M.D.–Ph.D. interested in computational image analysis, digital pathology, and neuropathology. Personal account: all opinions are my own.

Madison, WI
Joined September 2013
Way to go, Zhi! 👍💯 You're a rock star all around, both in and out of the lab. I'm fortunate to have you as a friend and collaborator!
So honored to be named one of @CityAndStatePA 2026 #Trailblazers in Healthcare! cityandstatepa.com/power-lis… At Penn, our work focuses on developing AI technologies for computational pathology and precision medicine, with the goal of transforming complex medical images and multimodal data into tools that can ultimately improve disease diagnosis and treatment. @PennPathLabMed
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Nirschl & Kolb labs are recruiting a Scientist I/II to develop novel PET tracers for protein aggregates in Alzheimer’s, Parkinson’s, FTD & ALS! Seeking experts in radioligand binding, protein biochemistry, SPR, and/or tissue assays. Apply by Aug. 25: jobs.wisc.edu/jobs/translati…
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Thanks, @ZhiHuangPhD! Shout-out to @Prof_Lundberg, a brilliant scientist and wonderful person who has been at the HPA for years! The Human @ProteinAtlas has been ongoing for >20 years. and is a testament to large-scale open science initiatives. #hpa #digitalpathology #ihc
🚀 Introducing iSight: toward expert–AI collaboration for #immunohistochemistry (IHC) assessment Preprint: arxiv.org/abs/2602.04063 🚀 What we built: 🖼️ HPA10M, the world’s largest open-access IHC dataset: huggingface.co/datasets/nirs… • 10,495,672 IHC images (Over 10M!) • 17,000+ protein markers • 45 normal tissues + 20 cancer types • Fully curated, standardized, and publicly available on @huggingface. We trained iSight, a multi-task AI system for automated IHC assessment • Jointly predicts staining location, intensity, and quantity • Outperforms fine-tuned pathology foundation models • Produces well-calibrated, clinically interpretable outputs @PennPathLabMed #DigitalPathology #AIinHealthcare #Immunohistochemistry #HumanAI #Pathology
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The @ProteinAtlas was absolutely essential to this work. The HPA graciously made their data CC-BY-SA-4.0, which enabled this work. I'm so fortunate to be a part of this outstanding team! And thanks to my postdoc mentor, @yeung_levy who encouraged me to pursue this direction.
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Jeff Nirschl retweeted
Check out PaperSearchQA, which I'll present at EACL in Morocco this March! We built an RL training environment for teaching LLMs to search and reason over scientific papers. 60k question-answer pairs + 16M papers to search over + benchmarks. RL training improves the model.
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Jeff Nirschl retweeted
Excited to share that our lab’s latest work, Melan-Dx, a knowledge-enhanced vision-language framework for improving the differential diagnosis of melanocytic neoplasms in pathology, is now published in @npjDigitalMed! Read it at: nature.com/articles/s41746-0… @PennPathLabMed #DigitalPathology #Dermpath
Skin cancer diagnosis isn’t just about seeing. It’s about knowing what you’re seeing. A new AI system improves melanoma diagnosis by combining pathology images with expert knowledge, not just pixels. READ HERE: nature.com/articles/s41746-0…
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We're hiring! The Nirschl & Kolb (@hckolb ) labs @UWMadison are seeking a Scientist I/II to help develop novel PET tracers for neurodegenerative diseases. - Tissue assays, autoradiography, SPR, protein biochem experience desired. Apply here: jobs.wisc.edu/jobs/nirschl-s… #PETimaging
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Amazing work, Zhi!
Wow! TissueLab.org has reached over 1700 users in the first 30 days and almost 500 downloads 🚀🔥! What an impressive achievement by my team. So proud of my students! We will keep shipping the code, fixing the bugs, and improve user experiences. Check out the first co-evolving agentic AI system for medical image analysis! 👉arxiv.org/abs/2509.20279 #TissueLab #AIAgent #AgenticAI #pathology #radiology
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Jeff Nirschl retweeted
📢 Excited to introduce TissueLab — the first co-evolving, open-source agentic AI ecosystem to transform medical image analysis, copilot clinical decisions & accelerate scientific discovery, with SOTA performance compared to other VLM and GPT-5. Simply ask any research/clinical question! TissueLab will: ✅ Design the workflow for you. ✅ Write the python code. ✅ Execute the workflow and generate answer. 🧵1/n Online portal: tissuelab.org Read preprint: arxiv.org/abs/2509.20279 Blog: linkedin.com/pulse/how-agent…
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🧬 What if we could build a virtual cell to predict how it responds to drugs or genetic perturbations? Super excited to introduce CellFlux at #ICML2025 — an image generative model that simulates cellular morphological changes from microscopy images. yuhui-zh15.github.io/CellFlu… 💡 Key Innovation: We frame perturbation prediction as a distribution-to-distribution learning problem, mapping control cells to perturbed cells within the same batch to mitigate biological batch artifacts, and solve it using flow matching. 📊 Results: ✅ 35% higher image fidelity ✅ 12% greater biological accuracy ✅ New capabilities: batch effect correction & trajectory modeling 🎯 Impact: Paving the way for faster drug discovery and deeper biological insights. 📍 Poster: Tue 7/15, 11:00 AM – 1:30 PM, #301 🙏Huge thanks to all my brilliant collaborators: @hhhhh2033528 (co-lead; now Harvard AIM PhD! 🎉) @ChenyuW64562111 @TianhongLi6 @zoewefers @jnirsch @jmhb0 @DaisyYDing @Ale9806_ @Prof_Lundberg @yeung_levy! #MachineLearning #ComputerVision #ComputationalBiology #DrugDiscovery #AIforScience #CVforScience
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Jeff Nirschl retweeted
"Dr. Dirk Keene, a professor and the director of neuropathology at UW Medicine who leads the brain bank, said if federal funding dries up, he’ll go to almost any end to 'honor the gift' of people's donation." nbcnews.com/health/health-ne…
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Today, the Wisconsin Brain Donor Program and Wisconsin ADRC join the national observance of #BrainDonorAwarenessDay to recognize and honor the individuals and families who have made the extraordinary decision to donate their brains to science. Learn more at adrc.wisc.edu/brain-donation.
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My lab is starting at UW-Madison! This is a unique opportunity to contribute to impactful computational neuropathology research in a collaborative environment. Join the Nirschl Lab and help drive discoveries that improve our understanding of neurodegenerative disorders!🧠
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Scientific software developer jobs.wisc.edu/jobs/digital-p… Job number: 314388-AS Researcher and Laboratory Manager (wet lab) - Computational Neuropathology jobs.wisc.edu/jobs/researche… Job number: 314623-AS
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Jeff Nirschl retweeted
My closed collaborator Prof. Jeff Nirschl @jnirsch has started his research lab at University of Wisconsin!!🎉 Dr. Nirschl has a rare combination of deep expertise in both medicine/pathology and AI/ML. Please check out the two open positions in his lab: Scientific software developer jobs.wisc.edu/jobs/digital-p… Researcher and Laboratory Manager - Computational Neuropathology jobs.wisc.edu/jobs/researche…
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Jeff Nirschl retweeted
Introducing MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research #CVPR2025 ✅ 1k multimodal reasoning VQAs testing MLLMs for science 🧑‍🔬 Biology researchers manually created the questions 🤖 RefineBot: a method for fixing QA language shortcuts 🧵
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Jeff Nirschl retweeted
🚨Large video-language models LLaVA-Video can do single-video tasks. But can they compare videos? Imagine you’re learning a sports skill like kicking: can an AI tell how your kick differs from an expert video? 🚀 Introducing "Video Action Differencing" (VidDiff), ICLR 2025 🧵
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🚀 Introducing Temporal Preference Optimization (TPO) – a video-centric post-training framework that enhances temporal grounding in long-form videos for Video-LMMs! 🎥✨ 🔍 Key Highlights: ✅ Self-improvement via preference learning – Models learn to differentiate well-grounded from inaccurate responses without manual annotations. ✅ Multi-level temporal grounding – Effectively captures both localized segments and comprehensive video sequences. ✅ Efficient and scalable – Utilizes only 10k video QA pairs for post-training and can scale seamlessly to larger datasets. ✅ Proven performance – TPO enhances two state-of-the-art Video-LMMs on LongVideoBench, MLVU, and Video-MME. 🔥 LLaVA-Video-TPO is now the top-performing 7B model on Video-MME, highlighting TPO's potential in advancing temporal reasoning. This work was co-led with the talented undergraduate @rui__li, alongside fantastic collaborators @Zhang_Yu_hui and Zeyu Wang, and advised by @yeung_levy!
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Biomedical datasets are often confined to specific domains, missing valuable insights from adjacent fields. To bridge this gap, we present BIOMEDICA: an open-source framework to extract and serialize PMC-OA. 📄Paper: lnkd.in/dUUgA6rR 🌐Website: lnkd.in/dnqZZW4M
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