Twitxy Saved

Faisal Mahmood

Verified account This account is verified. Learn more

@AI4Pathology

Associate Prof. @Harvard | Faculty @harvardmed @MassGenBrigham @broadinstitute @harvard_data | Director, MGB AI Institute
Boston, MA 🇺🇸 mahmoodlab.org Joined March 2010
1.7K Following 7.2K Followers 815 Posts

Latest posts 5

Pinned post

Faisal Mahmood Verified account @AI4Pathology
Today we are thrilled to announce Clinical System One (CS1), a fast and efficient general-purpose decision model for medicine.

Read our preprint 📄: arxiv.org/abs/2610.27099
Watch the video 🎬👇
Blog: linkedin.com/pulse/reading-…

Healthcare has a scale problem. Every health system holds decades of notes, reports, and timelines. They contain answers to questions we rarely get to ask of more than a few patients at a time. Which patients could join this trial? Who missed a follow-up? What happened to everyone who took this drug? Reading all of it, for every question, has always been too slow and too expensive. That was true even with LLMs.

Thats why our team built Clinical System One (CS1). Its a small, fast decision model tailored for clinical records. Trained on 12.4 million questions and 3.6 million patients, CS1-4B beats open decision models on reading real-world patient records across diverse healthcare systems, and it runs on a single desktop GPU. We show the power of composing CS1 with traditional System 2 LLMs into agentic systems that read dense patient timelines and assess trial eligibility from a pool of a thousand candidates. Imagine trials that find every eligible patient automatically, registries that fill themselves, and care gaps surfaced across a whole population. Thats the future were building toward.
2:17
19 replies 53 reposts 387 likes 21K views View on X
Faisal Mahmood Verified account @AI4Pathology
Can an EHR model trained at one hospital read another hospital's records?

Excited to introduce our new paper, "Discrete Neural Interlingua for Ontology-Agnostic EHR Modeling," accepted at NeurIPS 2026. See you in Sydney 🦘🏖️!

Paper: arxiv.org/abs/2610.27047
Code: github.com/mahmoodlab/MED…
Model: huggingface.co/MahmoodLab/MED…

Video: See👇

The same clinical concept can be an ICD code, a SNOMED term, a local identifier, or free text, and standard EHR tokenizers treat each one as an unrelated symbol. A model trained on MIMIC-III with a closed vocabulary can use only 13% of eICU events. It isn't only a cross-hospital problem. For example, inside one hospital, "acute kidney injury" can be a billing code, a flowsheet identifier, and free text in a note, and the vocabulary shifts again with every coding transition and EHR migration. The redundancy is there before a model ever leaves the building.

MEDIATOR is a discrete, ontology-agnostic tokenizer. Any clinical concept written as text maps to one of 100,000 shared tokens, so "acute kidney failure" (ICD-9), "AKI" (a local code), and "acute kidney injury" (free text) become the same token. It is trained on cross-ontology synonyms from UMLS and guided by LLM-enriched descriptions, code co-occurrence, and a medical relation graph. It is a drop-in token interface for standard EHR Transformers: no manual code mapping, and new code systems can be tokenized without retraining.

Main results:

• In-domain: +4.0 AUPRC points (8% relative) over SOTA, across 20 MIMIC-III tasks. Merging within-dataset redundancy pays off before you transfer anything.

• Zero-shot transfer: on eICU with no vocabulary alignment, MEDIATOR uses all 3.58 million events and improves AUPRC over MedTok by 8.6 points (29% relative) across 14 tasks, up to +21.2 on subarachnoid hemorrhage. Restricted to the same inputs as the closed-vocabulary baselines, it is still the best tokenizer.

• Transferable attribution: one shared token space means attributions compare directly across hospitals. For cirrhosis mortality, token importance is rank-correlated between MIMIC-III and eICU at Spearman ρ = 0.92.

Tokenizing a dataset's entire vocabulary is a one-time step of about 70 seconds on one GPU. Code and weights are public, and the co-occurrence teacher can be rebuilt from public data with near-identical results.

Congradulations to Caiwei Tian Tong Ding and everyone else.
#NeurIPS2026 #ClinicalInformatics #EHR #MachineLearning
1:37
16 replies 26 reposts 153 likes 8K views View on X
Faisal Mahmood Verified account @AI4Pathology
🎊 Excited to share our new study, Beyond Sparse Captions: Aligning Slide-Level Text and Patch-Level Vision in Pathology accepted at NeurIPS 2026 as a Spotlight article (top 1.3% articles) from our superstars @Daniel__Shao and Eugene (Dongmin) Bang.

Code: github.com/mahmoodlab/LIM…
Model: huggingface.co/MahmoodLab/CON…
Paper: arxiv.org/abs/2610.17233
0:58
3 replies 10 reposts 72 likes 4.1K views View on X