
Prof @NUFeinbergMed, Machine & Hybrid Intelligence Lab at Northwestern. Courtesy Prof @UCF retweet &/ like !=endorsement
Chicago, IL
Joined May 2009
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We ntroduce 𝗕𝗿𝗼𝗻𝗰𝗵𝗼𝗔𝗰𝗰𝗲𝘀𝘀, open-access CT dataset and benchmark for outcome-driven bronchoscopy accessibility prediction (our 𝗠𝗜𝗖𝗖𝗔𝗜 𝟮𝟬𝟮𝟲 work).
🌐 𝗣𝗿𝗼𝗷𝗲𝗰𝘁, 𝗽𝗮𝗽𝗲𝗿 and data: shorturl.at/moN2d
#MedicalImaging #Bronchoscopy #medicalAI
ulas bagci retweeted
"Ill-defined hypovascular mass."
Three words from a real radiology report. A tumor in the head of the pancreas. No size. No number. A radiologist reads these words and sees the tumor. We taught AI to see it too.
Ill-defined: the tumor has no clear edge. You cannot trace where it stops and the healthy pancreas begins.
Hypovascular: after the contrast dye, healthy pancreas lights up. The tumor stays dark.
Put together: a dark spot with blurry edges. Other reports say low-attenuation, heterogeneous, calcified, infiltrative. Each word is a visual fact a radiologist checked with their own eyes.
The same report measures a liver lesion at 15 mm. That is a number. AI learns numbers well: how many tumors, where, and how big (R-Super, #MICCAI2025). Descriptive words are harder. Nobody had taught AI the words of a tumor.
TextoMorph learned the words from 34,035 radiology reports. Tell it "ill-defined, hypovascular," and it draws that tumor on a CT scan: blurry edge, dark center. Tell it "well-defined, cystic," and it draws a different one. Our detection AI then practices on the tumors it used to miss.
Radiologists do nothing extra. The reports they already write teach the AI. Patients get an AI that learns what a tumor looks like, not only how big it is. Researchers and students get the code and models, #OpenSource: github.com/MrGiovanni/TextoM…, and article: ieeexplore.ieee.org/document…
Xinran Li led this work, with our partners at @nvidia, @UCSF, and the team in the post below.
Let AI read every word.
A team led by @JohnsHopkins researchers has developed a new system called TextoMorph, introduced in @IEEE_TMI. 🧵 (1/9)
feat. @Zongwei_Zhou, @YuilleAlan, @pedrorasb, @yy5ccuva, collaborators from @nvidia, @UCSF, @SunYatsen_Uni, & @HongKongPolyU, w/ @lustgartenfdn & @NIH support
ulas bagci retweeted
Buying random hospital scans is a very costly way to build AI for cancer.
About 61 million people in the U.S. get a CT scan each year. Fewer than 1 in 25 is diagnosed with cancer that year. For pancreatic cancer, it is about 1 in 900. And none of these scans comes with the tumor annotated in 3D.
CancerVerse is built the other way around. More than a third of its patients, about 5,000, have cancer. To find 5,000 cancer patients at random, you would have to buy CT scans from about 150,000 people. And experts annotated every tumor, voxel by voxel.
CancerVerse covers 13 cancer types.
For seven, these are the first public tumor masks: stomach, bladder, gallbladder, prostate, adrenal gland, duodenum, and spleen. Stomach cancer alone kills about 660,000 people a year worldwide.
The other six (liver, kidney, pancreas, colon, esophagus, uterus) had some public annotations. CancerVerse adds more, plus scans of the same patients over time.
This surprised me. AI for medical imaging has been hot for a decade. But in 2026, we could still claim a first. This is a big milestone.
We are not done. CancerVerse will grow to even more cancers, and you can help. If you have medical scans, our team turns the raw pixels into data AI can learn from. Then we release it together from @JohnsHopkins, with your team on it. Message me to start.
Our role model is MIMIC. It showed the world what open, longitudinal, multimodal patient data can do. As a healthcare researcher, I know how hard it is to bring data like this together and make it public. Thank you, Alistair Johnson, Tom Pollard, Steven Horng, MD, MMSc, FACEP, and the whole MIMIC team.
But CancerVerse is not simply MIMIC with CT. It is built for cancer: 3D longitudinal CT, expert tumor annotation, and 8,799 people confirmed free of these cancers for more than a year after their last scan.
Those healthy scans matter more than people expect. They are what tell you how often an AI raises a false alarm (IMPORTANT!!!).
Martijn P. A. Starmans, the #MICCAI Open Data initiative puts special emphasis on underrepresented diseases. We hope CancerVerse helps. @MICCAI_Society
Colleagues and students at #MICCAI2026, come discuss it with us.
🎗️ Poster Session 4, board W-AM-017
🎗️ Wednesday, September 30, 10:30 to 12:30
🎗️ Hall Rhin, Strasbourg Convention Center
Proud of our team at @JHUCompSci . Congratulations, @wenxuanli131 , @pedrorasb , and @zhou74818 on the Best Paper and Young Scientist Award nominations (#MICCAI2026)!
CancerVerse is free for research (#OpenScience). Download it. Build your AI that sees cancer coming.
ulas bagci retweeted
If you’re having trouble with your “vision-language models” — like they need huge amounts of data before they start learning, like they don’t know where to look, like they keep missing small diseases (and in healthcare, small size can be a big deal), like they get the measurements wrong, like they write reports that don’t match the images, or like they still can’t beat a simple U-Net, ..., come back and check out segmentation.
Segmentation is a foundation of medical image analysis. It may be (just slightly) less fashionable these years, partly because creating per-voxel annotations takes so much effort. For years, we’ve started our papers with some version of the same sentence: “Annotating medical images is tedious, time-consuming, and requires specialist expertise.”
But what if those per-voxel annotations are already available, and more annotated datasets are becoming available?
We present Merlin Plus. Building on @Stanford Merlin dataset, published in @Nature, we created 1,153 tumor per-voxel annotations across 9 organs, each produced by radiologists. These annotations show where the tumors are, voxel by voxel, giving models clear examples to learn from.
I predict, based on some early evidence, that self-supervised learning and vision-language learning could benefit greatly from datasets like this. Showing models where things are could make learning easier—and reduce the need for enormous amounts of data and compute.
Give your vision-language model sharper eyes. We’ve made these multi-tumor annotations available so you can try: lnkd.in/eGU6D_Dn
Replying to @JHUCompSci
In “Merlin Plus: A Large-Scale, Multi-Cancer, Image-Mask-Report Dataset,” @pedrorasb, @wenxuanli131, @YuilleAlan, @Zongwei_Zhou, @yy5ccuva, @Dr_ASChaudhari, @curtlanglotz, &more present the 1st CT dataset w/ radiologist-made tumor masks for 9 organs: github.com/MrGiovanni/Merlin… (7/8)
ulas bagci retweeted
An AI model trained from routine electronic health record data of 3.7 million individuals predicted cancer 1 year before clinical onset, no less promoted accuracy in detection, staging, treatment response, and prognosis
cell.com/cell/fulltext/S0092…
New paper in @CommsMedicine:
Compared 4 LLMs vs. 8 expert clinicians on interpreting brain metastases guidelines (ASTRO & ASCO).
LLMs: up to 100% accuracy, κ = 1.000
Experts: max 58.82%, κ ≤ 0.504
#MedicalAI #Oncology #LLM #BrainMetastases #OpenAccess
📄 doi.org/10.1038/s43856-025-0…
ulas bagci retweeted
AI scores 90% on one math test and 13% on another—the benchmarks are the problem
When we test an AI model on a benchmark, we assume the score tells us something meaningful about its capabilities. But what if the benchmark is measuring the wrong things—or several things at once without knowing it? And what if a 90% score on one math test tells us almost nothing about performance on a harder math test from the same domain?
That's exactly what happens. DeepSeek-R1-Distilled-Qwen-14B scores 90.5% on GSM8K but only 13.3% on OlymMATH Hard—when both supposedly test mathematical reasoning.
The answer reveals a deep flaw in how we evaluate AI: most benchmarks don't measure what they claim to measure, and their aggregate scores have little predictive power for unseen tasks.
Lexin Zhou and coauthors attack this head-on. They introduce 18 general rubrics—the DeLeAn rubric set—spanning cognitive capabilities like logical reasoning, metacognition, verbal comprehension, and knowledge in formal, natural, and applied sciences. Each rubric assigns a demand level from 0 to 5+ to any task instance. These levels are absolute, not relative to a population of models or benchmarks.
Running GPT-4o as an automated annotator across 16,108 instances from 20 benchmarks, they build the ADeLe battery: a unified representation of task demands across 18 dimensions. They then run 15 LLMs—from Babbage-002 to OpenAI o1 and DeepSeek-R1-Distilled—to derive ability profiles: 18-dimensional vectors describing what each model can reliably solve at each demand level.
The results are revealing. Knowledge dimensions scale primarily with model size. But quantitative reasoning, logical reasoning, and—strikingly—mind modeling and social cognition are boosted specifically in chain-of-thought reasoning models, even in smaller distilled variants. Most benchmarks fail basic construct validity: lacking either sensitivity or specificity, inadvertently measuring unrelated factors like question rarity or answer format.
The predictive power is the key result. A simple random forest trained on demand annotations achieves AUROC ~0.84 at a fraction of the compute of fine-tuned baselines—and degrades far less in out-of-distribution settings, precisely the regime that matters for real deployment.
This changes how model selection should work. Rather than relying on aggregate benchmark scores that may not transfer to your specific task, demand-based profiling lets you anticipate whether a model will succeed on literature annotation, reaction prediction, or experimental design before committing to a full pipeline integration—enabling smarter model routing and more reliable AI deployment in applied research.
Paper: Zhou et al., Nature (2026): nature.com/articles/s41586-0…
ulas bagci retweeted
The AI Scientist: Towards Fully Automated AI Research, Now Published in Nature
Nature: nature.com/articles/s41586-0…
Blog: sakana.ai/ai-scientist-natur…
When we first introduced The AI Scientist, we shared an ambitious vision of an agent powered by foundation models capable of executing the entire machine learning research lifecycle.
From inventing ideas and writing code to executing experiments and drafting the manuscript, the system demonstrated that end-to-end automation of the scientific process is possible.
Soon after, we shared a historic update: the improved AI Scientist-v2 produced the first fully AI-generated paper to pass a rigorous human peer-review process.
Today, we are happy to announce that “The AI Scientist: Towards Fully Automated AI Research,” our paper describing all of this work, along with fresh new insights, has been published in @Nature!
This Nature publication consolidates these milestones and details the underlying foundation model orchestration. It also introduces our Automated Reviewer, which matches human review judgments and actually exceeds standard inter-human agreement.
Crucially, by using this reviewer to grade papers generated by different foundation models, we discovered a clear scaling law of science. As the underlying foundation models improve, the quality of the generated scientific papers increases correspondingly. This implies that as compute costs decrease and model capabilities continue to exponentially increase, future versions of The AI Scientist will be substantially more capable.
Building upon our previous open-source releases (github.com/SakanaAI/AI-Scien…), this open-access Nature publication comprehensively details our system's architecture, outlines several new scaling results, and discusses the promise and challenges of AI-generated science.
This substantial milestone is the result of a close and fruitful collaboration between researchers at Sakana AI, the University of British Columbia (UBC) and the Vector Institute, and the University of Oxford. Congrats to the team!
@_chris_lu_ @cong_ml @RobertTLange @_yutaroyamada @shengranhu @j_foerst @hardmaru @jeffclune
ulas bagci retweeted
🧠🤖 Foundation models are shaking up medical imaging! @Neda_TV et al show how these models streamline workflows, boost accuracy, personalize care, & generate synthetic images. For real impact, we need trust, explainability, & integration! #AI #Radiology
pubs.rsna.org/doi/10.1148/ra…
ulas bagci retweeted
Ulas Bagci, Andrew Gordon and Ahsun Riaz received recognition as Mentors of the Year at the Northwestern University Radiology Research Day on June 5, 2025. Their work reflects Northwestern's strong teaching and mentoring values. @ulasbagci @AhsunR
ulas bagci retweeted
A landmark paper on research that has led to several patents. pubs.rsna.org/doi/10.1148/ra… #deeplearning #MRI #AI @DavidDushfunian @ulasbagci
ulas bagci retweeted
Physics-Informed Autoencoder for Prostate Tissue Microstructure Profiling with Hybrid Multidimensional MRI
The Physics-Informed Autoencoder (PIA) is a self-supervised deep learning model🤖 that accurately and efficiently measures prostate tissue biomarkers using hybrid multidimensional MRI, outperforming traditional nonlinear least squares (NLLS) methods. By embedding a biophysical diffusion-relaxation model into a neural network, PIA achieves high agreement with histopathology🔬across epithelium, stroma, and lumen compartments, even under noisy conditions. In both in silico and in vivo validation, PIA demonstrated strong correlations with prostate cancer aggressiveness and delivered results up to 10,000 times faster than NLLS.
These findings highlight PIA's promise as a robust, noninvasive, and explainable tool for #ProstateCancer detection and characterization.
@ulasbagci
@UChicagoRADS
@NURadiology
#MRI #AI #MachineLearning
@OncoAlert 🚨
@nataliagandur @bavilima @Silke_Gillessen @AOmlin
ulas bagci retweeted
We are proud to announce that Andrea Bejar, a research fellow in the Bagci lab, has been accepted for the 2025-26 cohort of the Chicago Area Schweitzer Fellowship. Congratulations, Andrea! @ulasbagci
ulas bagci retweeted
🚀 Introducing our proceedings on efficient MedSAMs in CVPR2024!
Promptable segmentation foundation models are revolutionizing medical imaging, yet their high computational demands hinder clinical adoption. To address this, we launched the first international competition in CVPR 2024 on efficient segmentation foundation models.
🏆 Key highlights:
🔹A large-scale benchmark spanning nine imaging modalities from 20+ institutions.
🔹Top teams developed lightweight segmentation models with efficient inference pipelines, dramatically reduced computational costs while maintaining state-of-the-art accuracy.
🔹 The best-performing algorithms are now integrated into open-source 3D Slicer software with a user-friendly interface to bridge research and clinical practice.
Proceedings: link.springer.com/book/10.10…
Summary: arxiv.org/abs/2412.16085
ulas bagci retweeted
Thrilled to announce that TotalSegmentator MRI has been published in @radiology_rsna @RSNA
Check out the paper: doi.org/10.1148/radiol.24161…
And the editorial by @FelipeKitamura: doi.org/10.1148/radiol.25014…
@JakobWasserthal @UniSpitalBasel @UniBasel_en
ulas bagci retweeted
Join us for this workshop on multimodal data integration hosted by the NIH Common Fund.
Join the conversation on 3/11-3/12 to help the #NIHCommonFund prioritize opportunities in enabling #PrecisionMedicine with #AI through the integration of #MedicalImaging with other #Data types! Register today: go.nih.gov/awiS2id
ulas bagci retweeted
An effective day brainstorming and learning - for both the scholars & the mentors
As our guest lecturer @ulasbagci says " AI will not replace physicians, but physicians who learn AI will replace them in healthcare research"
Thanks @ASGEendoscopy ! -with @AliSoroushMD
ulas bagci retweeted
In January, we feature our Quantitative Image Analysis & Artificial Intelligence research area.
academic.oup.com/bjrai/artic… #AI @ulasbagci @YuriVelichko
Advances for Managing Pancreatic Cystic Lesions: Integrating Imaging and AI Innovations
#pancreas #ipmn #cysts #pancan
#pancreaticcancer #ai #medicalai
#imaging #radiology #radiologyai
Read our review paper: mdpi.com/2072-6694/16/24/426…
ulas bagci retweeted
The pancreas is an organ that has been challenging to analyze. Gorkem Durak and Ulas Bagci offer remarks on using AI to image it, in this month's Journal of the Pancreas Online. bit.ly/49xUlcV @gorkemdurak_rad @ulasbagci






























