science

Publications

We believe in the power of open science to drive innovation and foster collaboration. Here are the published papers from our funded researchers.

The following publications report findings from projects funded by the Biswas Family Foundation.

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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:
Preprints
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, Associate Professor of Biomedical Informatics, Harvard Medical School 

Category:
Preprints
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:
Preprints
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, Associate Professor of Biomedical Informatics, Harvard Medical School 

Category:
Papers
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:
Preprints
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, Associate Professor of Biomedical Informatics, Harvard Medical School 

Category:
Papers
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:
Preprints
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:
Preprints
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, Associate Professor of Biomedical Informatics, Harvard Medical School 

Category:
Papers
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, Associate Professor of Biomedical Informatics, Harvard Medical School 

Category:
Papers

Genecorpus-104M dataset

Hugging Face
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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:
Data Ecosystem

Geneformer-V2

Hugging Face
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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:
Software

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