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requirements.txt

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+# Foundational Libraries (core dependencies)
+setuptools==59.5.0
+numpy==1.23.5            # Pin numpy to ensure compatibility
+scipy==1.9.3             # Install scipy after numpy
+pandas==1.5.3            # Pin pandas to avoid dask incompatibilities
+
+# Libraries dependent on numpy, pandas, or scipy
+numba==0.58.1
+dask==2023.4.1           # Use a stable version compatible with pandas==1.5.3
+scikit-learn==1.2.2
+imageio==2.34.0
+matplotlib==3.7.1
+seaborn==0.12.2
+wordcloud==1.9.3
+
+# Machine Learning and Deep Learning
+torchmetrics==0.10.3
+pytorch-lightning==1.9.5
+transformers==4.29.2
+deepspeed==0.9.2
+accelerate==0.19.0
+diffusers==0.16.1
+optuna==3.1.1
+fair-esm==2.0.0
+
+# Specialized Libraries
+lightning-flash==0.8.2
+axial-positional-embedding==0.2.1
+linear-attention-transformer==0.19.1
+linformer==0.2.3
+
+# Bioinformatics
+biopython==1.79
+
+# General Utilities
+tqdm==4.65.0
+pynvml==11.5.0
+

torch_requirements.sh

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+#!/bin/bash
+
+conda install pytorch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 pytorch-cuda=11.7 -c pytorch -c nvidia