Related papers: SMaSH: A Benchmarking Toolkit for Human Genome Var…
Spatio-temporal point processes (STPPs) are potent mathematical tools for modeling and predicting events with both temporal and spatial features. Despite their versatility, most existing methods for learning STPPs either assume a restricted…
We present a new benchmark for evaluating Deep Search--a realistic and complex form of retrieval-augmented generation (RAG) that requires source-aware, multi-hop reasoning over diverse, sparsed, but related sources. These include documents,…
Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…
This paper presents a simple, effective, and cost-efficient strategy to improve LLM performance by scaling test-time compute. Our strategy builds upon the repeated-sampling-then-voting framework, with a novel twist: incorporating multiple…
This work presents a statistically principled method for estimating the required number of instances in the experimental comparison of multiple algorithms on a given problem class of interest. This approach generalises earlier results by…
Test-time scaling has emerged as a powerful paradigm for enhancing the reasoning capabilities of large language models (LLMs) by allocating additional computational resources during inference. However, this paradigm is inherently…
Benchmarking the performance of quantum optimization algorithms is crucial for identifying utility for industry-relevant use cases. Benchmarking processes vary between optimization applications and depend on user-specified goals. The…
Cryptographic digests (e.g., MD5, SHA-256) are designed to provide exact identity. Any single-bit change in the input produces a completely different hash, which is ideal for integrity verification but limits their usefulness in many…
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
Quality assessment of images and videos emphasizes both local details and global semantics, whereas general data sampling methods (e.g., resizing, cropping or grid-based fragment) fail to catch them simultaneously. To address the…
We propose SLAMFuse, an open-source SLAM benchmarking framework that provides consistent crossplatform environments for evaluating multi-modal SLAM algorithms, along with tools for data fuzzing, failure detection, and diagnosis across…
Despite advances in feature representation, leveraging geometric relations is crucial for establishing reliable visual correspondences under large variations of images. In this work we introduce a Hough transform perspective on…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…
Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…
Multiple sequence alignment (MSA) is a core operation for comparing genome sequences and is widely used in bio-informatics. MAFFT, a practical MSA tool, repeatedly shifts a pair of sequences and computes a distance. Because the number of…
In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…