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Transformer that translates fragment ion peaks into peptide sequences for database-free de novo sequencing in large-scale proteomics, with InstaNovo+ extending it as a multinomial diffusion model that iteratively refines predicted sequences, plus InstaNovo-P for phosphoproteomics and Winnow for calibrated confidence with FDR control (130+ stars, Apache 2.0, actively maintained)

Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

PyTorch-based embedding instance segmentation algorithm optimized for accurate, efficient, and portable cell and nucleus segmentation across fluorescence and brightfield microscopy images, achieving state-of-the-art speed and accuracy with lightweight model sizes suitable for edge deployment (224+ stars, Apache 2.0)

Toolbox for comparative genomics of MAGs

A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.

A two-step desktop GUI application for RNA-seq differential gene expression (DEG) analysis. Step 1 reads raw GDC/TCGA STAR gene-count files together with a GDC sample sheet, matches samples to a Tumor/Normal design, and runs PyDESeq2 to produce normalized counts and DEG statistics. Step 2 generates publication-style volcano plots, MA plots, summary bar charts, and expression heatmaps (with optional gene labeling) from the results, exportable as PNG, PDF, SVG, or TIFF. Requires no coding from the user.

Closed-loop multi-agent system from hypothesis to verification across 12 scientific tasks, #1 on MLE-Bench (36.44%)

For a convenient overview and download list, visit our model page for this model.

Local-first, conversational AI research partner for multi-omics analysis with CLI, desktop app, and 95+ reproducible skills; keeps raw data local while routing natural-language requests to Python/R/CLI tools with persistent memory, autonomous analysis paths, and multi-method consensus workflows (TianGzlab, 155+ stars, Apache 2.0, 2026)

A genomic surveillance framework for Staphylococcus aureus

Agent skills (SKILL.md + deterministic tools) for the AI4S workflow — topic exploration, literature survey, runnable experiments, publication-grade papers, and integrity audit, with every citation and number traceable to its source (by ai4s-research, maintainers of this list; MIT, 2026)

464 fine-tuned DNABERT models for regulatory variant effect prediction

This tool estimates the completeness of KEGG pathway modules from the presence or absence of KEGG orthologues (KOs)

Biological vision foundation model trained on TreeOfLife-200M, yielding extraordinary accuracy on diverse biological visual tasks including habitat classification and trait prediction despite a narrow training objective (Ohio State University Imageomics Institute)

A local command-line tool for ancestral sequence reconstruction with gap-state inference using IQ-TREE. It supports nucleotide, amino acid, and codon sequence alignments and reports site-wise posterior probabilities of ancestral states.

REFUTE is an open benchmark for scientific critique honesty and epistemic calibration on recent life-science and biomedical literature. It tests whether models keep claims inside what the evidence allows (overclaim / planted-flaw / falsifier selection) and whether stated confidence is calibrated, with judge-free MCQ axes plus open-ended critique scoring.

LLM agents for working with the SRA (Sequence Read Archive) and associated bioinformatics databases, enabling natural language querying of high-throughput sequencing data and metadata across genomic repositories (Arc Institute, 169+ stars, 2024-2026)

PMGen (Peptide MHC Generator) is a comprehensive pipeline for predicting peptide-MHC (pMHC) complex structures and designing optimized peptide sequences.

Trinity-Mini-AI-Scientist

In search engines, rerankers are crucial for improving the accuracy of your retrieval system.

In search engines, rerankers are crucial for improving the accuracy of your retrieval system.

In retrieval systems, embedding models determine the quality of your search.

Machine learning model predicting cellular perturbation response across diverse contexts with State Transition (ST) and State Embedding (SE) variants, featuring CLI tooling, PyPI distribution, and Virtual Cell Challenge integration (575+ stars)

MoLFormer is a class of models pretrained on SMILES string representations of up to 1.1B molecules from ZINC and PubChem. This repository is for the model pretrained on 10% of both datasets.

First open-source agentic AI physicist turning research questions into structured workflows with rigorous verification and multi-step analytical work for long-horizon physics projects; integrates with Claude Code, Codex, Gemini CLI, and OpenCode (804+ stars, Apache 2.0, 2026)

The commands below use the glyph package. Install it from the code repository:

Advanced OCR with PP-StructureV3 document parsing, 13% accuracy improvement, supports 80+ languages

SDK & library for AI-driven scientific computing applications

Open-source biomedical AI platform integrating multimodal foundation models (BioMedGPT, PharmolixFM, LangCell) with agentic workflows and 45+ Claude Code skills for drug discovery, protein engineering, and single-cell omics analysis (PharMolix & Tsinghua AIR, 1K+ stars, 2023-2026)

Graph neural network interatomic potential package supporting efficient multi-GPU parallel molecular dynamics simulations, enabling large-scale atomistic modeling with machine learning potentials (MDIL-SNU, MIT License)

This is a QLoRA adapter for query-focused structured extraction from one PubMed title and abstract. It was trained as part of BioEvidence Copilot and targets the repository's versioned ModelEvidenceExtraction JSON Schema.

SMBGC Annotation using Neural Networks Trained on Interpro Signatures

Healthcare Brain Procedure Surgery NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of surgical procedures, diagnostic tests, interventions, and procedural details from unstructured clinical text.

Curated, multilingual library of 182 installable AI agent skills for end-to-end academic research spanning literature discovery, scientific writing, grant development, bioinformatics, drug discovery, clinical research, machine learning, and data analysis (779+ stars, MIT License, 2026)

Healthcare Brain Vitals NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of vital signs, body measurements, and physiological parameters from clinical text.

Healthcare Brain Laboratory NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of laboratory test results, values, units, reference ranges, and abnormality flags from unstructured clinical text.

Healthcare Brain Diagnosis ICD NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of diagnoses, conditions, and support for ICD-10/SNOMED code mapping from unstructured clinical text.

Healthcare Brain Medication NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of medication names, dosages, routes, frequencies, and administration details from unstructured clinical text.

Healthcare Brain Clinical Findings NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of clinical findings, diseases, conditions, anatomical locations, and clinical modifiers from unstructured clinical text.

Healthcare Brain NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated detection and de-identification of Protected Health Information (PHI) and Personally Identifiable Information (PII) in unstructured clinical text.

CliniGuard Laboratory NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of laboratory test results, values, units, reference ranges, and abnormality flags from unstructured clinical text.

Open-source implementation of AlphaEvolve's evolutionary coding agent paradigm, enabling LLMs to autonomously discover and optimize algorithms through iterative evolution, matching the approach behind DeepMind's breakthrough matrix multiplication discovery (6.2K+ stars, 2025)

CliniGuard Diagnosis ICD NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of diagnoses, conditions, and support for ICD-10/SNOMED code mapping from unstructured clinical text.

CliniGuard Medication NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of medication names, dosages, routes, frequencies, and administration details from unstructured clinical text.

CliniGuard Clinical Findings NER is a transformer-based clinical Named Entity Recognition model developed by Genzeon Platforms for automated extraction of clinical findings, diseases, conditions, anatomical locations, and clinical modifiers from unstructured clinical text.

102 executable tasks from 44 peer-reviewed papers across 4 disciplines with containerized evaluation

# DrugGen 2: A disease-aware language model for enhancing drug discovery DrugGen-2 is a disease‑aware language model specialized for generating drug-like SMILES structures based on both disease pathways and protein sequence.

A python-based workflow manager.