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PDSim is an R package that enables users to simulate commodity futures prices using the polynomial diffusion model introduced in Filipovic & Larsson (2016) through both a Shiny web application and R scripts. For user-supplied data, a…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Machine learning (ML) has seen promising developments in materials science, yet its efficacy largely depends on detailed crystal structural data, which are often complex and hard to obtain, limiting their applicability in real-world…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
Molecular Representation Learning is essential to solving many drug discovery and computational chemistry problems. It is a challenging problem due to the complex structure of molecules and the vast chemical space. Graph representations of…
Probabilistic models inform an increasingly broad range of business and policy decisions ultimately made by people. Recent algorithmic, computational, and software framework development progress facilitate the proliferation of Bayesian…
A major trend in academia and data science is the rapid adoption of Bayesian statistics for data analysis and modeling, leading to the development of probabilistic programming languages (PPL). A PPL provides a framework that allows users to…
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms. These chemical building blocks, or…
This paper presents a Matlab toolbox to perform basic image processing and visualization tasks, particularly designed for medical image processing. The functionalities available are similar to basic functions found in other non-Matlab…
PyUnfold is a Python package for incorporating imperfections of the measurement process into a data analysis pipeline. In an ideal world, we would have access to the perfect detector: an apparatus that makes no error in measuring a desired…
PySDM is an open-source Python package for simulating the dynamics of particles undergoing condensational and collisional growth, interacting with a fluid flow and subject to chemical composition changes. It is intended to serve as a…
E-graphs have emerged as a versatile data structure with applications in synthesis, optimization, and verification through techniques such as equality saturation. This paper introduces Python bindings for the experimental egglog library…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
Source code and its accompanying comments are complementary yet naturally aligned modalities-code encodes structural logic while comments capture developer intent. However, existing vulnerability detection methods mostly rely on…
HolPy is an interactive theorem proving system implemented in Python. It uses higher-order logic as the logical foundation. Its main features include a pervasive use of macros in producing, checking, and storing proofs, a JSON-based format…
In this position paper, we present a prototype of a visualizer for functional programs. Such programs, whose evaluation model is the reduction of an expression to a value through repeated application of rewriting rules, and which tend to…
In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…
This paper introduces Polyphorm, an interactive visualization and model fitting tool that provides a novel approach for investigating cosmological datasets. Through a fast computational simulation method inspired by the behavior of Physarum…
From the relative scarcity of training data to the lack of standardized benchmarks, the development of foundation models for polymers face significant and multi-faceted challenges. At the core, many of these issues are tied directly to the…
Modern software systems increasingly integrate machine learning (ML) due to its advancements and ability to enhance data-driven decision-making. However, this integration introduces significant challenges for software engineering,…