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The classical simulation of quantum computers is in general a computationally hard problem. To emulate the behavior of realistic devices, it is sufficient to sample bitstrings from circuits. Recently, arXiv:2112.08499 introduced the…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
We present iSLAT (the Interactive Spectral-Line Analysis Tool), a python-based graphical tool that allows users to interactively explore and manually fit line emission observed in molecular spectra. iSLAT adopts a simple slab model that…
The generation and collection of big data series are becoming an integral part of many emerging applications in sciences, IoT, finance, and web applications among several others. The terabyte-scale of data series has motivated recent…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
To address the scarcity of high-quality part annotations in existing datasets, we introduce PartImageNet++ (PIN++), a dataset that provides detailed part annotations for all categories in ImageNet-1K. With 100 annotated images per category,…
This paper presents an underlying framework for both automating and accelerating malware classification, more specifically, mapping malicious executables to known Advanced Persistent Threat (APT) groups. The main feature of this analysis is…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
Phylogenetic tree reconciliation is employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation.…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
Computationally expensive Radiative Transfer Models (RTMs) are widely used} to realistically reproduce the light interaction with the Earth surface and atmosphere. Because these models take long processing time, the common practice is to…
Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
The classification problem's complexity assessment is an essential element of many topics in the supervised learning domain. It plays a significant role in meta-learning -- becoming the basis for determining meta-attributes or…
Motivated by the need to emulate workload execution characteristics on high-performance and distributed heterogeneous resources, we introduce Synapse. Synapse is used as a proxy application (or "representative application") for real…
In recent years, the research community has raised serious questions about the reproducibility of scientific work. In particular, since many studies include some kind of computing work, reproducibility is also a technological challenge, not…
Embedded software systems, e.g. automotive, robotic or automation systems are highly configurable and consist of many software components being available in different variants and versions. To identify the degree of reusability between…
Past work in natural language processing interpretability focused mainly on popular classification tasks while largely overlooking generation settings, partly due to a lack of dedicated tools. In this work, we introduce Inseq, a Python…
Testing plays a pivotal role in ensuring software quality, yet conventional Search Based Software Testing (SBST) methods often struggle with complex software units, achieving suboptimal test coverage. Recent works using large language…
The similarity between protein sequences is a directly and easly computed quantity from which to deduce information about their evolutionary distance and to detect homologous proteins. The SIMAP database -- Similarity Matrix of Proteins --…