Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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PrePR-CT github.com
Graph-based model using cell-type-specific co-expression networks as inductive priors for small-data chemical perturbation response prediction.
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PASO github.com
Pathway-aware multi-omics drug response model combining pathway-difference features, multi-scale convolutions, Transformer encoding, and drug SMILES.
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OmicsFM github.com
Modality-agnostic molecular-expression foundation model with matched proteomics, bulk-transcriptomics, and single-cell-transcriptomics checkpoints.
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ChromFound github.com
Genome-aware scATAC-seq foundation model pretrained on 1.97M cells across tissues and disease contexts for zero-shot cell representations, annotation, and cross-omics prediction.
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TESSERA github.com
Cancer-genome foundation model jointly pretrained on somatic SNVs and copy-number alterations from TCGA using masked reconstruction and cross-modal contrastive learning.
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cycleCDR github.com
Interpretable cycle-consistency framework for modeling cellular responses to drug perturbations.
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DeepAEG github.com
GNN embedding + attention mechanism.
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MCPINN github.com
Drug discovery via compound-protein interaction and machine learning.
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NbBayesLM github.com
Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. Paper
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Chem-PerturBridge github.com
Harmonized compendium and processing pipelines for small-molecule perturbation transcriptomics across heterogeneous assays and gene panels.
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drGAT github.com
Attention-based model for drug response prediction with gene explainability.
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THERAPI github.com
Cell-line-to-patient transfer framework that aligns tumor transcriptomes with cancer cell lines and integrates perturbation and gene-level representations for patient drug response prediction.
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Casanovo Foundation github.com
Tandem mass-spectrometry proteomics foundation model that reuses a pretrained Casanovo spectrum encoder for spectrum quality, chimericity, and post-translational-modification prediction.
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DGDRP github.com
Multi-view embedding neural network.
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DrugAgent github.com
Multi-agent biomedical evidence synthesis framework for computational drug discovery with reliability-aware aggregation.
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SpatialGlue github.com
Graph attention network for spatial multi-omics integration jointly embedding spatial transcriptomics with chromatin accessibility or proteomics.
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SaProt github.com
Structure-aware protein language model using structure-aware tokens that encode both sequence and backbone geometry for improved function prediction.
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TOSICA github.com
Transformer-based framework for one-stop interpretable cell-type annotation supporting cross-dataset and cross-species transfer.
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HiDRA github.com
Hierarchical network model incorporating gene and pathway-level information for cancer drug response prediction.
