I’ve been working with @alat-rights towards overhauling the DeepChem website. We’re trying to gather a list of organizations who’ve used DeepChem (so we can display logos on the new website for our users). If your organization has used DeepChem or you can reputably certify that an organization has used DeepChem, please chime in here!
Organizations Using DeepChem
To start off a few organizations who I know have used DeepChem:
- Stanford (did my PhD there)
- CMU (collaborators)
- Deep Forest Sciences (first hand attestation)
- Novo Nordisk (see job thread DeepChem Jobs Thread)
- Nurix (DeepChem Jobs Thread)
- Merck (see https://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00146)
- Pfizer (see https://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00290)
- Reverie Labs (see https://arxiv.org/abs/2010.09885)
- Schrodinger (see https://www.schrodinger.com/science-articles/autoqsardeepchem)
- Weights and Biases (see https://wandb.ai/stacey/deepchem_molsol/reports/DeepChem-Molecular-Solubility--VmlldzoxMjQxMjM)
- AWS/Amazon (see https://aws.amazon.com/blogs/machine-learning/using-deepchem-with-amazon-sagemaker-for-virtual-screening/)
- ATOM (Lawrence Livermore Laboratory) (see https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b01053)
- ATOM (GlaxoSmithKline) (see https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b01053)
- Numerate, now acquired by Valo Health (see https://pubs.acs.org/doi/pdf/10.1021/acs.molpharmaceut.7b01144)
- Broad Institute (see https://twitter.com/mrinal1989/status/1433256671841853440)
I know of many others but don’t have a direct public attestation for them offhand. Will fill out this thread as I come across more!
Here are some research organizations that have used DeepChem (adapted from papers and discoveries post):
- University of Wisconsin Madison (see https://onlinelibrary.wiley.com/doi/abs/10.1002/minf.201900101)
- Johannes Kepler University (see https://pubs.rsc.org/ko/content/articlehtml/2018/sc/c8sc00148k)
- Janssen Pharmaceutical (see https://pubs.rsc.org/ko/content/articlehtml/2018/sc/c8sc00148k)
- Open Analytics NV (see https://pubs.rsc.org/ko/content/articlehtml/2018/sc/c8sc00148k)
- Bayer AG (see https://pubs.rsc.org/ko/content/articlehtml/2018/sc/c8sc00148k)
- Xiamen University (see https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-0414-z)
- University of Missouri, Columbia (see https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-0414-z)
- Chinese Academy of Sciences (see https://link.springer.com/chapter/10.1007/978-3-030-60245-1_20)
- Australian National University (see https://pubs.acs.org/doi/10.1021/acs.jcim.8b00901)
- Owkin, Inc (see https://www.sciencedirect.com/science/article/abs/pii/S2468111318300744#!)
- University of Texas at Arlington (see https://arxiv.org/pdf/1708.04675.pdf)
Note on methodology: for papers, I’m counting all institutions listed on a paper that uses DeepChem. In practice it’s possible that only some of the institutions may have used DeepChem, although in principle all authors should be familiar with core tools/methods used in the work.
University of California, San Francisco (see https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(20)30547-6)
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MIT (my personal use)
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We have used DeepChem in some of our research as a molecule vectorizer, and presented at ACS Symposium- poster is here: https://storage.googleapis.com/gsi_at_acs_symposium_2020/ACS%20Symposium%202020%20Poster%20V2.png
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The LLNL/GlaxoSmithKline (AMPL) reference would be more accurately attributed to the ATOM Research Initiative (www.atomscience.org) which is a multi-institute consortium. Thanks!
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Just changed the attribution above!
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- University of Geneva (see https://arxiv.org/pdf/1812.04439.pdf)
- German Research Center for Environmental Health (see https://arxiv.org/pdf/1812.04439.pdf)
- Firmenich SA (see https://arxiv.org/pdf/1812.04439.pdf)
- IBM Watson (see https://pubmed.ncbi.nlm.nih.gov/32077698/)
- Jiangsu University of Technology (see https://pubmed.ncbi.nlm.nih.gov/33058459/)
- Expedia (see https://link.springer.com/chapter/10.1007/978-3-030-30493-5_79)
- Hunan University (see https://ieeexplore.ieee.org/abstract/document/8983267)
- Global Health Drug Discovery Institute China (see https://arxiv.org/pdf/2102.04064.pdf)
- ATOM (Frederick National Laboratory for Cancer Research) (see https://dmd.aspetjournals.org/content/dmd/49/2/169.full.pdf)
- University of Vienna (see https://pubmed.ncbi.nlm.nih.gov/31978306/)
- SRI International (see https://arxiv.org/pdf/2011.03518.pdf)
- ShanghaiTech University (see https://www.sciencedirect.com/science/article/abs/pii/S2468823120305290#!)
- University of Strathclyde (see https://iopscience.iop.org/article/10.1088/1361-648X/aad076/meta)
- University of Tartu (see https://iopscience.iop.org/article/10.1088/1361-648X/aad076/meta)
- Skolkovo Institute of Science and Technology (see https://iopscience.iop.org/article/10.1088/1361-648X/aad076/meta)
- University of Central Florida (see https://www.frontiersin.org/articles/10.3389/fphar.2019.01526/full)
- University of Tokyo (see https://arxiv.org/pdf/1911.04738.pdf)
- RIKEN (see https://arxiv.org/pdf/1911.04738.pdf)
- Northwestern (see https://arxiv.org/pdf/1811.08283.pdf)
- University of Macau (see https://pubmed.ncbi.nlm.nih.gov/30571137/)
- Central South University (see https://pubmed.ncbi.nlm.nih.gov/30571137/)
- Institute of Chinese Medical Sciences (see https://pubmed.ncbi.nlm.nih.gov/30571137/)
- University of Alberta (see https://www.nature.com/articles/s41598-021-88939-5)
- The Barcelona Institute of Science and Technology (see https://www.nature.com/articles/s41467-021-24150-4.pdf)
- International University of Catalonia (see https://www.nature.com/articles/s41467-021-24150-4.pdf)
- National Taiwan University (see https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab367/6366324)
- CSIR-National Chemical Laboratory Pune (see https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758f4842e653d40db4903/original/machine-learning-the-redox-potentials-of-phenazine-derivatives-a-comparative-study-on-molecular-features.pdf)
- East China University of Science and Technology (see https://arxiv.org/pdf/2106.14232.pdf)
- Zhejiang University (see https://arxiv.org/pdf/2106.14232.pdf)
Hi All,
The University of Bristol’s School of Chemistry is using it in undergraduate and postgraduate teaching as well as research (although no papers have yet been published).
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