Demonstration venue · read-only. Every page can be browsed; the buttons that would change it are switched off. Create an account to run TaxoReview on your own data. A simulation from public publication records: the people listed were not invited and did not agree to review.
? Tutorial for this page

Frederikke Isa Marin

dblp:361/6460 · DBLP profile ↗
← Back
1ranked-venue papers
1as first author
1since 2021 · last 2024
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Language models and text generation · 100%

Topics — the 3 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis
DNA language model
0.812024
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · ICLR 2024
Bioinformatics and computational biology
genome annotation
0.812024
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · ICLR 2024
Bioinformatics and computational biology
genomics
0.812024
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · ICLR 2024

Methods — techniques the papers use, named apart from their topics

language model embeddings · 0.8language model embedding · 0.8
YearPublicationVenuePosition
2024 BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks
abstract
The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce **BEND**, a **BEN**chmark for **D**NA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.
Frederikke Isa Marin, Felix Teufel, Marc Horlacher, Dennis Madsen, Dennis Pultz, Ole Winther, Wouter Boomsma
ICLR1