Daily Papers

Knowledge graph (KG) link prediction aims to infer new facts based on existing facts in the KG. Recent studies have shown that using the graph neighborhood of a node via graph neural networks (GNNs) provides more useful information compared to just using the query information. Conventional GNNs for KG link prediction follow the standard message-passing paradigm on the entire KG, which leads to superfluous computation, over-smoothing of node representations, and also limits their expressive power. On a large scale, it becomes computationally expensive to aggregate useful information from the entire KG for inference. To address the limitations of existing KG link prediction frameworks, we propose a novel retrieve-and-read framework, which first retrieves a relevant subgraph context for the query and then jointly reasons over the context and the query with a high-capacity reader. As part of our exemplar instantiation for the new framework, we propose a novel Transformer-based GNN as the reader, which incorporates graph-based attention structure and cross-attention between query and context for deep fusion. This simple yet effective design enables the model to focus on salient context information relevant to the query. Empirical results on two standard KG link prediction datasets demonstrate the competitive performance of the proposed method. Furthermore, our analysis yields valuable insights for designing improved retrievers within the framework.

As a branch of advanced artificial intelligence, dialogue systems are prospering. Multi-turn response selection is a general research problem in dialogue systems. With the assistance of background information and pre-trained language models, the performance of state-of-the-art methods on this problem gains impressive improvement. However, existing studies neglect the importance of external commonsense knowledge. Hence, we design a Siamese network where a pre-trained Language model merges with a Graph neural network (SinLG). SinLG takes advantage of Pre-trained Language Models (PLMs) to catch the word correlations in the context and response candidates and utilizes a Graph Neural Network (GNN) to reason helpful common sense from an external knowledge graph. The GNN aims to assist the PLM in fine-tuning, and arousing its related memories to attain better performance. Specifically, we first extract related concepts as nodes from an external knowledge graph to construct a subgraph with the context response pair as a super node for each sample. Next, we learn two representations for the context response pair via both the PLM and GNN. A similarity loss between the two representations is utilized to transfer the commonsense knowledge from the GNN to the PLM. Then only the PLM is used to infer online so that efficiency can be guaranteed. Finally, we conduct extensive experiments on two variants of the PERSONA-CHAT dataset, which proves that our solution can not only improve the performance of the PLM but also achieve an efficient inference.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

Information retrieval based knowledge base question answering (KBQA) first retrieves a subgraph to reduce search space, then reasons on the subgraph to select answer entities. Existing approaches have three issues that impede the retrieval of such subgraphs. Firstly, there is no off-the-shelf toolkit for semantic-relevant subgraph retrieval. Secondly, existing methods are knowledge-graph-dependent, resulting in outdated knowledge graphs used even in recent studies. Thirdly, previous solutions fail to incorporate the best available techniques for entity linking or path expansion. In this paper, we present SRTK, a user-friendly toolkit for semantic-relevant subgraph retrieval from large-scale knowledge graphs. SRTK is the first toolkit that streamlines the entire lifecycle of subgraph retrieval across multiple knowledge graphs. Additionally, it comes with state-of-the-art subgraph retrieval algorithms, guaranteeing an up-to-date solution set out of the box.

Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.

A legal knowledge graph constructed from court cases, judgments, laws and other legal documents can enable a number of applications like question answering, document similarity, and search. While the use of knowledge graphs for distant supervision in NLP tasks is well researched, using knowledge graphs for downstream graph tasks like node similarity presents challenges in selecting node types and their features. In this demo, we describe our solution for predicting similar nodes in a case graph derived from our legal knowledge graph.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

As part of its scholarly data efforts, the Internet Archive (IA) releases a first version of a citation graph dataset, named refcat, derived from scholarly publications and additional data sources. It is composed of data gathered by the fatcat cataloging project (the catalog that underpins IA Scholar), related web-scale crawls targeting primary and secondary scholarly outputs, as well as metadata from the Open Library project and Wikipedia. This first version of the graph consists of over 1.3B citations. We release this dataset under a CC0 Public Domain Dedication, accessible through Internet Archive. The source code used for the derivation process, including exact and fuzzy citation matching, is released under an MIT license. The goal of this report is to describe briefly the current contents and the derivation of the dataset.

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

To deduce new facts on a knowledge graph (KG), a link predictor learns from the graph structure and collects local evidence to find the answer to a given query. However, existing methods suffer from a severe scalability problem due to the utilization of the whole KG for prediction, which hinders their promise on large scale KGs and cannot be directly addressed by vanilla sampling methods. In this work, we propose the one-shot-subgraph link prediction to achieve efficient and adaptive prediction. The design principle is that, instead of directly acting on the whole KG, the prediction procedure is decoupled into two steps, i.e., (i) extracting only one subgraph according to the query and (ii) predicting on this single, query dependent subgraph. We reveal that the non-parametric and computation-efficient heuristics Personalized PageRank (PPR) can effectively identify the potential answers and supporting evidence. With efficient subgraph-based prediction, we further introduce the automated searching of the optimal configurations in both data and model spaces. Empirically, we achieve promoted efficiency and leading performances on five large-scale benchmarks. The code is publicly available at: https://github.com/tmlr-group/one-shot-subgraph.

How might one test the hypothesis that networks were sampled from the same distribution? Here, we compare two statistical tests that use subgraph counts to address this question. The first uses the empirical subgraph densities themselves as estimates of those of the underlying distribution. The second test uses a new approach that converts these subgraph densities into estimates of the graph cumulants of the distribution (without any increase in computational complexity). We demonstrate -- via theory, simulation, and application to real data -- the superior statistical power of using graph cumulants. In summary, when analyzing data using subgraph/motif densities, we suggest using the corresponding graph cumulants instead.

We tackle NED by comparing entities in short sentences with graphs. Creating a context vector from graphs through deep learning is a challenging problem that has never been applied to NED. Our main contribution is to present an experimental study of recent neural techniques, as well as a discussion about which graph features are most important for the disambiguation task. In addition, a new dataset () is created to allow a clean and scalable evaluation of NED with entries, and to be used as a reference in future research. In the end our results show that a Bi-LSTM encoding of the graph triplets performs best, improving upon the baseline models and scoring an F1 value of 91.6% on the test set

Multi-hop logical reasoning is an established problem in the field of representation learning on knowledge graphs (KGs). It subsumes both one-hop link prediction as well as other more complex types of logical queries. Existing algorithms operate only on classical, triple-based graphs, whereas modern KGs often employ a hyper-relational modeling paradigm. In this paradigm, typed edges may have several key-value pairs known as qualifiers that provide fine-grained context for facts. In queries, this context modifies the meaning of relations, and usually reduces the answer set. Hyper-relational queries are often observed in real-world KG applications, and existing approaches for approximate query answering cannot make use of qualifier pairs. In this work, we bridge this gap and extend the multi-hop reasoning problem to hyper-relational KGs allowing to tackle this new type of complex queries. Building upon recent advancements in Graph Neural Networks and query embedding techniques, we study how to embed and answer hyper-relational conjunctive queries. Besides that, we propose a method to answer such queries and demonstrate in our experiments that qualifiers improve query answering on a diverse set of query patterns.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

While Retrieval-Augmented Generation (RAG) enhances the accuracy and relevance of responses by generative language models, it falls short in graph-based contexts where both textual and topological information are important. Naive RAG approaches inherently neglect the structural intricacies of textual graphs, resulting in a critical gap in the generation process. To address this challenge, we introduce Graph Retrieval-Augmented Generation (GRAG), which significantly enhances both the retrieval and generation processes by emphasizing the importance of subgraph structures. Unlike RAG approaches that focus solely on text-based entity retrieval, GRAG maintains an acute awareness of graph topology, which is crucial for generating contextually and factually coherent responses. Our GRAG approach consists of four main stages: indexing of k-hop ego-graphs, graph retrieval, soft pruning to mitigate the impact of irrelevant entities, and generation with pruned textual subgraphs. GRAG's core workflow-retrieving textual subgraphs followed by soft pruning-efficiently identifies relevant subgraph structures while avoiding the computational infeasibility typical of exhaustive subgraph searches, which are NP-hard. Moreover, we propose a novel prompting strategy that achieves lossless conversion from textual subgraphs to hierarchical text descriptions. Extensive experiments on graph multi-hop reasoning benchmarks demonstrate that in scenarios requiring multi-hop reasoning on textual graphs, our GRAG approach significantly outperforms current state-of-the-art RAG methods while effectively mitigating hallucinations.

Graph Neural Networks (GNNs) have gained traction across different domains such as transportation, bio-informatics, language processing, and computer vision. However, there is a noticeable absence of research on applying GNNs to supply chain networks. Supply chain networks are inherently graph-like in structure, making them prime candidates for applying GNN methodologies. This opens up a world of possibilities for optimizing, predicting, and solving even the most complex supply chain problems. A major setback in this approach lies in the absence of real-world benchmark datasets to facilitate the research and resolution of supply chain problems using GNNs. To address the issue, we present a real-world benchmark dataset for temporal tasks, obtained from one of the leading FMCG companies in Bangladesh, focusing on supply chain planning for production purposes. The dataset includes temporal data as node features to enable sales predictions, production planning, and the identification of factory issues. By utilizing this dataset, researchers can employ GNNs to address numerous supply chain problems, thereby advancing the field of supply chain analytics and planning. Source: https://github.com/CIOL-SUST/SupplyGraph

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

We describe new datasets for studying generalization from easy to hard examples.

We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated structures in the Visual Genome dataset. Our analysis shows that object labels are highly predictive of relation labels but not vice-versa. We also find that there are recurring patterns even in larger subgraphs: more than 50% of graphs contain motifs involving at least two relations. Our analysis motivates a new baseline: given object detections, predict the most frequent relation between object pairs with the given labels, as seen in the training set. This baseline improves on the previous state-of-the-art by an average of 3.6% relative improvement across evaluation settings. We then introduce Stacked Motif Networks, a new architecture designed to capture higher order motifs in scene graphs that further improves over our strong baseline by an average 7.1% relative gain. Our code is available at github.com/rowanz/neural-motifs.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Research question answering requires accurate retrieval and contextual understanding of scientific literature. However, current Retrieval-Augmented Generation (RAG) methods often struggle to balance complex document relationships with precise information retrieval. In this paper, we introduce Contextualized Graph Retrieval-Augmented Generation (CG-RAG), a novel framework that integrates sparse and dense retrieval signals within graph structures to enhance retrieval efficiency and subsequently improve generation quality for research question answering. First, we propose a contextual graph representation for citation graphs, effectively capturing both explicit and implicit connections within and across documents. Next, we introduce Lexical-Semantic Graph Retrieval (LeSeGR), which seamlessly integrates sparse and dense retrieval signals with graph encoding. It bridges the gap between lexical precision and semantic understanding in citation graph retrieval, demonstrating generalizability to existing graph retrieval and hybrid retrieval methods. Finally, we present a context-aware generation strategy that utilizes the retrieved graph-structured information to generate precise and contextually enriched responses using large language models (LLMs). Extensive experiments on research question answering benchmarks across multiple domains demonstrate that our CG-RAG framework significantly outperforms RAG methods combined with various state-of-the-art retrieval approaches, delivering superior retrieval accuracy and generation quality.

Since long, corporations are looking for knowledge sources which can provide structured description of data and can focus on meaning and shared understanding. Structures which can facilitate open world assumptions and can be flexible enough to incorporate and recognize more than one name for an entity. A source whose major purpose is to facilitate human communication and interoperability. Clearly, databases fail to provide these features and ontologies have emerged as an alternative choice, but corporations working on same domain tend to make different ontologies. The problem occurs when they want to share their data/knowledge. Thus we need tools to merge ontologies into one. This task is termed as ontology matching. This is an emerging area and still we have to go a long way in having an ideal matcher which can produce good results. In this paper we have shown a framework to matching ontologies using graphs.

Understanding the origins of militarized conflict is a complex, yet important undertaking. Existing research seeks to build this understanding by considering bi-lateral relationships between entity pairs (dyadic causes) and multi-lateral relationships among multiple entities (systemic causes). The aim of this work is to compare these two causes in terms of how they correlate with conflict between two entities. We do this by devising a set of textual and graph-based features which represent each of the causes. The features are extracted from Wikipedia and modeled as a large graph. Nodes in this graph represent entities connected by labeled edges representing ally or enemy-relationships. This allows casting the problem as an edge classification task, which we term dyad classification. We propose and evaluate classifiers to determine if a particular pair of entities are allies or enemies. Our results suggest that our systemic features might be slightly better correlates of conflict. Further, we find that Wikipedia articles of allies are semantically more similar than enemies.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

Knowledge graphs (KGs) have the advantage of providing fine-grained detail for question-answering systems. Unfortunately, building a reliable KG is time-consuming and expensive as it requires human intervention. To overcome this issue, we propose a novel framework to automatically construct a KG from unstructured documents that does not require external alignment. We first extract surface-form knowledge tuples from unstructured documents and encode them with contextual information. Entities with similar context semantics are then linked through internal alignment to form a graph structure. This allows us to extract the desired information from multiple documents by traversing the generated KG without a manual process. We examine its performance in retrieval based QA systems by reformulating the WikiMovies and MetaQA datasets into a tuple-level retrieval task. The experimental results show that our method outperforms traditional retrieval methods by a large margin.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

With the web getting bigger and assimilating knowledge about different concepts and domains, it is becoming very difficult for simple database driven applications to capture the data for a domain. Thus developers have come out with ontology based systems which can store large amount of information and can apply reasoning and produce timely information. Thus facilitating effective knowledge management. Though this approach has made our lives easier, but at the same time has given rise to another problem. Two different ontologies assimilating same knowledge tend to use different terms for the same concepts. This creates confusion among knowledge engineers and workers, as they do not know which is a better term then the other. Thus we need to merge ontologies working on same domain so that the engineers can develop a better application over it. This paper shows the development of one such matcher which merges the concepts available in two ontologies at two levels; 1) at string level and 2) at semantic level; thus producing better merged ontologies. We have used a graph matching technique which works at the core of the system. We have also evaluated the system and have tested its performance with its predecessor which works only on string matching. Thus current approach produces better results.

Repositories of large software systems have become commonplace. This massive expansion has resulted in the emergence of various problems in these software platforms including identification of (i) bug-prone packages, (ii) critical bugs, and (iii) severity of bugs. One of the important goals would be to mine these bugs and recommend them to the developers to resolve them. The first step to this is that one has to accurately detect the extent of severity of the bugs. In this paper, we take up this task of predicting the severity of bugs in the near future. Contextualized neural models built on the text description of a bug and the user comments about the bug help to achieve reasonably good performance. Further information on how the bugs are related to each other in terms of the ways they affect packages can be summarised in the form of a graph and used along with the text to get additional benefits.

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

Multi-hop query answering over a Knowledge Graph (KG) involves traversing one or more hops from the start node to answer a query. Path-based and logic-based methods are state-of-the-art for multi-hop question answering. The former is used in link prediction tasks. The latter is for answering complex logical queries. The logical multi-hop querying technique embeds the KG and queries in the same embedding space. The existing work incorporates First Order Logic (FOL) operators, such as conjunction (wedge), disjunction (vee), and negation (neg), in queries. Though current models have most of the building blocks to execute the FOL queries, they cannot use the dense information of multi-modal entities in the case of Multi-Modal Knowledge Graphs (MMKGs). We propose RConE, an embedding method to capture the multi-modal information needed to answer a query. The model first shortlists candidate (multi-modal) entities containing the answer. It then finds the solution (sub-entities) within those entities. Several existing works tackle path-based question-answering in MMKGs. However, to our knowledge, we are the first to introduce logical constructs in querying MMKGs and to answer queries that involve sub-entities of multi-modal entities as the answer. Extensive evaluation of four publicly available MMKGs indicates that RConE outperforms the current state-of-the-art.

Several recent efforts have been devoted to enhancing pre-trained language models (PLMs) by utilizing extra heterogeneous knowledge in knowledge graphs (KGs) and achieved consistent improvements on various knowledge-driven NLP tasks. However, most of these knowledge-enhanced PLMs embed static sub-graphs of KGs ("knowledge context"), regardless of that the knowledge required by PLMs may change dynamically according to specific text ("textual context"). In this paper, we propose a novel framework named Coke to dynamically select contextual knowledge and embed knowledge context according to textual context for PLMs, which can avoid the effect of redundant and ambiguous knowledge in KGs that cannot match the input text. Our experimental results show that Coke outperforms various baselines on typical knowledge-driven NLP tasks, indicating the effectiveness of utilizing dynamic knowledge context for language understanding. Besides the performance improvements, the dynamically selected knowledge in Coke can describe the semantics of text-related knowledge in a more interpretable form than the conventional PLMs. Our source code and datasets will be available to provide more details for Coke.

I introduce a new large-scale dataset of historical wire articles from U.S. Southern newspapers, spanning 1960-1975 and covering multiple wire services: The Associated Press, United Press International, Newspaper Enterprise Association. Unlike prior work focusing on front-page content, this dataset captures articles across the entire newspaper, offering broader insight into mid-century Southern coverage. The dataset includes a version that has undergone an LLM-based text cleanup pipeline to reduce OCR noise, enhancing its suitability for quantitative text analysis. Additionally, duplicate versions of articles are retained to enable analysis of editorial differences in language and framing across newspapers. Each article is tagged by wire service, facilitating comparative studies of editorial patterns across agencies. This resource opens new avenues for research in computational social science, digital humanities, and historical linguistics, providing a detailed perspective on how Southern newspapers relayed national and international news during a transformative period in American history. The dataset will be made available upon publication or request for research purposes.

Quantifying the similarity between a group of companies has proven to be useful for several purposes, including company benchmarking, fraud detection, and searching for investment opportunities. This exercise can be done using a variety of data sources, such as company activity data and financial data. However, ledger account data is widely available and is standardized to a large extent. Such ledger accounts within a financial statement can be represented by means of a tree, i.e. a special type of graph, representing both the values of the ledger accounts and the relationships between them. Given their broad availability and rich information content, financial statements form a prime data source based on which company similarities or distances could be computed. In this paper, we present a graph distance metric that enables one to compute the similarity between the financial statements of two companies. We conduct a comprehensive experimental study using real-world financial data to demonstrate the usefulness of our proposed distance metric. The experimental results show promising results on a number of use cases. This method may be useful for investors looking for investment opportunities, government officials attempting to identify fraudulent companies, and accountants looking to benchmark a group of companies based on their financial statements.

Existing commonsense knowledge bases often organize tuples in an isolated manner, which is deficient for commonsense conversational models to plan the next steps. To fill the gap, we curate a large-scale multi-turn human-written conversation corpus, and create the first Chinese commonsense conversation knowledge graph which incorporates both social commonsense knowledge and dialog flow information. To show the potential of our graph, we develop a graph-conversation matching approach, and benchmark two graph-grounded conversational tasks.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

We present a large longitudinal dataset of tweets from two sets of users that are suspected to be affiliated with ISIS. These sets of users are identified based on a prior study and a campaign aimed at shutting down ISIS Twitter accounts. These users have engaged with known ISIS accounts at least once during 2014-2015 and are still active as of 2021. Some of them have directly supported the ISIS users and their tweets by retweeting them, and some of the users that have quoted tweets of ISIS, have uncertain connections to ISIS seed accounts. This study and the dataset represent a unique approach to analyzing ISIS data. Although much research exists on ISIS online activities, few studies have focused on individual accounts. Our approach to validating accounts as well as developing a framework for differentiating accounts' functionality (e.g., propaganda versus operational planning) offers a foundation for future research. We perform some descriptive statistics and preliminary analyses on our collected data to provide deeper insight and highlight the significance and practicality of such analyses. We further discuss several cross-disciplinary potential use cases and research directions.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

Knowledge Graphs (KGs) have been used to support a wide range of applications, from web search to personal assistant. In this paper, we describe three generations of knowledge graphs: entity-based KGs, which have been supporting general search and question answering (e.g., at Google and Bing); text-rich KGs, which have been supporting search and recommendations for products, bio-informatics, etc. (e.g., at Amazon and Alibaba); and the emerging integration of KGs and LLMs, which we call dual neural KGs. We describe the characteristics of each generation of KGs, the crazy ideas behind the scenes in constructing such KGs, and the techniques developed over time to enable industry impact. In addition, we use KGs as examples to demonstrate a recipe to evolve research ideas from innovations to production practice, and then to the next level of innovations, to advance both science and business.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

Contextual Text Block Detection (CTBD) is the task of identifying coherent text blocks within the complexity of natural scenes. Previous methodologies have treated CTBD as either a visual relation extraction challenge within computer vision or as a sequence modeling problem from the perspective of natural language processing. We introduce a new framework that frames CTBD as a graph generation problem. This methodology consists of two essential procedures: identifying individual text units as graph nodes and discerning the sequential reading order relationships among these units as graph edges. Leveraging the cutting-edge capabilities of DQ-DETR for node detection, our framework innovates further by integrating a novel mechanism, a Dynamic Relation Transformer (DRFormer), dedicated to edge generation. DRFormer incorporates a dual interactive transformer decoder that deftly manages a dynamic graph structure refinement process. Through this iterative process, the model systematically enhances the graph's fidelity, ultimately resulting in improved precision in detecting contextual text blocks. Comprehensive experimental evaluations conducted on both SCUT-CTW-Context and ReCTS-Context datasets substantiate that our method achieves state-of-the-art results, underscoring the effectiveness and potential of our graph generation framework in advancing the field of CTBD.

Subgraphs of a larger global graph may be distributed across multiple devices, and only locally accessible due to privacy restrictions, although there may be links between subgraphs. Recently proposed subgraph Federated Learning (FL) methods deal with those missing links across local subgraphs while distributively training Graph Neural Networks (GNNs) on them. However, they have overlooked the inevitable heterogeneity between subgraphs comprising different communities of a global graph, consequently collapsing the incompatible knowledge from local GNN models. To this end, we introduce a new subgraph FL problem, personalized subgraph FL, which focuses on the joint improvement of the interrelated local GNNs rather than learning a single global model, and propose a novel framework, FEDerated Personalized sUBgraph learning (FED-PUB), to tackle it. Since the server cannot access the subgraph in each client, FED-PUB utilizes functional embeddings of the local GNNs using random graphs as inputs to compute similarities between them, and use the similarities to perform weighted averaging for server-side aggregation. Further, it learns a personalized sparse mask at each client to select and update only the subgraph-relevant subset of the aggregated parameters. We validate our FED-PUB for its subgraph FL performance on six datasets, considering both non-overlapping and overlapping subgraphs, on which it significantly outperforms relevant baselines. Our code is available at https://github.com/JinheonBaek/FED-PUB.

Fine-tuning pre-trained language models (PLMs) has recently shown a potential to improve knowledge graph completion (KGC). However, most PLM-based methods focus solely on encoding textual information, neglecting the long-tailed nature of knowledge graphs and their various topological structures, e.g., subgraphs, shortest paths, and degrees. We claim that this is a major obstacle to achieving higher accuracy of PLMs for KGC. To this end, we propose a Subgraph-Aware Training framework for KGC (SATKGC) with two ideas: (i) subgraph-aware mini-batching to encourage hard negative sampling and to mitigate an imbalance in the frequency of entity occurrences during training, and (ii) new contrastive learning to focus more on harder in-batch negative triples and harder positive triples in terms of the structural properties of the knowledge graph. To the best of our knowledge, this is the first study to comprehensively incorporate the structural inductive bias of the knowledge graph into fine-tuning PLMs. Extensive experiments on three KGC benchmarks demonstrate the superiority of SATKGC. Our code is available.

The web provides a rich, open-domain environment with textual, structural, and spatial properties. We propose a new task for grounding language in this environment: given a natural language command (e.g., "click on the second article"), choose the correct element on the web page (e.g., a hyperlink or text box). We collected a dataset of over 50,000 commands that capture various phenomena such as functional references (e.g. "find who made this site"), relational reasoning (e.g. "article by john"), and visual reasoning (e.g. "top-most article"). We also implemented and analyzed three baseline models that capture different phenomena present in the dataset.

An ability that underlies human syntactic knowledge is determining which words can appear in the similar structures (i.e. grouping words by their syntactic categories). These groupings enable humans to combine structures in order to communicate complex meanings. A foundational question is how do children acquire this ability underlying syntactic knowledge. In exploring this process, we will review various engineering approaches whose goal is similar to that of a child's -- without prior syntactic knowledge, correctly identify the parts of speech (POS) of the words in a sample of text. In reviewing these unsupervised tagging efforts, we will discuss common themes that support the advances in the models and their relevance for language acquisition. For example, we discuss how each model judges success (evaluation metrics), the "additional information" that constrains the POS learning (such as orthographic information), and the context used to determine POS (only previous word, words before and after the target, etc). The identified themes pave the way for future investigations into the cognitive processes that underpin the acquisition of syntactic categories and provide a useful layout of current state of the art unsupervised POS tagging models.

We introduce WonderJourney, a modularized framework for perpetual 3D scene generation. Unlike prior work on view generation that focuses on a single type of scenes, we start at any user-provided location (by a text description or an image) and generate a journey through a long sequence of diverse yet coherently connected 3D scenes. We leverage an LLM to generate textual descriptions of the scenes in this journey, a text-driven point cloud generation pipeline to make a compelling and coherent sequence of 3D scenes, and a large VLM to verify the generated scenes. We show compelling, diverse visual results across various scene types and styles, forming imaginary "wonderjourneys". Project website: https://kovenyu.com/WonderJourney/

About two million U.S. corporations and partnerships are linked to each other and human investors by about 15 million owner-subsidiary links. Comparable social networks such as corporate board memberships and socially-built systems such as the network of Internet links are "small worlds," meaning a network with a small diameter and link densities with a power-law distribution, but these properties had not yet been measured for the business entity network. This article shows that both inbound links and outbound links display a power-law distribution with a coefficient of concentration estimable to within a generally narrow confidence interval, overall, for subnetworks including only business entities, only for the great connected component of the network, and in subnetworks with edges associated with certain industries, for all years 2009-2021. In contrast to other networks with power-law distributed link densities, the network is mostly a tree, and has a diameter an order of magnitude larger than a small-world network with the same link distribution. The regularity of the power-law distribution indicates that its coefficient can be used as a new, well-defined macroeconomic metric for the concentration of capital flows in an economy. Economists might use it as a new measure of market concentration which is more comprehensive than measures based only on the few biggest firms. Comparing capital link concentrations across countries would facilitate modeling the relationship between business network characteristics and other macroeconomic indicators.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

We describe the SemEval task of extracting keyphrases and relations between them from scientific documents, which is crucial for understanding which publications describe which processes, tasks and materials. Although this was a new task, we had a total of 26 submissions across 3 evaluation scenarios. We expect the task and the findings reported in this paper to be relevant for researchers working on understanding scientific content, as well as the broader knowledge base population and information extraction communities.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Seminal research in the field of graph neural networks (GNNs) has revealed a direct correspondence between the expressive capabilities of GNNs and the k-dimensional Weisfeiler-Leman (kWL) test, a widely-recognized method for verifying graph isomorphism. This connection has reignited interest in comprehending the specific graph properties effectively distinguishable by the kWL test. A central focus of research in this field revolves around determining the least dimensionality k, for which kWL can discern graphs with different number of occurrences of a pattern graph P. We refer to such a least k as the WL-dimension of this pattern counting problem. This inquiry traditionally delves into two distinct counting problems related to patterns: subgraph counting and induced subgraph counting. Intriguingly, despite their initial appearance as separate challenges with seemingly divergent approaches, both of these problems are interconnected components of a more comprehensive problem: "graph motif parameters". In this paper, we provide a precise characterization of the WL-dimension of labeled graph motif parameters. As specific instances of this result, we obtain characterizations of the WL-dimension of the subgraph counting and induced subgraph counting problem for every labeled pattern P. We additionally demonstrate that in cases where the kWL test distinguishes between graphs with varying occurrences of a pattern P, the exact number of occurrences of P can be computed uniformly using only local information of the last layer of a corresponding GNN. We finally delve into the challenge of recognizing the WL-dimension of various graph parameters. We give a polynomial time algorithm for determining the WL-dimension of the subgraph counting problem for given pattern P, answering an open question from previous work.

We survey left 3-Engel elements in groups.

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

Extensive knowledge graphs (KGs) have been constructed to facilitate knowledge-driven tasks across various scenarios. However, existing work usually develops separate reasoning models for different KGs, lacking the ability to generalize and transfer knowledge across diverse KGs and reasoning settings. In this paper, we propose a prompt-based KG foundation model via in-context learning, namely KG-ICL, to achieve a universal reasoning ability. Specifically, we introduce a prompt graph centered with a query-related example fact as context to understand the query relation. To encode prompt graphs with the generalization ability to unseen entities and relations in queries, we first propose a unified tokenizer that maps entities and relations in prompt graphs to predefined tokens. Then, we propose two message passing neural networks to perform prompt encoding and KG reasoning, respectively. We conduct evaluation on 43 different KGs in both transductive and inductive settings. Results indicate that the proposed KG-ICL outperforms baselines on most datasets, showcasing its outstanding generalization and universal reasoning capabilities. The source code is accessible on GitHub: https://github.com/nju-websoft/KG-ICL.

Diderot's Encyclop\'edie is a reference work from XVIIIth century in Europe that aimed at collecting the knowledge of its era. Wikipedia has the same ambition with a much greater scope. However, the lack of digital connection between the two encyclopedias may hinder their comparison and the study of how knowledge has evolved. A key element of Wikipedia is Wikidata that backs the articles with a graph of structured data. In this paper, we describe the annotation of more than 10,300 of the Encyclop\'edie entries with Wikidata identifiers enabling us to connect these entries to the graph. We considered geographic and human entities. The Encyclop\'edie does not contain biographic entries as they mostly appear as subentries of locations. We extracted all the geographic entries and we completely annotated all the entries containing a description of human entities. This represents more than 2,600 links referring to locations or human entities. In addition, we annotated more than 9,500 entries having a geographic content only. We describe the annotation process as well as application examples. This resource is available at https://github.com/pnugues/encyclopedie_1751

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

We present a distributed data structure, which we call the rainbow skip graph. To our knowledge, this is the first peer-to-peer data structure that simultaneously achieves high fault tolerance, constant-sized nodes, and fast update and query times for ordered data. It is a non-trivial adaptation of the SkipNet/skip-graph structures of Harvey et al. and Aspnes and Shah, so as to provide fault-tolerance as these structures do, but to do so using constant-sized nodes, as in the family tree structure of Zatloukal and Harvey. It supports successor queries on a set of n items using O(log n) messages with high probability, an improvement over the expected O(log n) messages of the family tree.

This paper demonstrates how a graph-based semantic parser can be applied to the task of structured sentiment analysis, directly predicting sentiment graphs from text. We advance the state of the art on 4 out of 5 standard benchmark sets. We release the source code, models and predictions.

The Machine Learning for Combinatorial Optimization (ML4CO) NeurIPS 2021 competition aims to improve state-of-the-art combinatorial optimization solvers by replacing key heuristic components with machine learning models. On the dual task, we design models to make branching decisions to promote the dual bound increase faster. We propose a knowledge inheritance method to generalize knowledge of different models from the dataset aggregation process, named KIDA. Our improvement overcomes some defects of the baseline graph-neural-networks-based methods. Further, we won the 1st Place on the dual task. We hope this report can provide useful experience for developers and researchers. The code is available at https://github.com/megvii-research/NeurIPS2021-ML4CO-KIDA.

Text-Attributed Graphs (TAGs) augment graph structures with natural language descriptions, facilitating detailed depictions of data and their interconnections across various real-world settings. However, existing TAG datasets predominantly feature textual information only at the nodes, with edges typically represented by mere binary or categorical attributes. This lack of rich textual edge annotations significantly limits the exploration of contextual relationships between entities, hindering deeper insights into graph-structured data. To address this gap, we introduce Textual-Edge Graphs Datasets and Benchmark (TEG-DB), a comprehensive and diverse collection of benchmark textual-edge datasets featuring rich textual descriptions on nodes and edges. The TEG-DB datasets are large-scale and encompass a wide range of domains, from citation networks to social networks. In addition, we conduct extensive benchmark experiments on TEG-DB to assess the extent to which current techniques, including pre-trained language models, graph neural networks, and their combinations, can utilize textual node and edge information. Our goal is to elicit advancements in textual-edge graph research, specifically in developing methodologies that exploit rich textual node and edge descriptions to enhance graph analysis and provide deeper insights into complex real-world networks. The entire TEG-DB project is publicly accessible as an open-source repository on Github, accessible at https://github.com/Zhuofeng-Li/TEG-Benchmark.

Despite the impressive advancements of Large Language Models (LLMs) in generating text, they are often limited by the knowledge contained in the input and prone to producing inaccurate or hallucinated content. To tackle these issues, Retrieval-augmented Generation (RAG) is employed as an effective strategy to enhance the available knowledge base and anchor the responses in reality by pulling additional texts from external databases. In real-world applications, texts are often linked through entities within a graph, such as citations in academic papers or comments in social networks. This paper exploits these topological relationships to guide the retrieval process in RAG. Specifically, we explore two kinds of topological connections: proximity-based, focusing on closely connected nodes, and role-based, which looks at nodes sharing similar subgraph structures. Our empirical research confirms their relevance to text relationships, leading us to develop a Topology-aware Retrieval-augmented Generation framework. This framework includes a retrieval module that selects texts based on their topological relationships and an aggregation module that integrates these texts into prompts to stimulate LLMs for text generation. We have curated established text-attributed networks and conducted comprehensive experiments to validate the effectiveness of this framework, demonstrating its potential to enhance RAG with topological awareness.

Context: Recent research indicates that Web queries written by software developers are not very successful in retrieving relevant results, performing measurably worse compared to general purpose Web queries. Most approaches up to this point have addressed this problem with software engineering-specific automated query reformulation techniques, which work without developer involvement but are limited by the content of the original query. In other words, these techniques automatically improve the existing query but can not contribute new, previously unmentioned, concepts. Objective: In this paper, we propose a technique to guide software developers in manually improving their own Web search queries. We examine a conversational approach that follows unsuccessful queries with a clarification question aimed at eliciting additional query terms, thus providing to the developer a clear dimension along which the query could be improved. Methods: We describe a set of clarification questions derived from a corpus of software developer queries and a neural approach to recommending them for a newly issued query. Results: Our evaluation indicates that the recommendation technique is accurate, predicting a valid clarification question 80% of the time and outperforms simple baselines, as well as, state-of-the-art Learning To Rank (LTR) baselines. Conclusion: As shown in the experimental results, the described approach is capable at recommending appropriate clarification questions to software developers and considered useful by a sample of developers ranging from novices to experienced professionals.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Assume n, m are positive integers and G is a graph. Let P_{n,m} be the graph obtained from the path with vertices {-m, -(m-1), ldots, 0, ldots, n} by adding a loop at vertex 0. The double cone Delta_{n,m}(G) over a graph G is obtained from the direct product G times P_{n,m} by identifying V(G) times {n} into a single vertex (star, n), identifying V(G) times {-m} into a single vertex (star, -m), and adding an edge connecting (star, -m) and (star, n). This paper determines the fractional chromatic number of Delta_{n,m}(G). In particular, if n < m or n=m is even, then chi_f(Delta_{n,m}(G)) = chi_f(Delta_n(G)), where Delta_n(G) is the nth cone over G. If n=m is odd, then chi_f(Delta_{n,m}(G)) > chi_f(Delta_n(G)). The chromatic number of Delta_{n,m}(G) is also discussed.

Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of cellular sheaves: a knowledge graph embedding can be described as an approximate global section of an appropriate knowledge sheaf over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.

This paper presents the computational challenge on differential geometry and topology that happened within the ICLR 2021 workshop "Geometric and Topological Representation Learning". The competition asked participants to provide creative contributions to the fields of computational geometry and topology through the open-source repositories Geomstats and Giotto-TDA. The challenge attracted 16 teams in its two month duration. This paper describes the design of the challenge and summarizes its main findings.

AI alignment research is the field of study dedicated to ensuring that artificial intelligence (AI) benefits humans. As machine intelligence gets more advanced, this research is becoming increasingly important. Researchers in the field share ideas across different media to speed up the exchange of information. However, this focus on speed means that the research landscape is opaque, making it difficult for young researchers to enter the field. In this project, we collected and analyzed existing AI alignment research. We found that the field is growing quickly, with several subfields emerging in parallel. We looked at the subfields and identified the prominent researchers, recurring topics, and different modes of communication in each. Furthermore, we found that a classifier trained on AI alignment research articles can detect relevant articles that we did not originally include in the dataset. We are sharing the dataset with the research community and hope to develop tools in the future that will help both established researchers and young researchers get more involved in the field.

This is a report on the NSF Future Directions Workshop on Automatic Evaluation of Dialog. The workshop explored the current state of the art along with its limitations and suggested promising directions for future work in this important and very rapidly changing area of research.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

In this paper, we present an updated version of the NELA-GT-2018 dataset (N{\o}rregaard, Horne, and Adal{\i} 2019), entitled NELA-GT-2019. NELA-GT-2019 contains 1.12M news articles from 260 sources collected between January 1st 2019 and December 31st 2019. Just as with NELA-GT-2018, these sources come from a wide range of mainstream news sources and alternative news sources. Included with the dataset are source-level ground truth labels from 7 different assessment sites covering multiple dimensions of veracity. The NELA-GT-2019 dataset can be found at: https://doi.org/10.7910/DVN/O7FWPO

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

The task of Legal Statute Identification (LSI) aims to identify the legal statutes that are relevant to a given description of Facts or evidence of a legal case. Existing methods only utilize the textual content of Facts and legal articles to guide such a task. However, the citation network among case documents and legal statutes is a rich source of additional information, which is not considered by existing models. In this work, we take the first step towards utilising both the text and the legal citation network for the LSI task. We curate a large novel dataset for this task, including Facts of cases from several major Indian Courts of Law, and statutes from the Indian Penal Code (IPC). Modeling the statutes and training documents as a heterogeneous graph, our proposed model LeSICiN can learn rich textual and graphical features, and can also tune itself to correlate these features. Thereafter, the model can be used to inductively predict links between test documents (new nodes whose graphical features are not available to the model) and statutes (existing nodes). Extensive experiments on the dataset show that our model comfortably outperforms several state-of-the-art baselines, by exploiting the graphical structure along with textual features. The dataset and our codes are available at https://github.com/Law-AI/LeSICiN.

Besides entity-centric knowledge, usually organized as Knowledge Graph (KG), events are also an essential kind of knowledge in the world, which trigger the spring up of event-centric knowledge representation form like Event KG (EKG). It plays an increasingly important role in many downstream applications, such as search, question-answering, recommendation, financial quantitative investments, and text generation. This paper provides a comprehensive survey of EKG from history, ontology, instance, and application views. Specifically, to characterize EKG thoroughly, we focus on its history, definition, schema induction, acquisition, related representative graphs/systems, and applications. The development processes and trends are studied therein. We further summarize prospective directions to facilitate future research on EKG.

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM outputs, effectively mitigating issues such as ``hallucination'', lack of domain-specific knowledge, and outdated information. However, the complex structure of relationships among different entities in databases presents challenges for RAG systems. In response, GraphRAG leverages structural information across entities to enable more precise and comprehensive retrieval, capturing relational knowledge and facilitating more accurate, context-aware responses. Given the novelty and potential of GraphRAG, a systematic review of current technologies is imperative. This paper provides the first comprehensive overview of GraphRAG methodologies. We formalize the GraphRAG workflow, encompassing Graph-Based Indexing, Graph-Guided Retrieval, and Graph-Enhanced Generation. We then outline the core technologies and training methods at each stage. Additionally, we examine downstream tasks, application domains, evaluation methodologies, and industrial use cases of GraphRAG. Finally, we explore future research directions to inspire further inquiries and advance progress in the field.

Graph representation learning nowadays becomes fundamental in analyzing graph-structured data. Inspired by recent success of contrastive methods, in this paper, we propose a novel framework for unsupervised graph representation learning by leveraging a contrastive objective at the node level. Specifically, we generate two graph views by corruption and learn node representations by maximizing the agreement of node representations in these two views. To provide diverse node contexts for the contrastive objective, we propose a hybrid scheme for generating graph views on both structure and attribute levels. Besides, we provide theoretical justification behind our motivation from two perspectives, mutual information and the classical triplet loss. We perform empirical experiments on both transductive and inductive learning tasks using a variety of real-world datasets. Experimental experiments demonstrate that despite its simplicity, our proposed method consistently outperforms existing state-of-the-art methods by large margins. Moreover, our unsupervised method even surpasses its supervised counterparts on transductive tasks, demonstrating its great potential in real-world applications.

We present a large-scale dataset, ReCoRD, for machine reading comprehension requiring commonsense reasoning. Experiments on this dataset demonstrate that the performance of state-of-the-art MRC systems fall far behind human performance. ReCoRD represents a challenge for future research to bridge the gap between human and machine commonsense reading comprehension. ReCoRD is available at http://nlp.jhu.edu/record.

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.

The exploitation of syntactic graphs (SyGs) as a word's context has been shown to be beneficial for distributional semantic models (DSMs), both at the level of individual word representations and in deriving phrasal representations via composition. However, notwithstanding the potential performance benefit, the syntactically-aware DSMs proposed to date have huge numbers of parameters (compared to conventional DSMs) and suffer from data sparsity. Furthermore, the encoding of the SyG links (i.e., the syntactic relations) has been largely limited to linear maps. The knowledge graphs' literature, on the other hand, has proposed light-weight models employing different geometric transformations (GTs) to encode edges in a knowledge graph (KG). Our work explores the possibility of adopting this family of models to encode SyGs. Furthermore, we investigate which GT better encodes syntactic relations, so that these representations can be used to enhance phrase-level composition via syntactic contextualisation.

Recent work within the Argument Mining community has shown the applicability of Natural Language Processing systems for solving problems found within competitive debate. One of the most important tasks within competitive debate is for debaters to create high quality debate cases. We show that effective debate cases can be constructed using constrained shortest path traversals on Argumentative Semantic Knowledge Graphs. We study this potential in the context of a type of American Competitive Debate, called Policy Debate, which already has a large scale dataset targeting it called DebateSum. We significantly improve upon DebateSum by introducing 53180 new examples, as well as further useful metadata for every example, to the dataset. We leverage the txtai semantic search and knowledge graph toolchain to produce and contribute 9 semantic knowledge graphs built on this dataset. We create a unique method for evaluating which knowledge graphs are better in the context of producing policy debate cases. A demo which automatically generates debate cases, along with all other code and the Knowledge Graphs, are open-sourced and made available to the public here: https://github.com/Hellisotherpeople/DebateKG

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Knowledge-grounded dialog systems need to incorporate smooth transitions among knowledge selected for generating responses, to ensure that dialog flows naturally. For document-grounded dialog systems, the inter- and intra-document knowledge relations can be used to model such conversational flows. We develop a novel Multi-Document Co-Referential Graph (Coref-MDG) to effectively capture the inter-document relationships based on commonsense and similarity and the intra-document co-referential structures of knowledge segments within the grounding documents. We propose CorefDiffs, a Co-referential and Differential flow management method, to linearize the static Coref-MDG into conversational sequence logic. CorefDiffs performs knowledge selection by accounting for contextual graph structures and the knowledge difference sequences. CorefDiffs significantly outperforms the state-of-the-art by 9.5\%, 7.4\%, and 8.2\% on three public benchmarks. This demonstrates that the effective modeling of co-reference and knowledge difference for dialog flows are critical for transitions in document-grounded conversation

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

Many complicated network problems can be easily understood on small networks. Difficulties arise when small networks are combined into larger ones. Fortunately, the mathematical theory of sheaves was constructed to address just this kind of situation; it extends locally-defined structures to globally valid inferences by way of consistency relations. This paper exhibits examples in network monitoring and filter hardware where sheaves have useful descriptive power.

We study the set of networks, which consist of sources, sinks and neutral points, bijective to the permutations. The set of directed edges, which characterizes a network, is constructed from a polyomino or a Rothe diagram of a permutation through a Dyck tiling on a ribbon. We introduce a new combinatorial object similar to a tree-like tableau, which we call a forest. A forest is shown to give a permutation, and be bijective to a network corresponding to the inverse of the permutation. We show that the poset of networks is a finite graded lattice and admits an EL-labeling. By use of this EL-labeling, we show the lattice is supersolvable and compute the M\"obius function of an interval of the poset.

We announce a shared task on UCCA parsing in English, German and French, and call for participants to submit their systems. UCCA is a cross-linguistically applicable framework for semantic representation, which builds on extensive typological work and supports rapid annotation. UCCA poses a challenge for existing parsing techniques, as it exhibits reentrancy (resulting in DAG structures), discontinuous structures and non-terminal nodes corresponding to complex semantic units. Given the success of recent semantic parsing shared tasks (on SDP and AMR), we expect the task to have a significant contribution to the advancement of UCCA parsing in particular, and semantic parsing in general. Furthermore, existing applications for semantic evaluation that are based on UCCA will greatly benefit from better automatic methods for UCCA parsing. The competition website is https://competitions.codalab.org/competitions/19160

Answering complex questions about textual narratives requires reasoning over both stated context and the world knowledge that underlies it. However, pretrained language models (LM), the foundation of most modern QA systems, do not robustly represent latent relationships between concepts, which is necessary for reasoning. While knowledge graphs (KG) are often used to augment LMs with structured representations of world knowledge, it remains an open question how to effectively fuse and reason over the KG representations and the language context, which provides situational constraints and nuances. In this work, we propose GreaseLM, a new model that fuses encoded representations from pretrained LMs and graph neural networks over multiple layers of modality interaction operations. Information from both modalities propagates to the other, allowing language context representations to be grounded by structured world knowledge, and allowing linguistic nuances (e.g., negation, hedging) in the context to inform the graph representations of knowledge. Our results on three benchmarks in the commonsense reasoning (i.e., CommonsenseQA, OpenbookQA) and medical question answering (i.e., MedQA-USMLE) domains demonstrate that GreaseLM can more reliably answer questions that require reasoning over both situational constraints and structured knowledge, even outperforming models 8x larger.

This is a book about large language models. As indicated by the title, it primarily focuses on foundational concepts rather than comprehensive coverage of all cutting-edge technologies. The book is structured into four main chapters, each exploring a key area: pre-training, generative models, prompting techniques, and alignment methods. It is intended for college students, professionals, and practitioners in natural language processing and related fields, and can serve as a reference for anyone interested in large language models.

Generating knowledge grounded responses in both goal and non-goal oriented dialogue systems is an important research challenge. Knowledge Graphs (KG) can be viewed as an abstraction of the real world, which can potentially facilitate a dialogue system to produce knowledge grounded responses. However, integrating KGs into the dialogue generation process in an end-to-end manner is a non-trivial task. This paper proposes a novel architecture for integrating KGs into the response generation process by training a BERT model that learns to answer using the elements of the KG (entities and relations) in a multi-task, end-to-end setting. The k-hop subgraph of the KG is incorporated into the model during training and inference using Graph Laplacian. Empirical evaluation suggests that the model achieves better knowledge groundedness (measured via Entity F1 score) compared to other state-of-the-art models for both goal and non-goal oriented dialogues.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

Background. Due to the widespread adoption of Artificial Intelligence (AI) and Machine Learning (ML) for building software applications, companies are struggling to recruit employees with a deep understanding of such technologies. In this scenario, AutoML is soaring as a promising solution to fill the AI/ML skills gap since it promises to automate the building of end-to-end AI/ML pipelines that would normally be engineered by specialized team members. Aims. Despite the growing interest and high expectations, there is a dearth of information about the extent to which AutoML is currently adopted by teams developing AI/ML-enabled systems and how it is perceived by practitioners and researchers. Method. To fill these gaps, in this paper, we present a mixed-method study comprising a benchmark of 12 end-to-end AutoML tools on two SE datasets and a user survey with follow-up interviews to further our understanding of AutoML adoption and perception. Results. We found that AutoML solutions can generate models that outperform those trained and optimized by researchers to perform classification tasks in the SE domain. Also, our findings show that the currently available AutoML solutions do not live up to their names as they do not equally support automation across the stages of the ML development workflow and for all the team members. Conclusions. We derive insights to inform the SE research community on how AutoML can facilitate their activities and tool builders on how to design the next generation of AutoML technologies.

We propose two new methods for multi-document financial question answering. First, a method that uses semantic tagging, and then, queries the index to get the context (RAG_SEM). And second, a Knowledge Graph (KG_RAG) based method that uses semantic tagging, and, retrieves knowledge graph triples from a graph database, as context. KG_RAG uses knowledge graphs constructed using a small model that is fine-tuned using knowledge distillation using a large teacher model. The data consists of 18 10K reports of Apple, Microsoft, Alphabet, NVIDIA, Amazon and Tesla for the years 2021, 2022 and 2023. The list of questions in the data consists of 111 complex questions including many esoteric questions that are difficult to answer and the answers are not completely obvious. As evaluation metrics, we use overall scores as well as segmented scores for measurement including the faithfulness, relevance, correctness, similarity, an LLM based overall score and the rouge scores as well as a similarity of embeddings. We find that both methods outperform plain RAG significantly. KG_RAG outperforms RAG_SEM in four out of nine metrics.

Reasoning over knowledge graphs (KGs) is a challenging task that requires a deep understanding of the complex relationships between entities and the underlying logic of their relations. Current approaches rely on learning geometries to embed entities in vector space for logical query operations, but they suffer from subpar performance on complex queries and dataset-specific representations. In this paper, we propose a novel decoupled approach, Language-guided Abstract Reasoning over Knowledge graphs (LARK), that formulates complex KG reasoning as a combination of contextual KG search and logical query reasoning, to leverage the strengths of graph extraction algorithms and large language models (LLM), respectively. Our experiments demonstrate that the proposed approach outperforms state-of-the-art KG reasoning methods on standard benchmark datasets across several logical query constructs, with significant performance gain for queries of higher complexity. Furthermore, we show that the performance of our approach improves proportionally to the increase in size of the underlying LLM, enabling the integration of the latest advancements in LLMs for logical reasoning over KGs. Our work presents a new direction for addressing the challenges of complex KG reasoning and paves the way for future research in this area.

Recent years have witnessed an interesting phenomenon in which users come together to interrogate potentially harmful algorithmic behaviors they encounter in their everyday lives. Researchers have started to develop theoretical and empirical understandings of these user driven audits, with a hope to harness the power of users in detecting harmful machine behaviors. However, little is known about user participation and their division of labor in these audits, which are essential to support these collective efforts in the future. Through collecting and analyzing 17,984 tweets from four recent cases of user driven audits, we shed light on patterns of user participation and engagement, especially with the top contributors in each case. We also identified the various roles user generated content played in these audits, including hypothesizing, data collection, amplification, contextualization, and escalation. We discuss implications for designing tools to support user driven audits and users who labor to raise awareness of algorithm bias.

Knowledge Graph Question Answering (KGQA) aims to answer user-questions from a knowledge graph (KG) by identifying the reasoning relations between topic entity and answer. As a complex branch task of KGQA, multi-hop KGQA requires reasoning over the multi-hop relational chain preserved in KG to arrive at the right answer. Despite recent successes, the existing works on answering multi-hop complex questions still face the following challenges: i) The absence of an explicit relational chain order reflected in user-question stems from a misunderstanding of a user's intentions. ii) Incorrectly capturing relational types on weak supervision of which dataset lacks intermediate reasoning chain annotations due to expensive labeling cost. iii) Failing to consider implicit relations between the topic entity and the answer implied in structured KG because of limited neighborhoods size constraint in subgraph retrieval-based algorithms.To address these issues in multi-hop KGQA, we propose a novel model herein, namely Relational Chain based Embedded KGQA (Rce-KGQA), which simultaneously utilizes the explicit relational chain revealed in natural language question and the implicit relational chain stored in structured KG. Our extensive empirical study on three open-domain benchmarks proves that our method significantly outperforms the state-of-the-art counterparts like GraftNet, PullNet and EmbedKGQA. Comprehensive ablation experiments also verify the effectiveness of our method on the multi-hop KGQA task. We have made our model's source code available at github: https://github.com/albert-jin/Rce-KGQA.

Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease relations. We introduce a novel multimodal approach that unifies embeddings from specialized Language Models (LMs) with Graph Contrastive Learning (GCL) to enhance intra-entity relationships while employing a Knowledge Graph Embedding (KGE) model to capture inter-entity relationships for effective link prediction. To address limitations in existing BKGs, we present PrimeKG++, an enriched knowledge graph incorporating multimodal data, including biological sequences and textual descriptions for each entity type. By combining semantic and relational information in a unified representation, our approach demonstrates strong generalizability, enabling accurate link predictions even for unseen nodes. Experimental results on PrimeKG++ and the DrugBank drug-target interaction dataset demonstrate the effectiveness and robustness of our method across diverse biomedical datasets. Our source code, pre-trained models, and data are publicly available at https://github.com/HySonLab/BioMedKG

In this case study, the renowned Travelling Salesmen problem has been studied. Travelling Salesman problem is a most demanding computational problem in Computer Science. The Travelling Salesmen problem has been solved by two different ways using Hopfield Network. The main theory of the problem is to find distance and connectedness between nodes in a graph having edges between the nodes. The basic algorithm used for this problem is Djikstra's Algorithm. But till now , a number of such algorithms have evolved. Among them(some other algorithms) , are distinct and have been proved to solve the travelling salesmen problem by graph theory.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

Abstract meaning representation (AMR) highlights the core semantic information of text in a graph structure. Recently, pre-trained language models (PLMs) have advanced tasks of AMR parsing and AMR-to-text generation, respectively. However, PLMs are typically pre-trained on textual data, thus are sub-optimal for modeling structural knowledge. To this end, we investigate graph self-supervised training to improve the structure awareness of PLMs over AMR graphs. In particular, we introduce two graph auto-encoding strategies for graph-to-graph pre-training and four tasks to integrate text and graph information during pre-training. We further design a unified framework to bridge the gap between pre-training and fine-tuning tasks. Experiments on both AMR parsing and AMR-to-text generation show the superiority of our model. To our knowledge, we are the first to consider pre-training on semantic graphs.

In this study, we propose a novel graph neural network called propagate-selector (PS), which propagates information over sentences to understand information that cannot be inferred when considering sentences in isolation. First, we design a graph structure in which each node represents an individual sentence, and some pairs of nodes are selectively connected based on the text structure. Then, we develop an iterative attentive aggregation and a skip-combine method in which a node interacts with its neighborhood nodes to accumulate the necessary information. To evaluate the performance of the proposed approaches, we conduct experiments with the standard HotpotQA dataset. The empirical results demonstrate the superiority of our proposed approach, which obtains the best performances, compared to the widely used answer-selection models that do not consider the intersentential relationship.

We design a new technique for the distributional semantic modeling with a neural network-based approach to learn distributed term representations (or term embeddings) - term vector space models as a result, inspired by the recent ontology-related approach (using different types of contextual knowledge such as syntactic knowledge, terminological knowledge, semantic knowledge, etc.) to the identification of terms (term extraction) and relations between them (relation extraction) called semantic pre-processing technology - SPT. Our method relies on automatic term extraction from the natural language texts and subsequent formation of the problem-oriented or application-oriented (also deeply annotated) text corpora where the fundamental entity is the term (includes non-compositional and compositional terms). This gives us an opportunity to changeover from distributed word representations (or word embeddings) to distributed term representations (or term embeddings). This transition will allow to generate more accurate semantic maps of different subject domains (also, of relations between input terms - it is useful to explore clusters and oppositions, or to test your hypotheses about them). The semantic map can be represented as a graph using Vec2graph - a Python library for visualizing word embeddings (term embeddings in our case) as dynamic and interactive graphs. The Vec2graph library coupled with term embeddings will not only improve accuracy in solving standard NLP tasks, but also update the conventional concept of automated ontology development. The main practical result of our work is the development kit (set of toolkits represented as web service APIs and web application), which provides all necessary routines for the basic linguistic pre-processing and the semantic pre-processing of the natural language texts in Ukrainian for future training of term vector space models.

Reader reviews of literary fiction on social media, especially those in persistent, dedicated forums, create and are in turn driven by underlying narrative frameworks. In their comments about a novel, readers generally include only a subset of characters and their relationships, thus offering a limited perspective on that work. Yet in aggregate, these reviews capture an underlying narrative framework comprised of different actants (people, places, things), their roles, and interactions that we label the "consensus narrative framework". We represent this framework in the form of an actant-relationship story graph. Extracting this graph is a challenging computational problem, which we pose as a latent graphical model estimation problem. Posts and reviews are viewed as samples of sub graphs/networks of the hidden narrative framework. Inspired by the qualitative narrative theory of Greimas, we formulate a graphical generative Machine Learning (ML) model where nodes represent actants, and multi-edges and self-loops among nodes capture context-specific relationships. We develop a pipeline of interlocking automated methods to extract key actants and their relationships, and apply it to thousands of reviews and comments posted on Goodreads.com. We manually derive the ground truth narrative framework from SparkNotes, and then use word embedding tools to compare relationships in ground truth networks with our extracted networks. We find that our automated methodology generates highly accurate consensus narrative frameworks: for our four target novels, with approximately 2900 reviews per novel, we report average coverage/recall of important relationships of > 80% and an average edge detection rate of >89\%. These extracted narrative frameworks can generate insight into how people (or classes of people) read and how they recount what they have read to others.

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

Within this study, we propose a new approach for natural language processing using Bayesian networks to predict and analyze the context and how this approach can be applied to the Community Question Answering domain. We discuss how Bayesian networks can detect semantic relationships and dependencies between entities, and this is connected to different score-based approaches of structure-learning. We compared the Bayesian networks with different score metrics, such as the BIC, BDeu, K2 and Chow-Liu trees. Our proposed approach out-performs the baseline model at the precision metric. We also discuss the influence of penalty terms on the structure of Bayesian networks and how they can be used to analyze the relationships between entities. In addition, we examine the visualization of directed acyclic graphs to analyze semantic relationships. The article further identifies issues with detecting certain semantic classes that are separated in the structure of directed acyclic graphs. Finally, we evaluate potential improvements for the Bayesian network approach.

We present the "Annotation and Benchmarking on Understanding and Transparency of Machine Learning Lifecycles" (ABOUT ML) project as an initiative to operationalize ML transparency and work towards a standard ML documentation practice. We make the case for the project's relevance and effectiveness in consolidating disparate efforts across a variety of stakeholders, as well as bringing in the perspectives of currently missing voices that will be valuable in shaping future conversations. We describe the details of the initiative and the gaps we hope this project will help address.

We describe a method, based on Jennifer Nado's definition of classification procedures as targets of conceptual engineering, that implements such procedures using a large language model. We then apply this method using data from the Wikidata knowledge graph to evaluate concept definitions from two paradigmatic conceptual engineering projects: the International Astronomical Union's redefinition of PLANET and Haslanger's ameliorative analysis of WOMAN. We discuss implications of this work for the theory and practice of conceptual engineering. The code and data can be found on GitHub.

While multi-modal models have successfully integrated information from image, video, and audio modalities, integrating graph modality into large language models (LLMs) remains unexplored. This discrepancy largely stems from the inherent divergence between structured graph data and unstructured text data. Incorporating graph knowledge provides a reliable source of information, enabling potential solutions to address issues in text generation, e.g., hallucination, and lack of domain knowledge. To evaluate the integration of graph knowledge into language models, a dedicated dataset is needed. However, there is currently no benchmark dataset specifically designed for multimodal graph-language models. To address this gap, we propose GraphextQA, a question answering dataset with paired subgraphs, retrieved from Wikidata, to facilitate the evaluation and future development of graph-language models. Additionally, we introduce a baseline model called CrossGNN, which conditions answer generation on the paired graphs by cross-attending question-aware graph features at decoding. The proposed dataset is designed to evaluate graph-language models' ability to understand graphs and make use of it for answer generation. We perform experiments with language-only models and the proposed graph-language model to validate the usefulness of the paired graphs and to demonstrate the difficulty of the task.

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

As the production of and reliance on datasets to produce automated decision-making systems (ADS) increases, so does the need for processes for evaluating and interrogating the underlying data. After launching the Dataset Nutrition Label in 2018, the Data Nutrition Project has made significant updates to the design and purpose of the Label, and is launching an updated Label in late 2020, which is previewed in this paper. The new Label includes context-specific Use Cases &Alerts presented through an updated design and user interface targeted towards the data scientist profile. This paper discusses the harm and bias from underlying training data that the Label is intended to mitigate, the current state of the work including new datasets being labeled, new and existing challenges, and further directions of the work, as well as Figures previewing the new label.

We present 3DLNews, a novel dataset with local news articles from the United States spanning the period from 1996 to 2024. It contains almost 1 million URLs (with HTML text) from over 14,000 local newspapers, TV, and radio stations across all 50 states, and provides a broad snapshot of the US local news landscape. The dataset was collected by scraping Google and Twitter search results. We employed a multi-step filtering process to remove non-news article links and enriched the dataset with metadata such as the names and geo-coordinates of the source news media organizations, article publication dates, etc. Furthermore, we demonstrated the utility of 3DLNews by outlining four applications.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

Knowledge grounded dialogue system is designed to generate responses that convey information from given knowledge documents. However, it's a challenge for the current Seq2Seq model to acquire knowledge from complex documents and integrate it to perform correct responses without the aid of an explicit semantic structure. To address these issues, we present a novel graph structure, Ground Graph (G^2), which models the semantic structure of both dialogue contexts and knowledge documents to facilitate knowledge selection and integration for the task. Besides, a Ground Graph Aware Transformer (G^2AT) is proposed to enhance knowledge grounded response generation. Empirical results show that our proposed model outperforms previous state-of-the-art methods with more than 10\% and 20\% gains on response generation and factual consistency. Furthermore, our structure-aware approach shows excellent generalization ability in resource-limited situations.

This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

A graph homomorphism is a map between two graphs that preserves adjacency relations. We consider the problem of sampling a random graph homomorphism from a graph into a large network. We propose two complementary MCMC algorithms for sampling random graph homomorphisms and establish bounds on their mixing times and the concentration of their time averages. Based on our sampling algorithms, we propose a novel framework for network data analysis that circumvents some of the drawbacks in methods based on independent and neighborhood sampling. Various time averages of the MCMC trajectory give us various computable observables, including well-known ones such as homomorphism density and average clustering coefficient and their generalizations. Furthermore, we show that these network observables are stable with respect to a suitably renormalized cut distance between networks. We provide various examples and simulations demonstrating our framework through synthetic networks. We also demonstrate the performance of our framework on the tasks of network clustering and subgraph classification on the Facebook100 dataset and on Word Adjacency Networks of a set of classic novels.

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.

Peer review, as a cornerstone of scientific research, ensures the integrity and quality of scholarly work by providing authors with objective feedback for refinement. However, in the traditional peer review process, authors often receive vague or insufficiently detailed feedback, which provides limited assistance and leads to a more time-consuming review cycle. If authors can identify some specific weaknesses in their paper, they can not only address the reviewer's concerns but also improve their work. This raises the critical question of how to enhance authors' comprehension of review comments. In this paper, we present SEAGraph, a novel framework developed to clarify review comments by uncovering the underlying intentions behind them. We construct two types of graphs for each paper: the semantic mind graph, which captures the author's thought process, and the hierarchical background graph, which delineates the research domains related to the paper. A retrieval method is then designed to extract relevant content from both graphs, facilitating coherent explanations for the review comments. Extensive experiments show that SEAGraph excels in review comment understanding tasks, offering significant benefits to authors.

Text-rich Graph Knowledge Bases (TG-KBs) have become increasingly crucial for answering queries by providing textual and structural knowledge. However, current retrieval methods often retrieve these two types of knowledge in isolation without considering their mutual reinforcement and some hybrid methods even bypass structural retrieval entirely after neighboring aggregation. To fill in this gap, we propose a Mixture of Structural-and-Textual Retrieval (MoR) to retrieve these two types of knowledge via a Planning-Reasoning-Organizing framework. In the Planning stage, MoR generates textual planning graphs delineating the logic for answering queries. Following planning graphs, in the Reasoning stage, MoR interweaves structural traversal and textual matching to obtain candidates from TG-KBs. In the Organizing stage, MoR further reranks fetched candidates based on their structural trajectory. Extensive experiments demonstrate the superiority of MoR in harmonizing structural and textual retrieval with insights, including uneven retrieving performance across different query logics and the benefits of integrating structural trajectories for candidate reranking. Our code is available at https://github.com/Yoega/MoR.

Recently, context-dependent text-to-SQL semantic parsing which translates natural language into SQL in an interaction process has attracted a lot of attention. Previous works leverage context-dependence information either from interaction history utterances or the previous predicted SQL queries but fail in taking advantage of both since of the mismatch between natural language and logic-form SQL. In this work, we propose a History Information Enhanced text-to-SQL model (HIE-SQL) to exploit context-dependence information from both history utterances and the last predicted SQL query. In view of the mismatch, we treat natural language and SQL as two modalities and propose a bimodal pre-trained model to bridge the gap between them. Besides, we design a schema-linking graph to enhance connections from utterances and the SQL query to the database schema. We show our history information enhanced methods improve the performance of HIE-SQL by a significant margin, which achieves new state-of-the-art results on the two context-dependent text-to-SQL benchmarks, the SparC and CoSQL datasets, at the writing time.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

We propose KnowGL, a tool that allows converting text into structured relational data represented as a set of ABox assertions compliant with the TBox of a given Knowledge Graph (KG), such as Wikidata. We address this problem as a sequence generation task by leveraging pre-trained sequence-to-sequence language models, e.g. BART. Given a sentence, we fine-tune such models to detect pairs of entity mentions and jointly generate a set of facts consisting of the full set of semantic annotations for a KG, such as entity labels, entity types, and their relationships. To showcase the capabilities of our tool, we build a web application consisting of a set of UI widgets that help users to navigate through the semantic data extracted from a given input text. We make the KnowGL model available at https://huggingface.co/ibm/knowgl-large.

This document serves as an overview of the different mechanisms and areas of governance in the BigCode project. It aims to support transparency by providing relevant information about choices that were made during the project to the broader public, and to serve as an example of intentional governance of an open research project that future endeavors can leverage to shape their own approach. The first section, Project Structure, covers the project organization, its stated goals and values, its internal decision processes, and its funding and resources. The second section, Data and Model Governance, covers decisions relating to the questions of data subject consent, privacy, and model release.

CleverHans is a software library that provides standardized reference implementations of adversarial example construction techniques and adversarial training. The library may be used to develop more robust machine learning models and to provide standardized benchmarks of models' performance in the adversarial setting. Benchmarks constructed without a standardized implementation of adversarial example construction are not comparable to each other, because a good result may indicate a robust model or it may merely indicate a weak implementation of the adversarial example construction procedure. This technical report is structured as follows. Section 1 provides an overview of adversarial examples in machine learning and of the CleverHans software. Section 2 presents the core functionalities of the library: namely the attacks based on adversarial examples and defenses to improve the robustness of machine learning models to these attacks. Section 3 describes how to report benchmark results using the library. Section 4 describes the versioning system.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

Heterogeneous graph contrastive learning has received wide attention recently. Some existing methods use meta-paths, which are sequences of object types that capture semantic relationships between objects, to construct contrastive views. However, most of them ignore the rich meta-path context information that describes how two objects are connected by meta-paths. Further, they fail to distinguish negative samples, which could adversely affect the model performance. To address the problems, we propose MEOW, which considers both meta-path contexts and weighted negative samples. Specifically, MEOW constructs a coarse view and a fine-grained view for contrast. The former reflects which objects are connected by meta-paths, while the latter uses meta-path contexts and characterizes details on how the objects are connected. Then, we theoretically analyze the InfoNCE loss and recognize its limitations for computing gradients of negative samples. To better distinguish negative samples, we learn hard-valued weights for them based on node clustering and use prototypical contrastive learning to pull close embeddings of nodes in the same cluster. In addition, we propose a variant model AdaMEOW that adaptively learns soft-valued weights of negative samples to further improve node representation. Finally, we conduct extensive experiments to show the superiority of MEOW and AdaMEOW against other state-of-the-art methods.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Information extraction (IE) is an important task in Natural Language Processing (NLP), involving the extraction of named entities and their relationships from unstructured text. In this paper, we propose a novel approach to this task by formulating it as graph structure learning (GSL). By formulating IE as GSL, we enhance the model's ability to dynamically refine and optimize the graph structure during the extraction process. This formulation allows for better interaction and structure-informed decisions for entity and relation prediction, in contrast to previous models that have separate or untied predictions for these tasks. When compared against state-of-the-art baselines on joint entity and relation extraction benchmarks, our model, GraphER, achieves competitive results.

We present the FinCausal 2020 Shared Task on Causality Detection in Financial Documents and the associated FinCausal dataset, and discuss the participating systems and results. Two sub-tasks are proposed: a binary classification task (Task 1) and a relation extraction task (Task 2). A total of 16 teams submitted runs across the two Tasks and 13 of them contributed with a system description paper. This workshop is associated to the Joint Workshop on Financial Narrative Processing and MultiLing Financial Summarisation (FNP-FNS 2020), held at The 28th International Conference on Computational Linguistics (COLING'2020), Barcelona, Spain on September 12, 2020.

Organized crime inflicts human suffering on a genocidal scale: the Mexican drug cartels have murdered 150,000 people since 2006, upwards of 700,000 people per year are "exported" in a human trafficking industry enslaving an estimated 40 million people. These nefarious industries rely on sophisticated money laundering schemes to operate. Despite tremendous resources dedicated to anti-money laundering (AML) only a tiny fraction of illicit activity is prevented. The research community can help. In this brief paper, we map the structural and behavioral dynamics driving the technical challenge. We review AML methods, current and emergent. We provide a first look at scalable graph convolutional neural networks for forensic analysis of financial data, which is massive, dense, and dynamic. We report preliminary experimental results using a large synthetic graph (1M nodes, 9M edges) generated by a data simulator we created called AMLSim. We consider opportunities for high performance efficiency, in terms of computation and memory, and we share results from a simple graph compression experiment. Our results support our working hypothesis that graph deep learning for AML bears great promise in the fight against criminal financial activity.

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like question answering and search, they struggle to adapt to specialized knowledge, such as industrial workflows or knowledge work, without expensive fine-tuning or sub-optimal retrieval methods. Existing retrieval-augmented models, such as RAG, offer improvements but fail to account for structured domain knowledge, leading to suboptimal context generation. Ontologies, which conceptually organize domain knowledge by defining entities and their interrelationships, offer a structured representation to address this gap. OG-RAG constructs a hypergraph representation of domain documents, where each hyperedge encapsulates clusters of factual knowledge grounded using domain-specific ontology. An optimization algorithm then retrieves the minimal set of hyperedges that constructs a precise, conceptually grounded context for the LLM. This method enables efficient retrieval while preserving the complex relationships between entities. OG-RAG applies to domains where fact-based reasoning is essential, particularly in tasks that require workflows or decision-making steps to follow predefined rules and procedures. These include industrial workflows in healthcare, legal, and agricultural sectors, as well as knowledge-driven tasks such as news journalism, investigative research, consulting and more. Our evaluations demonstrate that OG-RAG increases the recall of accurate facts by 55% and improves response correctness by 40% across four different LLMs. Additionally, OG-RAG enables 30% faster attribution of responses to context and boosts fact-based reasoning accuracy by 27% compared to baseline methods.

Background. The rapid and growing popularity of machine learning (ML) applications has led to an increasing interest in MLOps, that is, the practice of continuous integration and deployment (CI/CD) of ML-enabled systems. Aims. Since changes may affect not only the code but also the ML model parameters and the data themselves, the automation of traditional CI/CD needs to be extended to manage model retraining in production. Method. In this paper, we present an initial investigation of the MLOps practices implemented in a set of ML-enabled systems retrieved from GitHub, focusing on GitHub Actions and CML, two solutions to automate the development workflow. Results. Our preliminary results suggest that the adoption of MLOps workflows in open-source GitHub projects is currently rather limited. Conclusions. Issues are also identified, which can guide future research work.

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

This paper describes a service learning project used in an upper-level and graduate-level database systems course. Students complete a small database project for a real client. The final product must match the client specification and needs, and include the database design and the final working database system with embedded user documentation. The solution must be implemented in a way to make it as easy to use as possible for the client. Students are expected to conduct professional meetings with their clients to understand the project, analyze the project's requirements, as well as design and implement the solution to the project. Students must have each milestone approved before starting the next phase of the project. The student learning objectives of a database system semester project are to: analyze a client's information system problem and determine the requirements for the solution; design a suitable database solution to the problem; use software design and development tools to design and develop a solution to the problem; communicate and interact with a client on a professional level; prepare effective documentation for both non-technical and technical software users; and interact ethically with all persons involved with a project. The broader impact objectives of a database system semester project are to: provide needed database solutions for organizations and businesses in the local area; provide a resume and portfolio-building opportunity for the students; provide a measure for assessing how well the program meets it mission; provide a mechanism for implementing service-based learning; provide a mechanism for outreach to local-area organizations and businesses; and provide a starting-point for undergraduate research projects.

Machine learning is the science of credit assignment: finding patterns in observations that predict the consequences of actions and help to improve future performance. Credit assignment is also required for human understanding of how the world works, not only for individuals navigating daily life, but also for academic professionals like historians who interpret the present in light of past events. Here I focus on the history of modern artificial intelligence (AI) which is dominated by artificial neural networks (NNs) and deep learning, both conceptually closer to the old field of cybernetics than to what's been called AI since 1956 (e.g., expert systems and logic programming). A modern history of AI will emphasize breakthroughs outside of the focus of traditional AI text books, in particular, mathematical foundations of today's NNs such as the chain rule (1676), the first NNs (linear regression, circa 1800), and the first working deep learners (1965-). From the perspective of 2022, I provide a timeline of the -- in hindsight -- most important relevant events in the history of NNs, deep learning, AI, computer science, and mathematics in general, crediting those who laid foundations of the field. The text contains numerous hyperlinks to relevant overview sites from my AI Blog. It supplements my previous deep learning survey (2015) which provides hundreds of additional references. Finally, to round it off, I'll put things in a broader historic context spanning the time since the Big Bang until when the universe will be many times older than it is now.

Graph measures that express closeness or distance between nodes can be employed for graph nodes clustering using metric clustering algorithms. There are numerous measures applicable to this task, and which one performs better is an open question. We study the performance of 25 graph measures on generated graphs with different parameters. While usually measure comparisons are limited to general measure ranking on a particular dataset, we aim to explore the performance of various measures depending on graph features. Using an LFR graph generator, we create a dataset of 11780 graphs covering the whole LFR parameter space. For each graph, we assess the quality of clustering with k-means algorithm for each considered measure. Based on this, we determine the best measure for each area of the parameter space. We find that the parameter space consists of distinct zones where one particular measure is the best. We analyze the geometry of the resulting zones and describe it with simple criteria. Given particular graph parameters, this allows us to recommend a particular measure to use for clustering.

A companion to the release of the latest version of the SPLADE library. We describe changes to the training structure and present our latest series of models -- SPLADE-v3. We compare this new version to BM25, SPLADE++, as well as re-rankers, and showcase its effectiveness via a meta-analysis over more than 40 query sets. SPLADE-v3 further pushes the limit of SPLADE models: it is statistically significantly more effective than both BM25 and SPLADE++, while comparing well to cross-encoder re-rankers. Specifically, it gets more than 40 MRR@10 on the MS MARCO dev set, and improves by 2% the out-of-domain results on the BEIR benchmark.

We open-source a state-of-the-art 7.5B-parameter generative model series named PhoGPT for Vietnamese, which includes the base pre-trained monolingual model PhoGPT-7B5 and its instruction-following variant, PhoGPT-7B5-Instruct. In addition, we also demonstrate its superior performance compared to previous open-source models through a human evaluation experiment. GitHub: https://github.com/VinAIResearch/PhoGPT

While most network embedding techniques model the relative positions of nodes in a network, recently there has been significant interest in structural embeddings that model node role equivalences, irrespective of their distances to any specific nodes. We present PhUSION, a proximity-based unified framework for computing structural and positional node embeddings, which leverages well-established methods for calculating node proximity scores. Clarifying a point of contention in the literature, we show which step of PhUSION produces the different kinds of embeddings and what steps can be used by both. Moreover, by aggregating the PhUSION node embeddings, we obtain graph-level features that model information lost by previous graph feature learning and kernel methods. In a comprehensive empirical study with over 10 datasets, 4 tasks, and 35 methods, we systematically reveal successful design choices for node and graph-level machine learning with embeddings.

In recent years, hate speech has gained great relevance in social networks and other virtual media because of its intensity and its relationship with violent acts against members of protected groups. Due to the great amount of content generated by users, great effort has been made in the research and development of automatic tools to aid the analysis and moderation of this speech, at least in its most threatening forms. One of the limitations of current approaches to automatic hate speech detection is the lack of context. Most studies and resources are performed on data without context; that is, isolated messages without any type of conversational context or the topic being discussed. This restricts the available information to define if a post on a social network is hateful or not. In this work, we provide a novel corpus for contextualized hate speech detection based on user responses to news posts from media outlets on Twitter. This corpus was collected in the Rioplatense dialectal variety of Spanish and focuses on hate speech associated with the COVID-19 pandemic. Classification experiments using state-of-the-art techniques show evidence that adding contextual information improves hate speech detection performance for two proposed tasks (binary and multi-label prediction). We make our code, models, and corpus available for further research.

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

In this study, we focus on the graph representation learning (a.k.a. network embedding) in attributed graphs. Different from existing embedding methods that treat the incorporation of graph structure and semantic as the simple combination of two optimization objectives, we propose a novel semantic graph representation (SGR) method to formulate the joint optimization of the two heterogeneous sources into a common high-order proximity based framework. Concretely, we first construct an auxiliary weighted graph, where the complex homogeneous and heterogeneous relations among nodes and attributes in the original graph are comprehensively encoded. Conventional embedding methods that consider high-order topology proximities can then be easily applied to the newly constructed graph to learn the representations of both node and attribute while capturing the nonlinear high-order intrinsic correlation inside or among graph structure and semantic. The learned attribute embeddings can also effectively support some semantic-oriented inference tasks (e.g., semantic community detection), helping to reveal the graph's deep semantic. The effectiveness of SGR is further verified on a series of real graphs, where it achieves impressive performance over other baselines.

Memes are the new-age conveyance mechanism for humor on social media sites. Memes often include an image and some text. Memes can be used to promote disinformation or hatred, thus it is crucial to investigate in details. We introduce Memotion 3, a new dataset with 10,000 annotated memes. Unlike other prevalent datasets in the domain, including prior iterations of Memotion, Memotion 3 introduces Hindi-English Codemixed memes while prior works in the area were limited to only the English memes. We describe the Memotion task, the data collection and the dataset creation methodologies. We also provide a baseline for the task. The baseline code and dataset will be made available at https://github.com/Shreyashm16/Memotion-3.0

Retrieving external knowledge and prompting large language models with relevant information is an effective paradigm to enhance the performance of question-answering tasks. Previous research typically handles paragraphs from external documents in isolation, resulting in a lack of context and ambiguous references, particularly in multi-document and complex tasks. To overcome these challenges, we propose a new retrieval framework IIER, that leverages Inter-chunk Interactions to Enhance Retrieval. This framework captures the internal connections between document chunks by considering three types of interactions: structural, keyword, and semantic. We then construct a unified Chunk-Interaction Graph to represent all external documents comprehensively. Additionally, we design a graph-based evidence chain retriever that utilizes previous paths and chunk interactions to guide the retrieval process. It identifies multiple seed nodes based on the target question and iteratively searches for relevant chunks to gather supporting evidence. This retrieval process refines the context and reasoning chain, aiding the large language model in reasoning and answer generation. Extensive experiments demonstrate that IIER outperforms strong baselines across four datasets, highlighting its effectiveness in improving retrieval and reasoning capabilities.

The field of conlang has evidenced an important growth in the last decades. This has been the product of a wide interest in the use and study of conlangs for artistic purposes. However, one important question is what it is happening with conlang in the academic world. This paper aims to have an overall understanding of the literature on conlang research. With this we aim to give a realistic picture of the field in present days. We have implemented a computational linguistic approach, combining bibliometrics and network analysis to examine all publications available in the Scopus database. Analysing over 2300 academic publications since 1927 until 2022, we have found that Esperanto is by far the most documented conlang. Three main authors have contributed to this: Garv\'ia R., Fiedler S., and Blanke D. The 1970s and 1980s have been the decades where the foundations of current research have been built. In terms of methodologies, language learning and experimental linguistics are the ones contributing to most to the preferred approaches of study in the field. We present the results and discuss our limitations and future work.

In this paper, we present the fifth installment of the NELA-GT datasets, NELA-GT-2022. The dataset contains 1,778,361 articles from 361 outlets between January 1st, 2022 and December 31st, 2022. Just as in past releases of the dataset, NELA-GT-2022 includes outlet-level veracity labels from Media Bias/Fact Check and tweets embedded in collected news articles. The NELA-GT-2022 dataset can be found at: https://doi.org/10.7910/DVN/AMCV2H

Sources of commonsense knowledge support applications in natural language understanding, computer vision, and knowledge graphs. Given their complementarity, their integration is desired. Yet, their different foci, modeling approaches, and sparse overlap make integration difficult. In this paper, we consolidate commonsense knowledge by following five principles, which we apply to combine seven key sources into a first integrated CommonSense Knowledge Graph (CSKG). We analyze CSKG and its various text and graph embeddings, showing that CSKG is well-connected and that its embeddings provide a useful entry point to the graph. We demonstrate how CSKG can provide evidence for generalizable downstream reasoning and for pre-training of language models. CSKG and all its embeddings are made publicly available to support further research on commonsense knowledge integration and reasoning.

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

In real world applications, knowledge graphs (KG) are widely used in various domains (e.g. medical applications and dialogue agents). However, for fact verification, KGs have not been adequately utilized as a knowledge source. KGs can be a valuable knowledge source in fact verification due to their reliability and broad applicability. A KG consists of nodes and edges which makes it clear how concepts are linked together, allowing machines to reason over chains of topics. However, there are many challenges in understanding how these machine-readable concepts map to information in text. To enable the community to better use KGs, we introduce a new dataset, FactKG: Fact Verification via Reasoning on Knowledge Graphs. It consists of 108k natural language claims with five types of reasoning: One-hop, Conjunction, Existence, Multi-hop, and Negation. Furthermore, FactKG contains various linguistic patterns, including colloquial style claims as well as written style claims to increase practicality. Lastly, we develop a baseline approach and analyze FactKG over these reasoning types. We believe FactKG can advance both reliability and practicality in KG-based fact verification.

As an efficient approach to understand, generate, and process natural language texts, research in natural language processing (NLP) has exhibited a rapid spread and wide adoption in recent years. Given the increasing amount of research work in this area, several NLP-related approaches have been surveyed in the research community. However, a comprehensive study that categorizes established topics, identifies trends, and outlines areas for future research remains absent to this day. Contributing to closing this gap, we have systematically classified and analyzed research papers included in the ACL Anthology. As a result, we present a structured overview of the research landscape, provide a taxonomy of fields-of-study in NLP, analyze recent developments in NLP, summarize our findings, and highlight directions for future work.

We present our submission to the AXOLOTL-24 shared task. The shared task comprises two subtasks: identifying new senses that words gain with time (when comparing newer and older time periods) and producing the definitions for the identified new senses. We implemented a conceptually simple and computationally inexpensive solution to both subtasks. We trained adapter-based binary classification models to match glosses with usage examples and leveraged the probability output of the models to identify novel senses. The same models were used to match examples of novel sense usages with Wiktionary definitions. Our submission attained third place on the first subtask and the first place on the second subtask.

Local graph clustering methods aim to detect small clusters in very large graphs without the need to process the whole graph. They are fundamental and scalable tools for a wide range of tasks such as local community detection, node ranking and node embedding. While prior work on local graph clustering mainly focuses on graphs without node attributes, modern real-world graph datasets typically come with node attributes that provide valuable additional information. We present a simple local graph clustering algorithm for graphs with node attributes, based on the idea of diffusing mass locally in the graph while accounting for both structural and attribute proximities. Using high-dimensional concentration results, we provide statistical guarantees on the performance of the algorithm for the recovery of a target cluster with a single seed node. We give conditions under which a target cluster generated from a fairly general contextual random graph model, which includes both the stochastic block model and the planted cluster model as special cases, can be fully recovered with bounded false positives. Empirically, we validate all theoretical claims using synthetic data, and we show that incorporating node attributes leads to superior local clustering performances using real-world graph datasets.

Existing PTLM-based models for TSC can be categorized into two groups: 1) fine-tuning-based models that adopt PTLM as the context encoder; 2) prompting-based models that transfer the classification task to the text/word generation task. In this paper, we present a new perspective of leveraging PTLM for TSC: simultaneously leveraging the merits of both language modeling and explicit target-context interactions via contextual target attributes. Specifically, we design the domain- and target-constrained cloze test, which can leverage the PTLMs' strong language modeling ability to generate the given target's attributes pertaining to the review context. The attributes contain the background and property information of the target, which can help to enrich the semantics of the review context and the target. To exploit the attributes for tackling TSC, we first construct a heterogeneous information graph by treating the attributes as nodes and combining them with (1) the syntax graph automatically produced by the off-the-shelf dependency parser and (2) the semantics graph of the review context, which is derived from the self-attention mechanism. Then we propose a heterogeneous information gated graph convolutional network to model the interactions among the attribute information, the syntactic information, and the contextual information. The experimental results on three benchmark datasets demonstrate the superiority of our model, which achieves new state-of-the-art performance.

With the recent advances in natural language processing (NLP), a vast number of applications have emerged across various use cases. Among the plethora of NLP applications, many academic researchers are motivated to do work that has a positive social impact, in line with the recent initiatives of NLP for Social Good (NLP4SG). However, it is not always obvious to researchers how their research efforts are tackling today's big social problems. Thus, in this paper, we introduce NLP4SGPAPERS, a scientific dataset with three associated tasks that can help identify NLP4SG papers and characterize the NLP4SG landscape by: (1) identifying the papers that address a social problem, (2) mapping them to the corresponding UN Sustainable Development Goals (SDGs), and (3) identifying the task they are solving and the methods they are using. Using state-of-the-art NLP models, we address each of these tasks and use them on the entire ACL Anthology, resulting in a visualization workspace that gives researchers a comprehensive overview of the field of NLP4SG. Our website is available at https://nlp4sg.vercel.app . We released our data at https://huggingface.co/datasets/feradauto/NLP4SGPapers and code at https://github.com/feradauto/nlp4sg .

Text detoxification is a textual style transfer (TST) task where a text is paraphrased from a toxic surface form, e.g. featuring rude words, to the neutral register. Recently, text detoxification methods found their applications in various task such as detoxification of Large Language Models (LLMs) (Leong et al., 2023; He et al., 2024; Tang et al., 2023) and toxic speech combating in social networks (Deng et al., 2023; Mun et al., 2023; Agarwal et al., 2023). All these applications are extremely important to ensure safe communication in modern digital worlds. However, the previous approaches for parallel text detoxification corpora collection -- ParaDetox (Logacheva et al., 2022) and APPADIA (Atwell et al., 2022) -- were explored only in monolingual setup. In this work, we aim to extend ParaDetox pipeline to multiple languages presenting MultiParaDetox to automate parallel detoxification corpus collection for potentially any language. Then, we experiment with different text detoxification models -- from unsupervised baselines to LLMs and fine-tuned models on the presented parallel corpora -- showing the great benefit of parallel corpus presence to obtain state-of-the-art text detoxification models for any language.

The Petit Larousse illustr\'e is a French dictionary first published in 1905. Its division in two main parts on language and on history and geography corresponds to a major milestone in French lexicography as well as a repository of general knowledge from this period. Although the value of many entries from 1905 remains intact, some descriptions now have a dimension that is more historical than contemporary. They are nonetheless significant to analyze and understand cultural representations from this time. A comparison with more recent information or a verification of these entries would require a tedious manual work. In this paper, we describe a new lexical resource, where we connected all the dictionary entries of the history and geography part to current data sources. For this, we linked each of these entries to a wikidata identifier. Using the wikidata links, we can automate more easily the identification, comparison, and verification of historically-situated representations. We give a few examples on how to process wikidata identifiers and we carried out a small analysis of the entities described in the dictionary to outline possible applications. The resource, i.e. the annotation of 20,245 dictionary entries with wikidata links, is available from GitHub url{https://github.com/pnugues/petit_larousse_1905/

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

We present a new knowledge-base of hasPart relationships, extracted from a large corpus of generic statements. Complementary to other resources available, it is the first which is all three of: accurate (90% precision), salient (covers relationships a person may mention), and has high coverage of common terms (approximated as within a 10 year old's vocabulary), as well as having several times more hasPart entries than in the popular ontologies ConceptNet and WordNet. In addition, it contains information about quantifiers, argument modifiers, and links the entities to appropriate concepts in Wikipedia and WordNet. The knowledge base is available at https://allenai.org/data/haspartkb

We advocate for a strong integration of Computational Creativity (CC) with research in large language and vision models (LLVMs) to address a key limitation of these models, i.e., creative problem solving. We present preliminary experiments showing how CC principles can be applied to address this limitation. Our goal is to foster discussions on creative problem solving in LLVMs and CC at prestigious ML venues. Our code is available at: https://github.com/lnairGT/creative-problem-solving-LLMs

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

We present POTATO, a task- and languageindependent framework for human-in-the-loop (HITL) learning of rule-based text classifiers using graph-based features. POTATO handles any type of directed graph and supports parsing text into Abstract Meaning Representations (AMR), Universal Dependencies (UD), and 4lang semantic graphs. A streamlit-based user interface allows users to build rule systems from graph patterns, provides real-time evaluation based on ground truth data, and suggests rules by ranking graph features using interpretable machine learning models. Users can also provide patterns over graphs using regular expressions, and POTATO can recommend refinements of such rules. POTATO is applied in projects across domains and languages, including classification tasks on German legal text and English social media data. All components of our system are written in Python, can be installed via pip, and are released under an MIT License on GitHub.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

Named Entity Disambiguation (NED) refers to the task of resolving multiple named entity mentions in a document to their correct references in a knowledge base (KB) (e.g., Wikipedia). In this paper, we propose a novel embedding method specifically designed for NED. The proposed method jointly maps words and entities into the same continuous vector space. We extend the skip-gram model by using two models. The KB graph model learns the relatedness of entities using the link structure of the KB, whereas the anchor context model aims to align vectors such that similar words and entities occur close to one another in the vector space by leveraging KB anchors and their context words. By combining contexts based on the proposed embedding with standard NED features, we achieved state-of-the-art accuracy of 93.1% on the standard CoNLL dataset and 85.2% on the TAC 2010 dataset.

We present the results and main findings of SemEval-2020 Task 12 on Multilingual Offensive Language Identification in Social Media (OffensEval 2020). The task involves three subtasks corresponding to the hierarchical taxonomy of the OLID schema (Zampieri et al., 2019a) from OffensEval 2019. The task featured five languages: English, Arabic, Danish, Greek, and Turkish for Subtask A. In addition, English also featured Subtasks B and C. OffensEval 2020 was one of the most popular tasks at SemEval-2020 attracting a large number of participants across all subtasks and also across all languages. A total of 528 teams signed up to participate in the task, 145 teams submitted systems during the evaluation period, and 70 submitted system description papers.

We provide a literature review about Automatic Text Summarization (ATS) systems. We consider a citation-based approach. We start with some popular and well-known papers that we have in hand about each topic we want to cover and we have tracked the "backward citations" (papers that are cited by the set of papers we knew beforehand) and the "forward citations" (newer papers that cite the set of papers we knew beforehand). In order to organize the different methods, we present the diverse approaches to ATS guided by the mechanisms they use to generate a summary. Besides presenting the methods, we also present an extensive review of the datasets available for summarization tasks and the methods used to evaluate the quality of the summaries. Finally, we present an empirical exploration of these methods using the CNN Corpus dataset that provides golden summaries for extractive and abstractive methods.

We present the Claire French Dialogue Dataset (CFDD), a resource created by members of LINAGORA Labs in the context of the OpenLLM France initiative. CFDD is a corpus containing roughly 160 million words from transcripts and stage plays in French that we have assembled and publicly released in an effort to further the development of multilingual, open source language models. This paper describes the 24 individual corpora of which CFDD is composed and provides links and citations to their original sources. It also provides our proposed breakdown of the full CFDD dataset into eight categories of subcorpora and describes the process we followed to standardize the format of the final dataset. We conclude with a discussion of similar work and future directions.

The process of annotating data within the legal sector is filled with distinct challenges that differ from other fields, primarily due to the inherent complexities of legal language and documentation. The initial task usually involves selecting an appropriate raw dataset that captures the intricate aspects of legal texts. Following this, extracting text becomes a complicated task, as legal documents often have complex structures, footnotes, references, and unique terminology. The importance of data cleaning is magnified in this context, ensuring that redundant information is eliminated while maintaining crucial legal details and context. Creating comprehensive yet straightforward annotation guidelines is imperative, as these guidelines serve as the road map for maintaining uniformity and addressing the subtle nuances of legal terminology. Another critical aspect is the involvement of legal professionals in the annotation process. Their expertise is valuable in ensuring that the data not only remains contextually accurate but also adheres to prevailing legal standards and interpretations. This paper provides an expanded view of these challenges and aims to offer a foundational understanding and guidance for researchers and professionals engaged in legal data annotation projects. In addition, we provide links to our created and fine-tuned datasets and language models. These resources are outcomes of our discussed projects and solutions to challenges faced while working on them.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy dataset expands the volume and diversity of existing molecular datasets. Our extensive benchmarks of the state-of-the-art graph neural network models on Alchemy clearly manifest the usefulness of new data in validating and developing machine learning models for chemistry and material science. We further launch a contest to attract attentions from researchers in the related fields. More details can be found on the contest website https://alchemy.tencent.com. At the time of benchamrking experiment, we have generated 119,487 molecules in our Alchemy dataset. More molecular samples are generated since then. Hence, we provide a list of molecules used in the reported benchmarks.

Context: Test-driven development (TDD) is a widely employed software development practice that involves developing test cases based on requirements prior to writing the code. Although various methods for automated test case generation have been proposed, they are not specifically tailored for TDD, where requirements instead of code serve as input. Objective: In this paper, we introduce a text-to-testcase generation approach based on a large language model (GPT-3.5) that is fine-tuned on our curated dataset with an effective prompt design. Method: Our approach involves enhancing the capabilities of basic GPT-3.5 for text-to-testcase generation task that is fine-tuned on our curated dataset with an effective prompting design. We evaluated the effectiveness of our approach using a span of five large-scale open-source software projects. Results: Our approach generated 7k test cases for open source projects, achieving 78.5% syntactic correctness, 67.09% requirement alignment, and 61.7% code coverage, which substantially outperforms all other LLMs (basic GPT-3.5, Bloom, and CodeT5). In addition, our ablation study demonstrates the substantial performance improvement of the fine-tuning and prompting components of the GPT-3.5 model. Conclusions: These findings lead us to conclude that fine-tuning and prompting should be considered in the future when building a language model for the text-to-testcase generation task

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

We investigated the evolution and transformation of scientific knowledge in the early modern period, analyzing more than 350 different editions of textbooks used for teaching astronomy in European universities from the late fifteenth century to mid-seventeenth century. These historical sources constitute the Sphaera Corpus. By examining different semantic relations among individual parts of each edition on record, we built a multiplex network consisting of six layers, as well as the aggregated network built from the superposition of all the layers. The network analysis reveals the emergence of five different communities. The contribution of each layer in shaping the communities and the properties of each community are studied. The most influential books in the corpus are found by calculating the average age of all the out-going and in-coming links for each book. A small group of editions is identified as a transmitter of knowledge as they bridge past knowledge to the future through a long temporal interval. Our analysis, moreover, identifies the most disruptive books. These books introduce new knowledge that is then adopted by almost all the books published afterwards until the end of the whole period of study. The historical research on the content of the identified books, as an empirical test, finally corroborates the results of all our analyses.

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

We study a new connection between a technical measure called mu-conductance that arises in the study of Markov chains for sampling convex bodies and the network community profile that characterizes size-resolved properties of clusters and communities in social and information networks. The idea of mu-conductance is similar to the traditional graph conductance, but disregards sets with small volume. We derive a sequence of optimization problems including a low-rank semi-definite program from which we can derive a lower bound on the optimal mu-conductance value. These ideas give the first theoretically sound bound on the behavior of the network community profile for a wide range of cluster sizes. The algorithm scales up to graphs with hundreds of thousands of nodes and we demonstrate how our framework validates the predicted structures of real-world graphs.

Graph neural networks achieve high accuracy in link prediction by jointly leveraging graph topology and node attributes. Topology, however, is represented indirectly; state-of-the-art methods based on subgraph classification label nodes with distance to the target link, so that, although topological information is present, it is tempered by pooling. This makes it challenging to leverage features like loops and motifs associated with network formation mechanisms. We propose a link prediction algorithm based on a new pooling scheme called WalkPool. WalkPool combines the expressivity of topological heuristics with the feature-learning ability of neural networks. It summarizes a putative link by random walk probabilities of adjacent paths. Instead of extracting transition probabilities from the original graph, it computes the transition matrix of a "predictive" latent graph by applying attention to learned features; this may be interpreted as feature-sensitive topology fingerprinting. WalkPool can leverage unsupervised node features or be combined with GNNs and trained end-to-end. It outperforms state-of-the-art methods on all common link prediction benchmarks, both homophilic and heterophilic, with and without node attributes. Applying WalkPool to a set of unsupervised GNNs significantly improves prediction accuracy, suggesting that it may be used as a general-purpose graph pooling scheme.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

The study of network robustness is a critical tool in the characterization and sense making of complex interconnected systems such as infrastructure, communication and social networks. While significant research has been conducted in all of these areas, gaps in the surveying literature still exist. Answers to key questions are currently scattered across multiple scientific fields and numerous papers. In this survey, we distill key findings across numerous domains and provide researchers crucial access to important information by--(1) summarizing and comparing recent and classical graph robustness measures; (2) exploring which robustness measures are most applicable to different categories of networks (e.g., social, infrastructure; (3) reviewing common network attack strategies, and summarizing which attacks are most effective across different network topologies; and (4) extensive discussion on selecting defense techniques to mitigate attacks across a variety of networks. This survey guides researchers and practitioners in navigating the expansive field of network robustness, while summarizing answers to key questions. We conclude by highlighting current research directions and open problems.

Node classification is a classical graph machine learning task on which Graph Neural Networks (GNNs) have recently achieved strong results. However, it is often believed that standard GNNs only work well for homophilous graphs, i.e., graphs where edges tend to connect nodes of the same class. Graphs without this property are called heterophilous, and it is typically assumed that specialized methods are required to achieve strong performance on such graphs. In this work, we challenge this assumption. First, we show that the standard datasets used for evaluating heterophily-specific models have serious drawbacks, making results obtained by using them unreliable. The most significant of these drawbacks is the presence of a large number of duplicate nodes in the datasets Squirrel and Chameleon, which leads to train-test data leakage. We show that removing duplicate nodes strongly affects GNN performance on these datasets. Then, we propose a set of heterophilous graphs of varying properties that we believe can serve as a better benchmark for evaluating the performance of GNNs under heterophily. We show that standard GNNs achieve strong results on these heterophilous graphs, almost always outperforming specialized models. Our datasets and the code for reproducing our experiments are available at https://github.com/yandex-research/heterophilous-graphs

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

We present the results and the main findings of SemEval-2020 Task 11 on Detection of Propaganda Techniques in News Articles. The task featured two subtasks. Subtask SI is about Span Identification: given a plain-text document, spot the specific text fragments containing propaganda. Subtask TC is about Technique Classification: given a specific text fragment, in the context of a full document, determine the propaganda technique it uses, choosing from an inventory of 14 possible propaganda techniques. The task attracted a large number of participants: 250 teams signed up to participate and 44 made a submission on the test set. In this paper, we present the task, analyze the results, and discuss the system submissions and the methods they used. For both subtasks, the best systems used pre-trained Transformers and ensembles.

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

While textual information significantly enhances the performance of pre-trained language models (PLMs) in knowledge graph completion (KGC), the static and noisy nature of existing corpora collected from Wikipedia articles or synsets definitions often limits the potential of PLM-based KGC models. To surmount these challenges, we introduce the Contextualization Distillation strategy, a versatile plug-in-and-play approach compatible with both discriminative and generative KGC frameworks. Our method begins by instructing large language models (LLMs) to transform compact, structural triplets into context-rich segments. Subsequently, we introduce two tailored auxiliary tasks, reconstruction and contextualization, allowing smaller KGC models to assimilate insights from these enriched triplets. Comprehensive evaluations across diverse datasets and KGC techniques highlight the efficacy and adaptability of our approach, revealing consistent performance enhancements irrespective of underlying pipelines or architectures. Moreover, our analysis makes our method more explainable and provides insight into generating path selection, as well as the choosing of suitable distillation tasks. All the code and data in this work will be released at https://github.com/David-Li0406/Contextulization-Distillation

Competitive Debate's increasingly technical nature has left competitors looking for tools to accelerate evidence production. We find that the unique type of extractive summarization performed by competitive debaters - summarization with a bias towards a particular target meaning - can be performed using the latest innovations in unsupervised pre-trained text vectorization models. We introduce CX_DB8, a queryable word-level extractive summarizer and evidence creation framework, which allows for rapid, biasable summarization of arbitarily sized texts. CX_DB8s usage of the embedding framework Flair means that as the underlying models improve, CX_DB8 will also improve. We observe that CX_DB8 also functions as a semantic search engine, and has application as a supplement to traditional "find" functionality in programs and webpages. CX_DB8 is currently used by competitive debaters and is made available to the public at https://github.com/Hellisotherpeople/CX_DB8

Traditional social media platforms, once envisioned as digital town squares, face growing criticism over corporate control, content moderation, and privacy concerns. Events such as Twitter's acquisition(now X) and major policy changes have driven users toward alternative platforms like Mastodon and Threads. However, this diversification has led to user dispersion and fragmented discussions across isolated social media platforms. To address these issues, federation protocols like ActivityPub have been adopted, with Mastodon leading efforts to build decentralized yet interconnected networks. In March 2024, Threads joined this federation by introducing its Fediverse Sharing service, which enables interactions such as posts, replies, and likes between Threads and Mastodon users as if on a unified platform. Building on this development, we introduce FediverseSharing, the first dataset capturing interactions between 20,000+ Threads users and 20,000+ Mastodon users over a ten-month period. This dataset serves as a foundation for studying cross-platform interactions and the impact of federation as previously two separate platforms integrate.

In the last decade, several organizations have produced documents intended to standardize, in the normative sense, and promote guidance to our recent and rapid AI development. However, the full spectrum of ideas presented in these documents has not yet been analyzed, except for a few meta-analyses and critical reviews of the field. In this work, we seek to expand on the work done by past researchers and create a tool for better data visualization of the contents and nature of these documents, to understand whether there is consensus or similarity between the principles espoused by various institutions, which may inspire debates on future regulations. We also provide some preliminary thoughts and questions that could guide the continuity of the research through a critical analysis of the results acquired by our methodology into a sample size of 200 documents.

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP

User profiling has long been an important problem that investigates user interests in many real applications. Some recent works regard users and their interacted objects as entities of a graph and turn the problem into a node classification task. However, they neglect the difference of distinct interaction types, e.g. user clicks an item v.s.user purchases an item, and thus cannot incorporate such information well. To solve these issues, we propose to leverage the relation-aware heterogeneous graph method for user profiling, which also allows capturing significant meta relations. We adopt the query, key, and value mechanism in a transformer fashion for heterogeneous message passing so that entities can effectively interact with each other. Via such interactions on different relation types, our model can generate representations with rich information for the user profile prediction. We conduct experiments on two real-world e-commerce datasets and observe a significant performance boost of our approach.