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Title: GitHub - QSong-github/MVCBench: Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes · GitHub

Open Graph Title: GitHub - QSong-github/MVCBench: Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes

X Title: GitHub - QSong-github/MVCBench: Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes

Description: Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes - QSong-github/MVCBench

Open Graph Description: Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes - QSong-github/MVCBench

X Description: Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes - QSong-github/MVCBench

Mail addresses
Boom985426@gmail.com
bobzhang@um.edu.mo
qsong1@ufl.edu

Opengraph URL: https://github.com/QSong-github/MVCBench

X: @github

direct link

Domain: github.com

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requirements.txthttps://github.com/QSong-github/MVCBench/blob/main/requirements.txt
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train_mvc.pyhttps://github.com/QSong-github/MVCBench/blob/main/train_mvc.py
READMEhttps://github.com/QSong-github/MVCBench
MIT licensehttps://github.com/QSong-github/MVCBench
https://github.com/QSong-github/MVCBench#mvcbench-a-multimodal-benchmark-for-drug-induced-virtual-cell-phenotypes
https://www.python.org/
https://github.com/QSong-github/MVCBench/blob/main/LICENSE
https://qsong-github.github.io/MVCBench/
https://huggingface.co/datasets/Boom5426/MVCBench
Project Pagehttps://qsong-github.github.io/MVCBench/
Manuscripthttps://www.biorxiv.org/content/10.64898/2026.04.22.720110v1
Datasethttps://huggingface.co/datasets/Boom5426/MVCBench
https://github.com/QSong-github/MVCBench#overview
https://github.com/QSong-github/MVCBench/blob/main/docs/static/images/Fig1.png
https://github.com/QSong-github/MVCBench#key-findings
https://github.com/QSong-github/MVCBench#-benchmark-zoo
https://github.com/QSong-github/MVCBench#-molecule-representation-methods
Nat. Commun. 2023https://www.nature.com/articles/s41467-023-43214-1
GitHubhttps://github.com/lihan97/kpgt
https://camo.githubusercontent.com/257d041ca581e075358f8d16d8097a28ba2059a1fc01f926d394692ed937b2b1/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f73746172732f6c6968616e39372f6b7067742e7376673f7374796c653d736f6369616c
ICLR 2025https://openreview.net/forum?id=BbZy8nI1si
GitHubhttps://github.com/liugangcode/InfoAlign
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Adv. Sci. 2024https://advanced.onlinelibrary.wiley.com/doi/10.1002/advs.202403998
GitHubhttps://github.com/Wang-Lin-boop/GeminiMol
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Adv. Sci. 2026https://www.biorxiv.org/content/10.1101/2025.03.18.643899v1
GitHubhttps://github.com/Wang-Lin-boop/ouroboros
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ICLR 2023https://openreview.net/forum?id=jevY-DtiZTR
GitHubhttps://github.com/junxia97/Mole-BERT
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arXiv 2022https://arxiv.org/abs/2209.01712
GitHubhttps://github.com/seyonechithrananda/bert-loves-chemistry
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EMNLP 2022https://arxiv.org/abs/2204.11817
GitHubhttps://github.com/blender-nlp/molt5
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JCIM 2024https://pubs.acs.org/doi/10.1021/acs.jcim.3c01250
GitHubhttps://github.com/chemprop/chemprop
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GitHubhttps://github.com/deepmodeling/Uni-Mol
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GitHubhttps://github.com/deepmodeling/Uni-Mol/tree/main/unimol2
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https://github.com/QSong-github/MVCBench#-gene-representation-methods-scfms
Nature 2023https://www.nature.com/articles/s41586-023-06139-9
HuggingFacehttps://huggingface.co/ctheodoris/Geneformer
bioRxiv 2022https://www.biorxiv.org/content/10.1101/2022.01.31.478596v1.full
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GitHubhttps://github.com/snap-stanford/uce
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Nat. Mach. Intell. 2022https://www.nature.com/articles/s42256-022-00534-z
GitHubhttps://github.com/TencentAILabHealthcare/scBERT
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ICLR 2024https://openreview.net/forum?id=BKXvPDekud
GitHubhttps://github.com/OmicsML/CellPLM
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arXiv 2023https://arxiv.org/pdf/2306.04371
GitHubhttps://github.com/PharMolix/OpenBioMed
https://camo.githubusercontent.com/c16df10db8e95b9c00404d5a578366d97fb18147c97f141f35d79334d8e02910/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f73746172732f506861724d6f6c69782f4f70656e42696f4d65642e7376673f7374796c653d736f6369616c
Nat. Methods 2024https://www.nature.com/articles/s41592-024-02201-0
GitHubhttps://github.com/bowang-lab/scGPT
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Nat. Methods 2024https://www.nature.com/articles/s41592-024-02305-7
GitHubhttps://github.com/biomap-research/scFoundation
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Nature 2025https://doi.org/10.1038/s41586-024-08411-y
GitHubhttps://github.com/Genentech/scimilarity
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ICML 2023https://icml.cc/virtual/2024/poster/34580
GitHubhttps://github.com/vandijklab/cell2sentence
https://camo.githubusercontent.com/f51b477b84ef321fed1cf926d2a18d74ce2607fcaa929076423a092c6ee3a7b9/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f73746172732f76616e64696a6b6c61622f63656c6c3273656e74656e63652e7376673f7374796c653d736f6369616c
bioRxiv 2025https://www.biorxiv.org/content/10.1101/2025.06.26.661135v2
GitHubhttps://github.com/ArcInstitute/state
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https://github.com/QSong-github/MVCBench#-datasets
https://github.com/QSong-github/MVCBench#gene-expression
Dataset Linkhttps://cigs.iomicscloud.com/
HuggingFacehttps://huggingface.co/datasets/tahoebio/Tahoe-100M
Clue.iohttps://clue.io/data/CMap2020#LINCS2020
https://github.com/QSong-github/MVCBench#cell-morphology
AWS Registryhttps://registry.opendata.aws/cellpainting-gallery/
https://github.com/QSong-github/MVCBench#multimodal-paired
Projecthttps://www.nature.com/articles/s41592-022-01667-0
MVCBench HuggingFacehttps://huggingface.co/datasets/Boom5426/MVCBench
https://github.com/QSong-github/MVCBench#-embedding-extraction
https://github.com/QSong-github/MVCBench#molecular-embeddings-eg-unimol2
Get_Molecular_Embedding.ipynbhttps://github.com/QSong-github/MVCBench/blob/main/examples/Get_Molecular_Embedding.ipynb
https://github.com/QSong-github/MVCBench#gene-embeddings-eg-state
Get_STATE_Embedding.ipynbhttps://github.com/QSong-github/MVCBench/blob/main/examples/Get_STATE_Embedding.ipynb
https://github.com/QSong-github/MVCBench#-getting-started
https://github.com/QSong-github/MVCBench#installation
https://github.com/QSong-github/MVCBench#data-organization
MVCBench on Hugging Facehttps://huggingface.co/datasets/Boom5426/MVCBench
https://github.com/QSong-github/MVCBench#main-training-scripts
scripts/run_gene_batch.shhttps://github.com/QSong-github/MVCBench/blob/main/data/boom/Agent/MVCBench/scripts/run_gene_batch.sh
scripts/run_image_batch.shhttps://github.com/QSong-github/MVCBench/blob/main/data/boom/Agent/MVCBench/scripts/run_image_batch.sh
scripts/run_mvc_batch.shhttps://github.com/QSong-github/MVCBench/blob/main/data/boom/Agent/MVCBench/scripts/run_mvc_batch.sh
https://github.com/QSong-github/MVCBench#example-commands
https://github.com/QSong-github/MVCBench#outputs
https://github.com/QSong-github/MVCBench#notes
examples/Get_Molecular_Embedding.ipynbhttps://github.com/QSong-github/MVCBench/blob/main/examples/Get_Molecular_Embedding.ipynb
examples/Get_STATE_Embedding.ipynbhttps://github.com/QSong-github/MVCBench/blob/main/examples/Get_STATE_Embedding.ipynb
src/configs.pyhttps://github.com/QSong-github/MVCBench/blob/main/data/boom/Agent/MVCBench/src/configs.py
https://github.com/QSong-github/MVCBench#️-citation
https://github.com/QSong-github/MVCBench#-contact
qsong-github.github.io/MVCBench/https://qsong-github.github.io/MVCBench/
Readme https://github.com/QSong-github/MVCBench#readme-ov-file
MIT license https://github.com/QSong-github/MVCBench#MIT-1-ov-file
Please reload this pagehttps://github.com/QSong-github/MVCBench
Activityhttps://github.com/QSong-github/MVCBench/activity
1 forkhttps://github.com/QSong-github/MVCBench/forks
Report repository https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FQSong-github%2FMVCBench&report=QSong-github+%28user%29
Releaseshttps://github.com/QSong-github/MVCBench/releases
Packages 0https://github.com/users/QSong-github/packages?repo_name=MVCBench
Please reload this pagehttps://github.com/QSong-github/MVCBench
Contributorshttps://github.com/QSong-github/MVCBench/graphs/contributors
Please reload this pagehttps://github.com/QSong-github/MVCBench
Python 86.9% https://github.com/QSong-github/MVCBench/search?l=python
Shell 13.1% https://github.com/QSong-github/MVCBench/search?l=shell
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

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