Therapeutics Data Commons

Excited to share our new paper in Nature Chemical Biology @nchembio AI is poised to transform #therapeutic #science The Commons is an initiative to access and evaluate #AI capability across therapeutic modalities and stages of discovery 1/4 nature.com/articles/s4158…

With the ToolUniverse (TU) CLI, there’s no need to set up an MCP server—agents can instantly access tools with a single command. Paste this to your AI agent to use it now! "Read aiscientist.tools/setup.md and update to the latest ToolUniverse. I want to use the tu CLI."

If you are at NeurIPS, join us tomorrow for the CUREBench Competition Workshop (curebench.ai) and see how @ScientistTools is driving large-scale evaluation and global benchmarking of AI models for therapeutics and precision medicine

@NeurIPSConf week Sat, Dec 6 🔹 CUREBench - International Competition on AI agents and reasoning models for therapeutics at scale curebench.ai @GaoShanghua @ScientistTools @RichardYXZhu @sui67713 @ZKong50693 @xiaorui_su with a keynote by @AziziShekoofeh Sun, Dec 7 🔹 6th AI for Science NeurIPS Workshop – The Reach and Limits of AI for Scientific Discovery ai4sciencecommunity.github.io @AdaFang_ We started this workshop series in 2021, when @AI_for_Science was still niche. It is exciting to see how the community and the field have grown and how much potential there is to transform scientific discovery Sat, Dec 6 🔹 AI Virtual Cells and Instruments – A New Era in Drug Discovery and Development ai4d3.github.io/2025/index.html @_michellemli We are also presenting many papers throughout the week. Here is the first batch and more to follow throughout the week: • A scalable data layer of knowledge graph AI: openreview.net/pdf?id=8OXD0yN… by Lucas Vittor, @ayushnoori @InakiArango, Joaquin Polonuer • Multi-agent collaboration in knowledge graph environments: openreview.net/pdf?id=xUDGChZ… @ayushnoori @InakiArango Lucas Vittor, Joaquin Polonuer • Evolutionary reasoning in protein language models: openreview.net/pdf?id=nR9S0Ie… @YEktefaie Kudos to all stellar students and many thanks to fantastic collaborators @HarvardDBMI @harvardmed @Harvard @broadinstitute @KempnerInst

Highlight of PDGrapher in @thecrimson nature.com/articles/s4155… Great work by @justguadaa Xiang Lin and collaboration with K. Veselkov and @mmbronstein

1⃣ more day⌛️ to submit your exciting research to our #NeurIPS workshop on AI Virtual Cells and Instruments! Submit an extended abstract & join our excellent lineup of presenters! 🌟 Please do not hesitate to reach out if you have any questions! ai4d3.github.io/2025/cfp.html

Update from CURE-Bench at @NeurIPSConf: 524 entrants and 298 submissions! Thank you to the CURE-Bench community! Working on AI for drug discovery and reasoning in medicine? Your agent belongs here New teams welcome. Tasks, rules, and leaderboard: curebench.ai #NeurIPS2025 #CUREBench @GaoShanghua @RichardYXZhu @ZKong50693 @xiaorui_su @CurtGinder Huge thanks to @cziscience @MilkenInstitute @BiswasFamilyFdn @cziscience Rare as One program @harvardmed @BrighamWomens @HarvardDBMI @KempnerInst @MIT @broadinstitute for making this possible

Pitch the dataset that could spark the next AI for Science revolution 🚀 The PDB revolutionized structural biology (and even helped win a🏅Nobel Prize in 2024). We’re hunting for the next breakthrough dataset that could unlock similar leaps across science—and we want your idea!

📣 Competition launch alert! CUREBench competition at @NeurIPSConf 2025 Start here: curebench.ai Benchmarking AI for therapeutic reasoning, drug discovery, treatment planning, and therapeutic decision-making 🎯 Track 1: Develop AI models that rely on parametric memory alone 🎯 Track 2: Build AI agents that use external tools and resources 🎯 Evaluation will be done by agentic judges and human disease experts, in collaboration with our partners @cziscience and @harvard 💰 $40,000 in prizes, Starter Kit, Travel Awards, and more ⏰ Entry deadline: October 15, 2025 A big thank you to our partners: @cziscience @MilkenInstitute @BiswasFamilyFdn @cziscience Rare as One program @harvardmed @BrighamWomens Organized by an amazing team: @GaoShanghua @RichardYXZhu @ZKong50693 @xiaorui_su @CurtGinder Sufian Aldogom, Ishita Das, Taylor Evans, Theo Tsiligkaridis. Big congrats to @GaoShanghua for spearheading this effort @HarvardDBMI @harvardmed @KempnerInst @MIT @broadinstitute

🌍 Excited to open up our global evaluation of AI for drug decision-making and therapeutic reasoning @GaoShanghua Want to shape the future of therapeutic AI, from understanding existing medicines to developing new treatments for diseases with limited options? Start here: txagentevals.curebench.ai How you can participate: 1️⃣ Evaluate TxAgent Test-drive TxAgent, our AI built for therapeutic reasoning across all drugs since 1939, powered by a universal toolbox of 200+ tools. Assess its reasoning on accuracy, clinical relevance, drug safety, and more, each evaluation takes ~10 minutes. Learn about TxAgent: zitniklab.hms.harvard.edu/TxAgent and github.com/mims-harvard/T… 2️⃣ Challenge the AI Submit your toughest therapeutic questions: rare diseases, unmet patient needs, or how to safely extend existing treatments, including combination therapies and personalized treatments. Help build an open library of challenges and shape smarter biomedical AI @GaoShanghua @ZKong50693 @RichardYXZhu @xiaorui_su @CurtGinder Sufian Aldogom Thanks to our many partners: @HarvardDBMI @harvardmed @Harvard @KempnerInst @harvard_data @MIT @broadinstitute @BrighamWomens @MilkenInstitute @BiswasFamilyFdn @cziscience

📢 AI-enabled drug discovery reaches clinical milestone rdcu.be/eugUu Few AI-designed drug candidates have gone beyond in silico benchmarks. Now, a study in @NatureMedicine @biogerontology reports a successful phase 2a trial of rentosertib, an AI-discovered drug and target combination for idiopathic pulmonary fibrosis What distinguishes this study (in addition to clinical data) is the upstream innovation pipeline This trial marks a turning point: it affirms a potential for AI to do more than generate molecules faster and cheaper; guide discovery, de-risk development and potentially reshape how we develop medicines A pertinent question is: why did this AI-generated drug candidate advance to clinical testing when so many others have not? 🎯 Cross-disease target discovery and 'time-machine' setup: AI models trained on past data predicted therapeutic targets years ahead of traditional methods, pinpointing TNIK as a promising target 🔬 Robust biological validation: Integrated multi-omic analyses, network biology, and extensive literature mining rapidly validated TNIK’s biological relevance for fibrosis ⚙️ Chemistry design: Generative AI models designed molecules targeting novel binding sites, prioritized drug-likeness and synthetic feasibility, and proactively optimized pharmacokinetics and potency from early stages @biogerontology @InSilicoMeds @HarvardDBMI @Harvard @harvardmed @harvard_data @KempnerInst @broadinstitute

🔍 Call for Reviewers: AI4D3@NeurIPS 2025 We're seeking experts in AI & drug discovery to review submissions for our NeurIPS workshop. 🗓️ Deadline: May 30, 2025 📍 Workshop: Dec 2025, San Diego ✅ Sign up: forms.gle/o3kWHdJ6nVfXhd… #AI4D3 #NeurIPS2025 #DrugDiscovery #AI

📢 🧬 New preprint! Can we predict which cancer patients will benefit, before treatment begins? @WanXiang_Shen Immunotherapy saves lives but many patients don’t respond to treatment, and we still lack reliable tools to predict who will benefit We introduce COMPASS, foundation AI model for immunotherapy response prediction across cancers and treatments medrxiv.org/content/10.110… immuno-compass.com github.com/mims-harvard/C… @HarvardDBMI @harvardmed @KempnerInst @harvard_data @broadinstitute @Harvard Thanks to incredible team @WanXiang_Shen Thinh H. Nguyen @_michellemli @YepHuang @IntaeMoon Nitya Nair Daniel Marbach 🧵👇

New in the Kempner's Deeper Learning blog: @AdaFang_ and @marinkazitnik introduce ATOMICA, a geometric foundation model that enables reasoning about biological systems with atom-level precision. bit.ly/KempnerATOMICA #AI #ML #MedTech

📄 Preprint: biorxiv.org/content/10.110… 🚀 Open source code, weights, and data: github.com/mims-harvard/A…

ATOMICA characterizes interesting clusters of putative bacterial zinc fingers and cytochrome proteins. We're working on getting some of these validated in the lab 🧫👩‍🔬. Stay tuned!

Using masked token accuracy to proxy representation quality, we see training of ATOMICA follows scaling laws where representation quality improves with increasing biomolecular data modalities 📈

ATOMICA builds multi-scale representations at the atom, block (amino acid / nucleotide / common chemical motif), and interaction complex scale. 💡 The key is capturing *interaction complexes* - to learn patterns fundamental to chemistry, such as hydrogen bonds & pi-pi stacking.

Introducing ATOMICA 💫 A model to universally represent molecular interactions (for proteins, nucleic acids, small molecules, and ions) at an all-atom scale 🧵

DBMI's @zakkohane & @marinkazitnik, plus @AdamRodmanMD & other collaborators, on how AI is transforming medicine. “Having an instant second opinion... will change, for the better, the nature of the doctor-patient relationship.” news.harvard.edu/gazette/story/…

👉 Preprint: arxiv.org/abs/2503.10970 👉 TxAgent: zitniklab.hms.harvard.edu/TxAgent 👉 Open code and data: github.com/mims-harvard/T… 👉 ToolUniverse: github.com/mims-harvard/T… We are excited about the next steps as we work with clinical researchers, disease foundations, and patient-led organizations to evaluate TxAgent in real-world practice