Shantanu Singh
computation biology, drug discovery, computer vision, microscopy, statistics, machine learning, all happening at carpenter-singh-lab.broadinstitute.org
- Reposted by Shantanu Singh💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵 1/6 #iccv2025
- Reposted by Shantanu SinghMorph Map is now published in Nature Methods. Excited to see what the community discovers with this resource mapping ~15,000 human genes! rdcu.be/ezGre
- Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...
- Reposted by Shantanu SinghBig shout out to the whole team: Alán F. Muñoz, Tim Treis, @shatavishadg.bsky.social , @fabiantheis.bsky.social ntheis.bsky.social, @drannecarpenter.bsky.social, @shantanu-singh.cc 6/6
- Reposted by Shantanu Singh🔬API-first feature extraction for image-based profiling workflows If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle. 1/6
- Reposted by Shantanu Singh🌟 𝗥𝗲𝗺𝗶𝗻𝗱𝗲𝗿 🌟 The deadline for abstract submissions for oral presentations at Cytodata 2025 in Berlin is approaching! 👉 𝗦𝘂𝗯𝗺𝗶𝘁 𝘆𝗼𝘂𝗿 𝗮𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝗯𝘆 𝗝𝘂𝗻𝗲 25! cytodata25.eu-openscreen.eu/registration/ #BerlinConference #Imageanalysis #Microscopy
- Delighted to see this out in print! It captures everything several of us in the field have been thinking about on the topic of measuring signal in high-dimensional profiling data, and I couldn't think of a better torchbearer and storyteller than @alxndrkalinin.bsky.social to champion this work.
- 🚨 New paper alert! We developed a versatile information retrieval framework that uses mean average precision (mAP) to robustly quantify sample activity and similarity in large-scale profiling data. Now out @natcomms.nature.com: doi.org/10.1038/s414... More in the 🧵 below: 1/7
- Reposted by Shantanu Singh🚨 New paper alert! We developed a versatile information retrieval framework that uses mean average precision (mAP) to robustly quantify sample activity and similarity in large-scale profiling data. Now out @natcomms.nature.com: doi.org/10.1038/s414... More in the 🧵 below: 1/7
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- Reposted by Shantanu Singh🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse... paper: www.biorxiv.org/content/10.1... w/ @computingnature.bsky.social 1/n
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- Reposted by Shantanu Singh📚😅🎉 Yay!! I just submitted the complete manuscript of my upcoming book to the publisher! Learn to easily and clearly interpret (almost) any stats model w/ R or Python. Simple ideas, consistent workflow, powerful tools, detailed case studies. Read it for free @ marginaleffects.com #RStats #PyData
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- Reposted by Shantanu SinghDelighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)
- Reposted by Shantanu SinghWe're once again hiring a summer (+?) #bioimage #bioimageanalysis #software intern! Due to requirements of the funding program, you must be a current student, as well as work onsite in MA (+ have US work permission). Details at the link below. Spend your summer making great tools with fun people!
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- 🧪 Summer internship alert, Feb 7 deadline New URL: hsph.harvard.edu/fellowship-s... (+ @harvardchanschool.bsky.social is now on 🦋!)
- Reposted by Shantanu SinghHey #StatsSky, what are you favorite papers to cite when you need to justify something that is obvious (I once had a reviewer ask we justify the use of logistic regression on a binary outcome) or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?
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- Reposted by Shantanu SinghInstead of listing my publications, as the year draws to an end, I want to shine the spotlight on the commonplace assumption that productivity must always increase. Good research is disruptive and thinking time is central to high quality scholarship and necessary for disruptive research.
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- Taking pictures of cells with a microscope, then extracting thousands of features from them is uncannily effective for quantifying cell state, esp. for genes and chemicals (e.g., Cell Painting). But we often average the rich single-cell data to simplify analysis. Can we do better? #bioML 🧪 1/n
- Robert van Dijk (www.linkedin.com/in/robert-v-...) developed CytoSummaryNet – a simple strategy to learn an optimal way to aggregate single-cell features into population-level profiles, outperforming traditional averaging on tasks like mechanism-of-action prediction. 2/n
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- 🧪 So proud of this work by the dream team of @johnarevalo.bsky.social and Ellen Su: a new graph dataset for predicting drug-target interactions, using information from Cell Painting. Stop by their poster in a few hours @ #NeurIPS! (details below) PS: John is on the job market 🚀 #bioML #MLSky
- Excited to present our spotlight paper at #NeurIPS! MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208 Poster: neurips.cc/virtual/2024... Paper: arxiv.org/abs/2406.08649
- Reposted by Shantanu Singh🎉 I'm starting my own lab at EMBL-EBI (Cambridge, UK; June 2025) 🎉 We will focus on identifying and characterizing chemical hazards to humans and ecosystems using computational biology methods. I am beginning the search for two postdocs now - stay tuned for more details! ewaldlab.org
- Reposted by Shantanu SinghExcited to present our spotlight paper at #NeurIPS! MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208 Poster: neurips.cc/virtual/2024... Paper: arxiv.org/abs/2406.08649
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- Reposted by Shantanu SinghNow on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...
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- PCPs on #MedSky must share this clear, compelling data with their >65 yo patients: getting last year’s COVID shot made you about 2.5 times less likely to end up in the hospital and 4 times less likely to die from COVID last winter—even if you’d had all the earlier shots and COVID before.
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- A delightful thread on the follow-up to the U-turn on double descent paper, extending explanations to neural network learning Context: 1. Seminal article on double descent arxiv.org/abs/2105.14368 2. U-turn paper, which ~demystified double descent (but not for NNs) arxiv.org/abs/2310.18988
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- Reposted by Shantanu SinghStudent Researcher positions in EMEA now accepting applications! Please repost. www.google.com/about/career...
- Reposted by Shantanu SinghNow that "scale is all we need" has predictably faltered... 1. Small AI models often perform better in context. 2. Obsession w bigness has bad consequences, from climate, to power concentration, to research capture. Me + @gaelvaroquaux.bsky.social @sashamtl.bsky.social arxiv.org/abs/2409.14160
- Reposted by Shantanu SinghJanelia is recruiting AI scientists and theory fellows to collaborate with experimental scientists on hard biological problems - these positions have a considerable level of independence and very competitive salaries. Join our great community! Ai.hhmi.org janelia.org/theoryfellow #neuroscience #AI
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- Does anyone recall seeing a starter pack for optical tools? I could bet I saw one pop up but can't find it now (context: looking to nominate innovative microscopy, drug discovery or bioML tech with real-world clinical impact, for a prize).
