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We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
As modern analogue/mixed-signal design increasingly relies on optimization-in-the-loop flows, such as AI and LLM-based sizing agents that repeatedly invoke SPICE-efficient, accurate high-performance simulators have become an indispensable…
The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…
We present iSAPP (Imperative Static Analyser for Probabilistic Polynomial Time), a complexity verifier tool that is sound and extensionally complete for the Probabilistic Polynomial Time (PP) complexity class. iSAPP works on an imperative…
Expectation propagation (EP) is a deterministic approximation algorithm that is often used to perform approximate Bayesian parameter learning. EP approximates the full intractable posterior distribution through a set of local approximations…
We present EZ, a novel current deposition algorithm for particle-in-cell (PIC) simulations. EZ calculates the current density on the electromagnetic grid due to macro-particle motion within a time step by solving the continuity equation of…
Predicting and characterizing phase transitions is crucial for understanding generic physical phenomena such as crystallization, protein folding and others. However, directly observing phase transitions is not always easy, and often one has…
This paper describes the Jas4pp framework for exploring physics cases and for detector-performance studies of future particle collision experiments. Jas4pp is a multi-platform Java program for numeric calculations, scientific visualization…
BayesPy is an open-source Python software package for performing variational Bayesian inference. It is based on the variational message passing framework and supports conjugate exponential family models. By removing the tedious task of…
Programs with high levels of complexity often face challenges in adjusting execution parameters, particularly when these parameters vary based on the execution context. These dynamic parameters significantly impact the program's…
In Earth System Modeling (ESM), meshes of different models usually do not match, requiring data mapping algorithms implemented in coupling software. Valcke et al. recently introduced a benchmark to evaluate such algorithms and compared…
It is often difficult to write code that you can ensure will be executed in the right order when programing for parallel compute tasks. Due to the way that today's parallel compute hardware, primarily Graphical Processing Units (GPUs),…
Existing extremum-seeking control (ESC) approaches typically rely on applying repeated perturbations to input parameters and performing measurements of the corresponding performance output. The required separation between the different…
Probabilistic Logic Programming (PLP), exemplified by Sato and Kameya's PRISM, Poole's ICL, De Raedt et al's ProbLog and Vennekens et al's LPAD, combines statistical and logical knowledge representation and inference. Inference in these…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
Summary: The F2CS server provides access to the software, F2CS2.00, that implements an automated prediction method of SCOP and CATH classifications of proteins, based on their FSSP Z-scores (Getz et al., 2002), Availability: Free, at…
Constraint Programming (CP) is a useful technology for modeling and solving combinatorial constrained problems. On the one hand, on can use a library like PyCSP3 for easily modeling problems arising in various application fields (e.g.,…
Static analysis is a powerful technique for automatic verification of programs but raises major engineering challenges when developing a full-fledged analyzer for a realistic language such as Java. This paper describes the Sawja library: a…
We present HSIM: a dedicated pipeline for simulating observations with the HARMONI integral field spectrograph on the European Extremely Large Telescope. HSIM takes high spectral and spatial resolution input data-cubes, encoding physical…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…