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We propose a set of kernel-based tools to evaluate the designs and tune the hyperparameters of conditional sequence models, with a focus on problems in computational biology. The backbone of our tools is a new measure of discrepancy between…

Modern computational neuroscience strives to develop complex network models to explain dynamics and function of brains in health and disease. This process goes hand in hand with advancements in the theory of neuronal networks and increasing…

As the number of novel data-driven approaches to material science continues to grow, it is crucial to perform consistent quality, reliability and applicability assessments of model performance. In this paper, we benchmark the Materials…

Big data systems address the challenges of capturing, storing, managing, analyzing, and visualizing big data. Within this context, developing benchmarks to evaluate and compare big data systems has become an active topic for both research…

Recent advances in deep research systems enable large language models to retrieve, synthesize, and reason over large-scale external knowledge. In medicine, developing clinical guidelines critically depends on such deep evidence integration.…

Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…

As AI-driven document understanding and processing tools become increasingly prevalent in real-world applications, the need for rigorous evaluation standards has grown increasingly urgent. Existing benchmarks and evaluations often focus on…

In this paper we present the Yale-CMU-Berkeley (YCB) Object and Model set, intended to be used to facilitate benchmarking in robotic manipulation, prosthetic design and rehabilitation research. The objects in the set are designed to cover a…

Current benchmarks for evaluating the reasoning capabilities of Large Language Models (LLMs) face significant limitations: task oversimplification, data contamination, and flawed evaluation items. These deficiencies necessitate more…

Benchmarking involves designing scientific test methods, tools, and frameworks to quantitatively and comparably assess specific performance indicators of certain test subjects. With the development of artificial intelligence, AI…

Biopharmaceutical manufacturing is a rapidly growing industry with impact in virtually all branches of medicines. Biomanufacturing processes require close monitoring and control, in the presence of complex bioprocess dynamics with many…

DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of…

A bacterial biofilm is an aggregate of micro-organisms growing fixed onto a solid surface, rather than floating freely in a liquid. Biofilms play a major role in various practical situations such as surgical infections and water treatment.…

Side-by-side comparison of detailed kinetic models using a new tool to aid recognition of species structures reveals significant discrepancies in the published rates of many reactions and thermochemistry of many species. We present a first…

A central problem in systems biology is to identify parameter values such that a biological model satisfies some behavioral constraints (\eg, time series). In this paper we focus on parameter synthesis for hybrid (continuous/discrete)…

Fetching, which includes approaching, grasping, and retrieving, is a critical challenge for robot manipulation tasks. Existing methods primarily focus on table-top scenarios, which do not adequately capture the complexities of environments…

Mathematical modeling based on time-delay differential equations is an important tool to study the role of delay in biological systems and to evaluate its impact on the asymptotic behavior of their dynamics. Delays are indeed found in many…

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA,…

Over the past decade, generative models have demonstrated success in enhancing fundus images. However, the evaluation of these models remains a challenge. A benchmark for fundus image enhancement is needed for three main reasons:(1)…