Demo Data from VLDB 2026 / reviewers in the wild / expert
Frederikke Isa Marin
dblp:361/6460
· DBLP profile ↗
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
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › sequence analysis
DNA language model |
0.8 | 1 | 2024 | BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · ICLR 2024 |
Bioinformatics and computational biology
genome annotation |
0.8 | 1 | 2024 | BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · ICLR 2024 |
Bioinformatics and computational biology
genomics |
0.8 | 1 | 2024 | 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
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | BEND: Benchmarking DNA Language Models on Biologically Meaningful TasksabstractThe 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 |
ICLR | 1 |