Related papers: RawBench: A Comprehensive Benchmarking Framework f…

Inverse design of materials has significantly advanced target-driven formulation optimization, yet existing materials machine learning benchmarks remain limited to forward property prediction, failing to systematically evaluate inverse…

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…

This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…

Accurate evaluation of weather forecasting models is critical for their reliable deployment in real-world applications. However, existing benchmarks predominantly rely on reanalysis products such as ERA5, which are generated through delayed…

Introduction of spectrum-sharing in 5G and subsequent generation networks demand base-station(s) with the capability to characterize the wideband spectrum spanned over licensed, shared and unlicensed non-contiguous frequency bands. Spectrum…

Biometric systems based on brain activity have been proposed as an alternative to passwords or to complement current authentication techniques. By leveraging the unique brainwave patterns of individuals, these systems offer the possibility…

Recent advances in deep learning have driven rapid progress in time series forecasting, yet many state-of-the-art models continue to struggle with robust performance in real-world applications, even when they achieve strong results on…

In unforeseen situations, such as nuclear power plant's or civilian radiation accidents, there is a need for effective and computationally inexpensive methods to determine the expression level of a selected gene panel, allowing for rough…

Nanopore sensing is a versatile technique for the analysis of molecules on the single-molecule level. However, extracting information from data with established algorithms usually requires time-consuming checks by an experienced researcher…

Translocation event detection from raw nanopore current signals is a fundamental step in nanopore signal analysis. Traditional data analysis methods rely on user-defined parameters to extract event information, making the interpretation of…

Noise characterization methods such as randomized benchmarking (RB) are critical for the development of scalable quantum computers. Modern RB protocols for multiqubit systems extract physically relevant error rates by exploiting the…

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…

In real-world information-seeking scenarios, users have dynamic and diverse needs, requiring RAG systems to demonstrate adaptable resilience. To comprehensively evaluate the resilience of current RAG methods, we introduce HawkBench, a…

Despite Retrieval-Augmented Generation (RAG) showing promising capability in leveraging external knowledge, a comprehensive evaluation of RAG systems is still challenging due to the modular nature of RAG, evaluation of long-form responses…

Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…

Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn generalizable representations of diverse…

Existing prompt-optimization techniques rely on local signals to update behavior, often neglecting broader and recurring patterns across tasks, leading to poor generalization; they further rely on full-prompt rewrites or unstructured…

Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…

DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…

Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…