scgpt

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

Benchmarks four single-cell foundation models: scGPT, UCE, SCimilarity, and Transcriptformer in a zero-shot setting across four downstream tasks:

PhenoSeq: Conditional Diffusion Model; Generating Transcriptomic Representations from Cell Painting Images

Recovering gene regulatory networks from Perturb-seq by fitting steady-state ODEs through frozen single-cell foundation models (GenBio @ ICML 2026)

Patient-aware benchmark of frozen scGPT versus Scanpy/PCA on 29,614 NSCLC single cells with held-out evaluation and sample-level analysis

Автосервис в Минске. Качественный ремонт авто.

Companion code for the PLOS ONE paper 'What topological and geometric structure do biological foundation models learn? Evidence from 141 hypotheses'.

Causal token interventions for validating gene regulatory network inference from single-cell foundation models

Reproducible pipelines comparing bulk RNA-seq, single-cell (pseudobulk), and scFM embeddings (scGPT, scFoundation) for per-drug response prediction in cancer cell lines.

BG Internship 2026 Group 7: scGPT embeddings, cAE batch correction, strict 35-month OS prediction (v5 pipeline).

scGPT fine-tuning on PBMC3k · 7-method benchmark · Nature Methods 2024 framework

Standardized benchmark for bulk RNA-seq deconvolution: 73 methods x 42 datasets (30 pseudo-bulk + 12 real-bulk). Classical regression, container methods, single-cell foundation-model embeddings, scGPT-LoRA, and ML baselines.

A drop-in modernization of bowang-lab/scGPT for Python 3.12 + torch 2.6 + flash-attn 3 (H100 sm_90a native). Original pretrained weights load unmodified — compatible, more modern, faster.

Code, results and paper for "The geometry of single-cell foundation models: what they inherit, what they add, and what shapes it"

CytoBridge: single-cell perturbation prediction with pathway-gated cross-attention; frozen benchmark for 'Beyond per-pair correlation: a drug-discrimination control exposes prediction collapse in single-cell multi-drug perturbation models'