Evidence map›Paper›PMID 41510245›Full record

ArticleResearch square2025

A Process-Centric Survey of AI for Scientific Discovery Through the EXHYTE Framework.

Md Musaddaqul Hasib, Sumin Jo, Harsh Sinha, Jifeng Song, Arun Das, Zhentao Liu, Hugh Galloway, Huey Huang, Kexun Zhang, Shou-Jiang Gao and 3 more

Abstract readPreprint
In one paragraph

Article in Research square, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Md Musaddaqul HasibCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Sumin JoDepartment of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
Harsh SinhaCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Jifeng SongCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Arun DasCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Zhentao LiuCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Hugh GallowayCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Huey HuangElectrical and Computer Engineering, University of Texas at Austin, Austin, TX, USA.
Kexun ZhangLanguage Technologies Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
Shou-Jiang GaoCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Yu-Chiao ChiuDepartment of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Lei LiLanguage Technologies Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
Yufei HuangCancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.

Funding

VECTOR CORE FACILITYP30CA047904 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI CHRISTOPHER J. BAKKENIST · 1988 to 2026
$158.0M
Cell Model for KSHV Infection and Genetic ManipulationR01CA096512 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI Shou-Jiang Gao · 2003 to 2026
$7.4M
Regulation of KSHV replication by N6-methyladenosine (m6A) - Diversity SupplementR01CA124332 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI GAO, SHOU-JIANG · 2007 to 2025
$5.0M
Impact of microbiota on AIDS-Kaposi’s sarcoma development and therapyR01CA284554 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Shou-Jiang Gao · 2023 to 2026
$3.1M
Citrulline-urea cycle in KSHV cellular transformationR01CA278812 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Shou-Jiang Gao · 2023 to 2026
$2.1M
m6A-suite: an informatics pipeline and resource for elucidating roles of m6A epitranscriptome in cancerU01CA279618 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI HUANG, YUFEI · 2023 to 2025
$1.8M
METTL16 and S-adenosylmethionine cycle in KSHV infectionR01CA291244 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Shou-Jiang Gao · 2025 to 2026
$1.3M
Novel computational approaches for pharmacogenomics of complex diseasesR35GM154967 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Yu-Chiao Chiu · 2024 to 2026
$1.2M
High-Throughput Computing for Genomics and Bioinformatics ResearchS10OD028483 · OD · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LEE, ADRIAN V · 2021 to 2021
$574k
Open science platform for cancer dependency prediction and analysis using deep learning and large language modelsR03CA305794 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Yu-Chiao Chiu · 2025 to 2026
$474k
Novel geometric deep learning models for tissue structure-aware spatial expression representations from spatially resolved single-cell transcriptomics dataR21GM155774 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI GAO, SHOU-JIANG, HUANG, YUFEI · 2024 to 2025
$433k
NCI NIH HHS P30 CA047904NCI NIH HHS R01 CA096512NCI NIH HHS R01 CA124332NCI NIH HHS R01 CA278812NCI NIH HHS R01 CA284554NCI NIH HHS R01 CA291244NCI NIH HHS R03 CA305794NCI NIH HHS U01 CA279618NIGMS NIH HHS R21 GM155774NIGMS NIH HHS R35 GM154967NIH HHS S10 OD028483
6 · The paper itself

Abstract

Large language models (LLMs) and agent systems are increasingly transforming scientific discovery, driving progress across chemistry, biology, materials science, and physics. Yet most existing work and surveys remain fragmented, focusing on isolated tasks such as idea generation or experiment design without addressing how these components fit within the broader discovery process. To bridge this gap, we introduce the EXHYTE cycle, an iterative framework that formalizes scientific discovery as a sequence of

Indexed as

AI for Scientific discoveryHypothesis generationIdea generationLarge language modelsthe EXHYTE cycle

Identifiers

PMID41510245
PMCPMC12776506

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.