Related papers: RawBench: A Comprehensive Benchmarking Framework f…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Despite significant progress in designing powerful adversarial evasion attacks for robustness verification, the evaluation of these methods often remains inconsistent and unreliable. Many assessments rely on mismatched models, unverified…
The rise of big data systems has created a need for benchmarks to measure and compare the capabilities of these systems. Big data benchmarks present unique scalability challenges. The supercomputing community has wrestled with these…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
Extracting structured information from visual documents (Visual Information Extraction, VIE) is a cornerstone of business automation. While recent Multimodal Large Language Models (MLLMs) have shown promising capabilities, existing…
We introduce DRBench, a benchmark for evaluating AI agents on complex, open-ended deep research tasks in enterprise settings. Unlike prior benchmarks that focus on simple questions or web-only queries, DRBench evaluates agents on multi-step…
Motivation: The mapping of RNA-seq reads to their transcripts of origin is a fundamental task in transcript expression estimation and differential expression scoring. Where ambiguities in mapping exist due to transcripts sharing sequence,…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
Evaluation of reasoning language models gained importance after it was observed that they can combine their existing capabilities into novel traces of intermediate steps before task completion and that the traces can sometimes help them to…
This paper presents AquaSignal, a modular and scalable pipeline for preprocessing, denoising, classification, and novelty detection of underwater acoustic signals. Designed to operate effectively in noisy and dynamic marine environments,…
Deep-learning survival models for electronic health record (EHR) data are hard to compare across papers because the upstream preprocessing step, which includes cohort definition, time discretisation, missingness handling, and censoring…
Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a…
We study the task of automatically finding evidence relevant to hypotheses in biomedical papers. Finding relevant evidence is an important step when researchers investigate scientific hypotheses. We introduce EvidenceBench to measure models…
Nanopore resistive pulse sensors are emerging technologies for single-molecule protein sequencing. But they can hardly detect small post-translational modifications (PTMs) such as hydroxylation in single-molecule level. While a combination…
In this study, we present a computational framework tailored for the precise detection and comprehensive analysis of nanoparticles within scanning electron microscopy (SEM) images. The primary objective of this framework revolves around the…
Hyperspectral pansharpening consists of fusing a high-resolution panchromatic band and a low-resolution hyperspectral image to obtain a new image with high resolution in both the spatial and spectral domains. These remote sensing products…
Across scientific domains, a fundamental challenge is to characterize and compute the mappings from underlying physical processes to observed signals and measurements. While nonlinear neural networks have achieved considerable success, they…