Repository Index

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

Open source tumor evidence matching for sequencing labs and hospitals without molecular tumor boards. Research prototype; oncologist review required.

• bioinformatics
• cancer-research
• computational-biology
• drug-repurposing

ChemML is a machine learning and informatics program suite for the chemical and materials sciences.

• quantum-mechanics
• materials-informatics
• data-science
• machine-learning

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network

Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.

• cheminformatics
• dft-calculations
• automation
• feature

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

TypeDB Bio: Biomedical Knowledge Graph

• bioinformatics
• knowledge-graph
• knowledge-base
• drug-discovery

Autonomous multi-agent framework to optimize scientific software

• acceleration
• agentic-ai
• ai-agents
• bioinformatics

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

A cheminformatics extension for the SQLAlchemy database toolkit.

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution