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  1. README.md +203 -0
  2. config.json +17 -0
  3. vocab.txt +0 -0
README.md ADDED
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+ ---
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+ # For reference on model card metadata, see the spec: https://github.com/huggingface/hub-docs/blob/main/modelcard.md?plain=1
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+ # Doc / guide: https://huggingface.co/docs/hub/model-cards
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+ {}
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+ ---
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+ # Bio Clinical BERT with MIMIC and Padchest
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+ <!-- Provide a quick summary of what the model is/does. -->
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+ The Publicly Available Clinical BERT Embeddings paper contains four unique BioclinicalBERT models: initialized with BERT-Base (biobert_v1.0_pubmed_pmc) or BioBERT (BioBERT-Base v1.0 + PubMed 200K + PMC 270K) & trained on either all MIMIC notes or only discharge summaries.
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+ This model card describes the Bio+Clinical BERT model, which was initialized from BioBERT & trained on all MIMIC notes and Padchest (translate to English by google translation).
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+ ## Model Details
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+ ### Model Description
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+ <!-- Provide a longer summary of what this model is. -->
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+ - **Developed by:** [More Information Needed]
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+ - **Shared by [optional]:** [More Information Needed]
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+ - **Model type:** [More Information Needed]
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+ - **Language(s) (NLP):** [More Information Needed]
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+ - **License:** [More Information Needed]
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+ - **Finetuned from model [optional]:** [More Information Needed]
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+ ### Model Sources [optional]
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+ <!-- Provide the basic links for the model. -->
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+ - **Repository:** [More Information Needed]
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+ - **Paper [optional]:** [More Information Needed]
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+ - **Demo [optional]:** [More Information Needed]
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+ ## Uses
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+ <!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->
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+ ### Direct Use
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+ <!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. -->
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+ [More Information Needed]
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+ ### Downstream Use [optional]
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+ <!-- This section is for the model use when fine-tuned for a task, or when plugged into a larger ecosystem/app -->
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+ [More Information Needed]
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+ ### Out-of-Scope Use
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+ <!-- This section addresses misuse, malicious use, and uses that the model will not work well for. -->
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+ [More Information Needed]
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+ ## Bias, Risks, and Limitations
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+ <!-- This section is meant to convey both technical and sociotechnical limitations. -->
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+ [More Information Needed]
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+ ### Recommendations
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+ <!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
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+ Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
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+ ## How to Get Started with the Model
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+ Use the code below to get started with the model.
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+ [More Information Needed]
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+ ## Training Details
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+ ### Training Data
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+ <!-- This should link to a Data Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
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+ [More Information Needed]
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+ ### Training Procedure
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+ <!-- This relates heavily to the Technical Specifications. Content here should link to that section when it is relevant to the training procedure. -->
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+ #### Preprocessing [optional]
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+ [More Information Needed]
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+ #### Training Hyperparameters
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+ - **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->
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+ #### Speeds, Sizes, Times [optional]
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+ <!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. -->
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+ [More Information Needed]
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+ ## Evaluation
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+ <!-- This section describes the evaluation protocols and provides the results. -->
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+ ### Testing Data, Factors & Metrics
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+ #### Testing Data
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+ <!-- This should link to a Data Card if possible. -->
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+ [More Information Needed]
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+ #### Factors
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+ <!-- These are the things the evaluation is disaggregating by, e.g., subpopulations or domains. -->
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+ [More Information Needed]
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+ #### Metrics
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+ <!-- These are the evaluation metrics being used, ideally with a description of why. -->
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+ [More Information Needed]
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+ ### Results
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+ [More Information Needed]
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+ #### Summary
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+ ## Model Examination [optional]
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+ <!-- Relevant interpretability work for the model goes here -->
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+ [More Information Needed]
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+ ## Environmental Impact
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+ <!-- Total emissions (in grams of CO2eq) and additional considerations, such as electricity usage, go here. Edit the suggested text below accordingly -->
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+ Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).
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+ - **Hardware Type:** [More Information Needed]
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+ - **Hours used:** [More Information Needed]
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+ - **Cloud Provider:** [More Information Needed]
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+ - **Compute Region:** [More Information Needed]
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+ - **Carbon Emitted:** [More Information Needed]
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+ ## Technical Specifications [optional]
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+ ### Model Architecture and Objective
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+ [More Information Needed]
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+ ### Compute Infrastructure
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+ [More Information Needed]
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+ #### Hardware
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+ [More Information Needed]
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+ #### Software
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+ ## Citation [optional]
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+ <!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->
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+ **BibTeX:**
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+ [More Information Needed]
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+ **APA:**
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+ ## Glossary [optional]
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+ <!-- If relevant, include terms and calculations in this section that can help readers understand the model or model card. -->
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+ [More Information Needed]
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+ ## More Information [optional]
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+ [More Information Needed]
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+ ## Model Card Authors [optional]
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+ [More Information Needed]
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+ ## Model Card Contact
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+ [More Information Needed]
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config.json ADDED
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+ {
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+ "attention_probs_dropout_prob": 0.1,
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+ "do_lower_case": false,
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+ "hidden_act": "gelu",
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+ "hidden_dropout_prob": 0.1,
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+ "hidden_size": 768,
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+ "initializer_range": 0.02,
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+ "intermediate_size": 3072,
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+ "layer_norm_eps": 1e-12,
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+ "max_position_embeddings": 512,
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+ "model_type": "bert",
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+ "num_attention_heads": 12,
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+ "num_hidden_layers": 12,
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+ "pad_token_id": 0,
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+ "type_vocab_size": 2,
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+ "vocab_size": 28996
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+ }
vocab.txt ADDED
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