science

Publications

The following publications discuss work from Biswas Family Foundation funded projects.

July 15, 2025

Learning Universal Representations of Intermolecular Interactions with ATOMICA

bioRxiv
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Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Manuscript
July 7, 2025

SPATIA: Multimodal Model for Prediction and Generation of Spatial Cell Phenotypes

arXiv
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Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Manuscript
June 29, 2025

Multimodal Medical Code Tokenizer

arXiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
June 11, 2025

One Patient, Many Contexts: Scaling Medical AI Through Contextual Intelligence

arXiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
June 4, 2025

ReXVQA: A Large-scale Visual Question Answering Benchmark for Generalist Chest X-ray Understanding

arXiv
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Associated Project:
The MAIDA Initiative: Democratizing Global Medical Imaging Data Sharing for Safer and Fairer AI
Principal Investigator:

Pranav Rajpurkar, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
June 3, 2025

Controllable Sequence Editing for Biological and Clinical Trajectories

arXiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
May 10, 2025

ReXGradient-160K: A Large-Scale Publicly Available Dataset of Chest Radiographs with Free-text Reports

arXiv
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Associated Project:
The MAIDA Initiative: Democratizing Global Medical Imaging Data Sharing for Safer and Fairer AI
Principal Investigator:

Pranav Rajpurkar, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
May 7, 2025

ClinVec: Unified Embeddings of Clinical Codes Enable Knowledge-Grounded AI in Medicine

medRXiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
May 5, 2025

Generalizable AI Predicts Immunotherapy Outcomes Across Cancers and Treatments

medRxiv
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Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Manuscript
April 27, 2025

Neighborhood Nonnegative Matrix Factorization Identifies Patterns and Spatially-Variable Genes in Large-Scale Spatial Transcriptomics Data

bioRxiv
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Associated Project:
Biswas Center for Transformative Computational Cancer Biology
Principal Investigator:

Katherine Pollard, PhD, Director of Data Science & Biotechnology, Gladstone Institutes

Category:
Manuscript
March 14, 2025

TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools

arXiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
March 4, 2025

Multimodal AI Predicts Clinical Outcomes of Drug Combinations from Preclinical Data

arXiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
January 22, 2025

KGARevion: An AI Agent for Knowledge-Intensive Biomedical QA

ICLR 2025 Conference
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Manuscript
December 15, 2024

ProCyon: A Multimodal Foundation Model for Protein Phenotypes

bioRxiv
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Associated Project:
Artificial intelligence for Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Manuscript
December 10, 2024

Unified Clinical Vocabulary Embeddings for Advancing Precision

medRxiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
November 21, 2024

Cellular Behavior Analysis from Live-Cell Imaging of TCR T Cell-Cancer Cell Interactions

bioRxiv
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Associated Project:
Biswas Center for Transformative Computational Cancer Biology
Principal Investigator:

Katherine Pollard, PhD, Director of Data Science & Biotechnology, Gladstone Institutes

Category:
Manuscript
November 15, 2024

Efficient Generation of Protein Pockets with PocketGen

Nature Machine Intelligence
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
November 12, 2024

Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics

NeurIPS AIDrugX
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Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Manuscript
October 31, 2024

Empowering Biomedical Discovery with AI Agents

Cell
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
August 29, 2024

ReXamine-Global: A Framework for Uncovering Inconsistencies in Radiology Report Generation Metrics

arXiv
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Associated Project:
The MAIDA Initiative: Democratizing Global Medical Imaging Data Sharing for Safer and Fairer AI
Principal Investigator:

Pranav Rajpurkar, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
August 19, 2024

Quantized Multi-Task Learning for Context-Specific Representations of Gene Network Dynamics

bioRxiv
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Associated Project:
Biswas Center for Transformative Computational Cancer Biology
Principal Investigator:

Katherine Pollard, PhD, Director of Data Science & Biotechnology, Gladstone Institutes

Category:
Manuscript
August 7, 2024

A Foundation Model for Clinician-Centered Drug Repurposing

Nature Medicine
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
July 27, 2024

Deep-learning prediction of gene expression from personal genomes

bioRxiv
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Associated Project:
Biswas Center for Transformative Computational Cancer Biology
Principal Investigator:

Katherine Pollard, PhD, Director of Data Science & Biotechnology, Gladstone Institutes 

Category:
Manuscript
July 22, 2024

Contextual AI Models for Single-Cell Protein Biology

Nature
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Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript

ReXGradient-160K: A Large-Scale Publicly Available Dataset of Chest Radiographs with Free-text Reports

Hugging Face
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Associated Project:
The MAIDA Initiative: Democratizing Global Medical Imaging Data Sharing for Safer and Fairer AI
Principal Investigator:

Pranav Rajpurkar, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Software
Associated Project:
The MAIDA Initiative: Democratizing Global Medical Imaging Data Sharing for Safer and Fairer AI
Principal Investigator:

Pranav Rajpurkar, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Software

TxAgent

GitHub
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Software

KGARevion

GitHub
Purple circular redirect arrow icon pointing to the right
Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School

Category:
Software

PINNACLE

GitHub
Purple circular redirect arrow icon pointing to the right
Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Software
Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Software

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