EnhancAR: Use evolution and deep learning to design enhancers with desired expression profiles! Had a lot of fun working with Andrew Duncan, Micaela Consens @alexijie.bsky.social @lcrawford.bsky.social Jennifer Mitchell and Alan Moses! www.biorxiv.org/content/10.6...

Join the Dionne Price Public Lecture on April 21 at 3 p.m., featuring Lorin Crawford (Microsoft Research), who will present “A Statistician’s Roadmap Toward an AI-Driven Paradigm for Precision Oncology.” Free to attend in person or virtually (registration required): tinyurl.com/y3vaeaup #STATSSKY

Excited to see our hierarchical cross-entropy strategy for improved cell type annotation out today in @natcomputsci.nature.com! Congratulations to the team! Try out the HCE loss with your own models and datasets: 📄: www.nature.com/articles/s43... 💻: github.com/microsoft/hc...

Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss - Nature Computational Science

A hierarchical cross-entropy loss is presented, which incorporates ontology structure into training and improves the out-of-distribution performance of large-scale single-cell annotation models withou...

nature.com

📢Out now! Sebastiano Cultrera di Montesano, Peter S. Winter, @lcrawford.bsky.social, and colleagues present a hierarchical cross-entropy loss that improves performance of single-cell annotation models. www.nature.com/articles/s43... 🖥️ 🧬

Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss - Nature Computational Science

A hierarchical cross-entropy loss is presented, which incorporates ontology structure into training and improves the out-of-distribution performance of large-scale single-cell annotation models withou...

nature.com

Come do a research internship with us! Details on the posting and how to upload a research statement given below!

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 9mo ago

You have until Dec 1 to apply to the bioml PhD research internship! This is where you apply to work with me, @alexijie.bsky.social @avapamini.bsky.social @lcrawford.bsky.social or Kristen Severson! (new) link and some instructions below apply.careers.microsoft.com/careers/job/...

"What James Watson got wrong about DNA" By the great Sohini Ramachandran (@sramach.bsky.social) and your boy for The Boston Globe (@bostonglobe.com). www.bostonglobe.com/2025/11/14/o...

What James Watson got wrong about DNA - The Boston Globe

The science he helped pioneer consistently undermines his view that genes determine everything about us.

bostonglobe.com

Alan did a ton of work on our latest revision. Message of the story still holds: more data does not necessarily lead to better downstream performance for many models. Check out all our new analyses here: www.biorxiv.org/content/10.1...

alandenadel.bsky.social@alandenadel.bsky.social · 9mo ago

We have recently uploaded our revised manuscript “Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance”. TL;DR: More models, more tasks => same results.

Come do an internship with us! Please apply

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 10mo ago

Are you a PhD student interested in ML and biology or health? Come do an internship with me, @avapamini.bsky.social, Alex Lu, @lcrawford.bsky.social, or Kristen Severson at MSRNE! Applications are due Dec 1: make sure you include a research statement! jobs.careers.microsoft.com/global/en/jo...

Gindra, Palla, Nguyen, Wagner, Tran, Theis, Saur, Crawford, Peng: A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics https://arxiv.org/abs/2508.01490 https://arxiv.org/pdf/2508.01490 https://arxiv.org/html/2508.01490

📣Online now! 📄Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies 🧑‍🤝‍🧑 @lcrawford.bsky.social @julian-stamp.bsky.social & co

Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies

The sparse marginal epistasis test overcomes computational limitations of previous mapping approaches by focusing its epistatic search to regions of the genome that have some known functional relation...

cell.com

Do protein language models store different structural elements in factorizable subnetworks? To find out, we masked out PLM weights to suppress performance on CATH subcategories or secondary structure elements while maintaining performance on other sequences or residues.

Members have elected Brian Millen as the 122nd president of the association. Also elected: Julia Sharp, Vice President; Martin Slawski, Council of Sections Representative; Ruixiao Lu, Council of Chapters Representative; Pedro Silva, International Representative. Congratulations! tinyurl.com/ptunrn5z

"Leadership in Trustworthy AI" COPSS-NISS Leadership Webinar with David Donoho (Stanford), Michael I. Jordan (UC Berkeley), and Tracy Ke (Harvard) - online Tuesday, April 29, 2025 at 12-1pm ET. Register at: www.niss.org/events/copss...

Great to see our paper presenting recall, a framework which calibrates clustering for the impact of data "double-dipping" in single-cell studies, out today in AJHG! Congratulations, @alandenadel.bsky.social and co-authors!

The American Journal of Human Genetics@ajhgnews.bsky.social · last yr.

🚨Online now! 📄Artificial variables help to avoid over-clustering in single-cell RNA sequencing 🧑‍🤝‍🧑 @alandenadel.bsky.social @lcrawford.bsky.social & co

New online! Adapting systems biology to address the complexity of human disease in the single-cell era

Adapting systems biology to address the complexity of human disease in the single-cell era

Nature Reviews Genetics, Published online: 10 March 2025; doi:10.1038/s41576-025-00821-6Differences between humans and experimental models create a translational gap that makes it difficult to extrapolate research findings. The authors review…

nature.com

🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding. Why does this matter? Reproducibility & fair comparison have been lacking—until now. Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti... A thread ⬇️

🎉Congratulations to the authors!🎉 The list of accepted papers for #RECOMB2025 is now live ➡️ recomb.org/recomb2025/a... What are your plans for Seoul? Let us know! www.youtube.com/watch?v=uztj... #seoul

Quick post to close out the week - in our newest preprint, @julian-stamp.bsky.social scales the marginal epistasis test to work on biobanks! The key is that using trait-specific information to induce sparsity in the modeled gene-interactions greatly improves both runtime and power

Julian Stamp@julian-stamp.bsky.social · 2y ago

Can we find epistasis in human traits? To help, in our preprint, we present the most scalable and powerful framework for detecting epistasis to date: the “sparse marginal epistasis test” (SME). Thank you @lcrawford.bsky.social, @sampatsmith.bsky.social, Dan Weinreich! doi.org/10.1101/2025... 1/6

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance [new]

Rethinking cancer drug synergy prediction: a call for standardization in machine learning applications https://www.biorxiv.org/content/10.1101/2024.12.24.630216v1

In our newest preprint, we show that simply increasing the size of pre-training datasets doesn't necessarily improve the performance of single-cell foundation models on downstream tasks. Really proud of @alandenadel.bsky.social for leading this effort! See his thread below for more details👇

alandenadel.bsky.social@alandenadel.bsky.social · 2y ago

Current methods in the field are trained on atlases ranging from 1 to 100 million cells. In our newest preprint, we show that these same approaches tend to plateau in performance with pre-training datasets that are only a fraction of the size.

This starter pack is in honor of Assistant Professor Antentor Hinton Jr (AJ) at Vanderbilt School of Medicine - Basic Sciences. AJ curated the first 100 Inspiring Black Scientists in America list and in collaboration with the Community of Scholars expanded this list to the 1000. go.bsky.app/DsJrwR

Looking to find your MSR colleagues? I put together a starter pack. Msg me if I missed you (or you just joined). go.bsky.app/NxtpELZ

In the spirit of trying to be more active on here... the deadline for our BioML internship is tomorrow 11/22. If you are currently a PhD student please consider applying --- all we need is a CV and research statement! jobs.careers.microsoft.com/global/en/jo...