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Tracking individual cells in live-cell imaging provides fundamental insights, inevitable for studying causes and consequences of phenotypic heterogeneity, responses to changing environmental conditions or stressors. Microbial cell tracking,…
This work introduces a new software package `Sesame' for the numerical computation of classical semiconductor equations. It supports 1 and 2-dimensional systems and provides tools to easily implement extended defects such as grain…
Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on score matrices and PSSMs obtained…
GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…
We introduce Quantum Mechanics for Proteins (QMProt), a dataset developed to support quantum computing applications in protein research. QMProt contains precise quantum-mechanical and physicochemical data, enabling accurate characterization…
An open source symbolic tool for vector fields analysis 'SymFields' is developed in Python. The SymFields module is constructed upon Python symbolic module sympy, which could only conduct scaler field analysis. With SymFields module, you…
We present SymNet, a network static analysis tool based on symbolic execution. SymNet quickly analyzes networks by injecting symbolic packets and tracing their path through the network. Our key novelty is SEFL, a language we designed for…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
Binary code clone analysis is an important technique which has a wide range of applications in software engineering (e.g., plagiarism detection, bug detection). The main challenge of the topic lies in the semantics-equivalent code…
PyPOTS is an open-source Python library dedicated to data mining and analysis on multivariate partially-observed time series with missing values. Particularly, it provides easy access to diverse algorithms categorized into five tasks:…
Mutation testing can be used to assess the fault-detection capabilities of a given test suite. To this aim, two characteristics of mutation testing frameworks are of paramount importance: (i) they should generate mutants that are…
We introduce SPFlow, an open-source Python library providing a simple interface to inference, learning and manipulation routines for deep and tractable probabilistic models called Sum-Product Networks (SPNs). The library allows one to…
Measuring and evaluating source code similarity is a fundamental software engineering activity that embraces a broad range of applications, including but not limited to code recommendation, duplicate code, plagiarism, malware, and smell…
We introduce OmniPrint, a synthetic data generator of isolated printed characters, geared toward machine learning research. It draws inspiration from famous datasets such as MNIST, SVHN and Omniglot, but offers the capability of generating…
This study proposes a deep learning-based approach for discovering loops in programming code according to their potential for parallelization. Two genetic algorithm-based code generators were developed to produce two distinct types of code:…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
We propose a new clustering algorithm, Extended Affinity Propagation, based on pairwise similarities. Extended Affinity Propagation is developed by modifying Affinity Propagation such that the desirable features of Affinity Propagation,…
Many software engineering techniques, such as fault localization, operate based on relevance relationships between tests and code. These relationships are often inferred through the use of dynamic test execution information (test execution…
Being able to duplicate published research results is an important process of conducting research whether to build upon these findings or to compare with them. This process is called "replicability" when using the original authors'…
Multidimensional scaling visualizes dissimilarities among objects and reduces data dimensionality. While many methods address symmetric proximity data, asymmetric and especially three-way proximity data (capturing relationships across…