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We present an algorithm for the classification of linear codes over finite fields, based on lattice point enumeration. We validate a correct implementation of our algorithm with known classification results from the literature, which we…

GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…

Graph rewrite systems are powerful tools to model and study complex problems in various fields of research. Their successful application to chemical reaction modelling on a molecular level was shown but no appropriate and simple system is…

KernelHaven is an open infrastructure for Software Product Line (SPL) analysis. It is intended both as a production-quality analysis tool set as well as a research support tool, e.g., to support researchers in systematically exploring…

We find ourselves on the brink of an exciting era in observational astrophysics, driven by groundbreaking facilities like JWST, Euclid, Rubin, Roman, SKA, or ELT. Simultaneously, computational astrophysics has shown significant strides,…

For deterministic and probabilistic programs we investigate the problem of program synthesis and program optimisation (with respect to non-functional properties) in the general setting of global optimisation. This approach is based on the…

We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and…

This paper targets the automated extraction of components of argumentative information and their relations from natural language text. Moreover, we address a current lack of systems to provide complete argumentative structure from arbitrary…

Interrogation of biological pathways is an integral part of omics data analysis. Large language models (LLMs) enable the generation of custom pathways and gene sets tailored to specific scientific questions. These targeted sets are…

We present the first public release of ShapePipe, an open-source and modular weak-lensing measurement, analysis, and validation pipeline written in Python. We describe the design of the software and justify the choices made. We provide a…

Accessing structures of molecules, crystals, and complex interfaces with atomic level details is vital to the understanding and engineering of materials, chemical reactions, and biochemical processes. Currently, determination of accurate…

Molecular line data for the rotational transitions of a number of astrophysically interesting species have been collected and are made publically available through the www. These data, including energy levels, statistical weights, Einstein…

Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs,…

A linear graph is a graph whose vertices are totally ordered. Biological and linguistic sequences with interactions among symbols are naturally represented as linear graphs. Examples include protein contact maps, RNA secondary structures…

Foundation models (FMs) have opened new avenues for machine learning applications due to their ability to adapt to new and unseen tasks with minimal or no further training. Time-series foundation models (TSFMs) -- FMs trained on time-series…

We present QDK/Chemistry, a software toolkit for quantum chemistry workflows targeting quantum computers. The toolkit addresses a key challenge in the field: while quantum algorithms for chemistry have matured considerably, the…

Artificial Intelligence (AI)-driven material design has been attracting great attentions as a groundbreaking technology across a wide spectrum of industries. Molecular design is particularly important owing to its broad application domains…

To address the challenges associated with data processing at scale, we propose Dataverse, a unified open-source Extract-Transform-Load (ETL) pipeline for large language models (LLMs) with a user-friendly design at its core. Easy addition of…

With the increasing interest in robotic synthesis in the context of organic chemistry, the automated extraction of chemical procedures from literature is critical. However, this task remains challenging due to the inherent ambiguity of…

The development of large language models and multi-modal models has enabled the appealing idea of generating novel molecules from text descriptions. Generative modeling would shift the paradigm from relying on large-scale chemical screening…