Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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TargetDiff github.com
3D equivariant diffusion model for structure-based drug design.
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UCE github.com
Universal Cell Embeddings: zero-shot single-cell embedding model trained on 36M cells across species, tissues, and assays without fine-tuning.
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PathomicFusion github.com
Integrated framework fusing histopathology and genomic features via CNN, GNN, and attention gating for cancer diagnosis and prognosis.
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GenePT github.com
Foundation LLM for single-cell data.
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GraphDTA github.com
Graph neural network–based DTI prediction using molecular graphs.
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DeepDTA github.com
Deep learning model using CNNs on protein sequences and drug SMILES.
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Borzoi github.com
Extended successor to Enformer for predicting RNA-seq coverage from long genomic sequence windows (524 kb) with improved resolution.
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PORPOISE github.com
Pan-cancer integrative histology-genomic analysis framework using multimodal deep learning for patient stratification.
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Caduceus github.com
Bidirectional equivariant long-range DNA sequence model based on Mamba.
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Ankh github.com
Efficient protein language model optimized for downstream prediction tasks including secondary structure, localization, and function annotation.
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MolTrans github.com
Transformer-based DTI model leveraging molecular substructures.
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MUSK github.com
Vision-language foundation model for precision oncology analyzing multimodal paired text and pathology image data for biomarker prediction and retrieval.
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AutoBA github.com
Automated multi-omics analysis agent that plans, executes, and repairs bioinformatics workflows from natural-language objectives.
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modernGENA github.com
ModernBERT-style DNA foundation-model family pretrained on hundreds of vertebrate genome assemblies for efficient long-sequence regulatory modeling.
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Numbat github.com
Haplotype-aware copy number variation inference from single-cell RNA-seq using hidden Markov models.
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CellCharter github.com
Identification and characterization of spatial cell niches from spatial transcriptomics using VAEs and Gaussian mixture models.
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MolT5 github.com
Language model for molecular tasks bridging text and SMILES, enabling molecule captioning and text-driven molecule generation.
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DTINet github.com
Network-based framework integrating heterogeneous biological data for DTI prediction.
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scPerturb github.com
Curated and continuously updated single-cell perturbation data resource spanning CRISPR and drug perturbation studies.
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JUMP Cell Painting Datasets github.com
Consortium-scale cell imaging perturbation datasets (chemical and genetic) for phenotypic profiling and drug discovery research.
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MOGONET github.com
Multi-omics graph convolutional network framework for patient classification and biomarker identification.
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TOAD github.com
Tumor Origin Assessment via Deep-learning; weakly-supervised multi-task model predicting cancer primary origin from H&E whole-slide images.
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CellOT github.com
Neural optimal transport framework for predicting single-cell responses to drug and genetic perturbations.
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MolGPT github.com
Transformer-based model for molecular generation.
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RiNALMo github.com
RNA language-model family pretrained on tens of millions of RNA sequences for secondary-structure and functional prediction tasks.
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Nicheformer github.com
Foundation model for single-cell and spatial omics using a transformer architecture with positional embeddings to encode spatial cell information.
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SATURN github.com
Transformer-based model integrating gene expression and protein sequences via a protein language model to learn unified multi-species cell embeddings.
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OpenBioLink github.com
Benchmark datasets for biological knowledge graph completion.
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ChatDrug github.com
LLM-based conversational pipeline for drug discovery, using natural language prompts for iterative drug editing and optimization.
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scPRINT github.com
Pretrained on 50M cells for scRNA-seq denoising & zero imputation.
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CellFlow github.com
Conditional flow-matching framework for modeling and predicting cellular phenotypes under chemical, genetic, and other perturbations.
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chemCPA github.com
Compositional perturbation autoencoder for predicting single-cell transcriptional responses to unseen drug perturbations and dose combinations.
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TransformerCPI github.com
CPI prediction using Transformer.
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STELLA github.com
Self-evolving biomedical research agent that expands its tool repertoire and supports literature reasoning, computational analysis, and laboratory-oriented scientific workflows.
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VirTues github.com
Spatial-proteomics foundation model learning marker-aware representations across proteins, cells, niches, and tissues from multiplexed imaging.
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DrugBAN github.com
Bilinear attention network for interpretable DTI prediction.
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COMMOT github.com
Optimal transport-based framework for screening cell-cell communication in spatial transcriptomics.
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BioMedAgent github.com
Self-evolving multi-agent framework for autonomous biomedical data analysis with tool discovery, workflow planning, code generation, execution, correction, and cross-omics analysis.
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scGPT-spatial github.com
Extension of scGPT for spatial transcriptomics with continual pretraining and a mixture-of-experts decoder for spatial gene expression analysis.
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FLIP (Fitness Landscape Inference for Proteins) github.com
Benchmark collection of protein fitness landscape datasets for evaluating protein ML models.
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LINGER github.com
Neural network for gene regulatory network inference from single-cell multiome (RNA+ATAC-seq) data with bulk data pretraining.
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GenoMAS github.com
Multi-agent framework for code-driven gene-expression analysis with planning, execution, debugging, backtracking, and GEO/TCGA-based scientific discovery.
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Medea github.com
Multi-agent therapeutic discovery system combining research planning, biological data analysis, literature reasoning, and multi-LLM deliberation across single-cell, cell-line, and patient contexts.
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GeneCompass github.com
Large-scale foundation model integrating DNA regulatory sequences and single-cell transcriptomics from 120M+ cells across multiple species for gene regulation prediction.
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NCEM github.com
GNN-based model for learning intercellular communication from spatial graphs of cells.
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Sei github.com
Sequence-to-function framework learning a genome-wide regulatory activity code from DNA sequences for variant effect prediction.
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CellFM github.com
800M-parameter single-cell foundation model pretrained on transcriptomics from 100 million human cells for annotation, integration, gene-function, and perturbation tasks.
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BioMaster github.com
Multi-agent system for automated and auditable bioinformatics workflows spanning RNA-seq, ChIP-seq, single-cell, spatial omics, Hi-C, long reads, metagenomics, and proteomics.
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FlashDeconv github.com
High-performance spatial transcriptomics deconvolution (~1M spots in ~3 min).
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CellPLM github.com
Cell pre-trained language model with inter-cell transformer architecture for diverse single-cell analysis tasks.
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