Related papers: STRIKE-GOLDD 4.0: user-friendly, efficient analysi…

Open-World Object Detection (OWOD) enriches traditional object detectors by enabling continual discovery and integration of unknown objects via human guidance. However, existing OWOD approaches frequently suffer from semantic confusion…

Combinatorial and guided screening of materials space with density-functional theory and related approaches has provided a wealth of hypothetical inorganic materials, which are increasingly tabulated in open databases. The OPTIMADE API is a…

PyBADS is a Python implementation of the Bayesian Adaptive Direct Search (BADS) algorithm for fast and robust black-box optimization (Acerbi and Ma 2017). BADS is an optimization algorithm designed to efficiently solve difficult…

Accurate protein structures are essential for understanding biological function, yet incorporating experimental data into protein generative models remains a major challenge. Most predictors of experimental observables are…

Data series motif discovery represents one of the most useful primitives for data series mining, with applications to many domains, such as robotics, entomology, seismology, medicine, and climatology, and others. The state-of-the-art motif…

A simplicial complex is a generalization of a graph: a collection of n-ary relationships (instead of binary as the edges of a graph), named simplices. In this paper, we develop a new tool to study the structure of simplicial complexes: we…

An important problem in the analysis of high-dimensional omics data is to identify subsets of molecular variables that are associated with a phenotype of interest. This requires addressing the challenges of high dimensionality, strong…

Structural global parameter identifiability indicates whether one can determine a parameter's value from given inputs and outputs in the absence of noise. If a given model has parameters for which there may be infinitely many values, such…

The prediction of crystal properties is essential for understanding structure-property relationships and accelerating the discovery of functional materials. However, conventional approaches relying on experimental measurements or density…

The availability of large data sets is providing an impetus for driving current artificial intelligent developments. There are, however, challenges for developing solutions with small data sets due to practical and cost-effective deployment…

Machine learning models are increasingly applied to biomedical data, yet their adoption in high stakes domains remains limited by poor robustness, limited interpretability, and instability of learned features under realistic data…

Many tools exist for extracting structural and physiochemical descriptors from linear peptides to predict their properties, but similar tools for hydrocarbon-stapled peptides are lacking.Here, we present StaPep, a Python-based toolkit…

Modern large-scale scientific discovery requires multidisciplinary collaboration across diverse computing facilities, including High Performance Computing (HPC) machines and the Edge-to-Cloud continuum. Integrated data analysis plays a…

Arithmetic puzzle games provide a controlled setting for studying difficulty in mathematical reasoning tasks, a core challenge in adaptive learning systems. We investigate the structural determinants of difficulty in a class of integer…

A common approach for feature selection is to examine the variable importance scores for a machine learning model, as a way to understand which features are the most relevant for making predictions. Given the significance of feature…

Sign-based optimization algorithms, such as SignSGD, have garnered significant attention for their remarkable performance in distributed learning and training large foundation models. Despite their empirical superiority, SignSGD is known to…

Out-of-distribution (OOD) detection is crucial for ensuring the reliability of deep learning models in real-world applications. Existing methods typically focus on feature representations or output-space analysis, often assuming a…

Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change…

Pattern discovery is a machine learning technique that aims to find sets of items, subsequences, or substructures that are present in a dataset with a higher frequency value than a manually set threshold. This process helps to identify…

Learning models of dynamical systems with external inputs, which may be, for example, nonsmooth or piecewise, is crucial for studying complex phenomena and predicting future state evolution, which is essential for applications such as…