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Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…
Image-adaptive lookup tables (LUTs) have achieved great success in real-time image enhancement tasks due to their high efficiency for modeling color transforms. However, they embed the complete transform, including the color…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
Decompilation converts machine code into human-readable form, enabling analysis and debugging without source code. However, fidelity issues often degrade the readability and semantic accuracy of decompiled output. Existing methods, such as…
In this work, we present a methodology and a corresponding code-base for constructing mock integral field spectrograph (IFS) observations of simulated galaxies in a consistent and reproducible way. Such methods are necessary to improve the…
Considering the diverse nature of real-world distributed applications that makes it hard to identify a representative subset of distributed benchmarks, we focus on their underlying distributed algorithms. We present and characterize a new…
High quality epidemiological modelling is essential in order to combat the spread of infectious diseases. In this contribution, we present SimPLoID, an epidemiological modelling framework based on the probabilistic logic programming…
Medical image analysis is critical yet challenged by the need of jointly segmenting organs or tissues, and numerous instances for anatomical structures and tumor microenvironment analysis. Existing studies typically formulated different…
Machine learning (ML) offers powerful methods for detecting and modeling associations often in data with large feature spaces and complex associations. Many useful tools/packages (e.g. scikit-learn) have been developed to make the various…
Pattern matching is a powerful tool which is part of many functional programming languages as well as computer algebra systems such as Mathematica. Among the existing systems, Mathematica offers the most expressive pattern matching.…
We introduce SIMCOPILOT, a benchmark that simulates the role of large language models (LLMs) as interactive, "copilot"-style coding assistants. Targeting both completion (finishing incomplete methods or code blocks) and infill tasks…
Graph similarity search is among the most important graph-based applications, e.g. finding the chemical compounds that are most similar to a query compound. Graph similarity computation, such as Graph Edit Distance (GED) and Maximum Common…
Pattern matching is a powerful tool for symbolic computations. Applications include term rewriting systems, as well as the manipulation of symbolic expressions, abstract syntax trees, and XML and JSON data. It also allows for an intuitive…
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information…
Image Segmentation has been an active field of research as it has a wide range of applications, ranging from automated disease detection to self-driving cars. In recent years, various research papers proposed different loss functions used…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
In recent years, the robotics community has extensively examined methods concerning the place recognition task within the scope of simultaneous localization and mapping applications.This article proposes an appearance-based loop closure…
CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…
Python bindings are a critical bridge between high-performance C++ libraries and the flexibility of Python, enabling rapid prototyping, reproducible experiments, and integration with simulation and learning frameworks in robotics research.…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…