Evidence map›Paper›PMID 40799805›Full record

ArticleArXiv2025

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA.

Aman Patel, Arpita Singhal, Austin Wang, Anusri Pampari, Maya Kasowski, Anshul Kundaje

Abstract readPreprint
In one paragraph

Article in ArXiv, 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

6 authors.

Aman PatelDepartment of Computer Science, School of Engineering, Stanford University.
Arpita SinghalDepartment of Computer Science, School of Engineering, Stanford University.
Austin WangDepartment of Computer Science, School of Engineering, Stanford University.
Anusri PampariDepartment of Computer Science, School of Engineering, Stanford University.
Maya KasowskiDepartment of Genetics, School of Medicine, Stanford University.
Anshul KundajeDepartment of Computer Science, School of Engineering, Stanford University.

Funding

INSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2M
GENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1M
Predicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory codeU01HG012069 · NHGRI · STANFORD UNIVERSITY · PI Anshul Kundaje · 2021 to 2026
$3.9M
Decoding the regulatory architecture of the human genome across cell types, individuals and diseaseU01HG009431 · NHGRI · STANFORD UNIVERSITY · PI PRITCHARD, JONATHAN K · 2017 to 2021
$3.5M
NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG009431NHGRI NIH HHS U01 HG012069NHGRI NIH HHS U24 HG007234
6 · The paper itself

Abstract

Recent advances in self-supervised models for natural language, vision, and protein sequences have catalyzed the development of genomic DNA language models (DNALMs). These models aim to learn generalizable representations of diverse DNA elements, potentially enabling various downstream genomic prediction, interpretation and design tasks. However, existing benchmarks do not adequately assess the capabilities of DNALMs on an important class of non-coding DNA elements critical for regulating gene activity. Here, we introduce DART-Eval, a suite of representative benchmarks focused on regulatory DNA to evaluate performance of DNALMs across zero-shot, probed, and fine-tuned settings against contemporary

Identifiers

PMID40799805
PMCPMC12340898

What OpenQuestion holds

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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.