Related papers: inMOTIFin: a lightweight end-to-end simulation sof…
Mutation testing consists of generating test cases that detect faults injected into software (generating mutants) which its original test suite could not. By running such an augmented set of test cases, it may discover actual faults that…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Python's dynamic type system, while offering significant flexibility and expressiveness, poses substantial challenges for static analysis and automated tooling, particularly in unannotated or partially annotated codebases. Existing type…
Data series motif discovery represents one of the most useful primitives for data series mining, with applications to many domains, such as robotics, entomology, seismology, medicine, and climatology, and others. The state-of-the-art motif…
Recent advances in long chain-of-thought (CoT) reasoning have largely prioritized answer accuracy and token efficiency, while overlooking aspects critical to trustworthiness. We argue that usable reasoning systems must be trustworthy,…
Homeostasis is a running theme in biology. Often achieved through feedback regulation strategies, homeostasis allows living cells to control their internal environment as a means for surviving changing and unfavourable environments. While…
IntLevPy provides a comprehensive description of the IntLevPy Package, a Python library designed for simulating and analyzing intermittent and L\'evy processes. The package includes functionalities for process simulation, including full…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Mathematical models of gene regulatory networks are widely used to study cell fate changes and transcriptional regulation. When designing such models, it is important to accurately account for sources of stochasticity. However, doing so can…
Data-adaptive (machine learning-based) effect estimators are increasingly popular to reduce bias in high-dimensional bioinformatic and clinical studies (e.g. real-world data, target trials, -omic discovery). Their relative statistical…
Empirical research on code review processes is increasingly central to understanding software quality and collaboration. However, collecting and analyzing review data remains a time-consuming and technically intensive task. Most researchers…
Motif discovery is one of the most challenging problems in bioinformatics today. DNA sequence motifs are becoming increasingly important in analysis of gene regulation. Motifs are short, recurring patterns in DNA that have a biological…
As one of the most successful generative models, diffusion models have demonstrated remarkable efficacy in synthesizing high-quality images. These models learn the underlying high-dimensional data distribution in an unsupervised manner.…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
The design and implementation of regulation motifs ensuring robust perfect adaptation are challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic pathways producing, for instance, drug precursors and…
We present RoboManipBaselines, an open-source software framework for imitation learning research in robotic manipulation. The framework supports the entire imitation learning pipeline, including data collection, policy training, and…
Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal.…
The discovery of motifs underlying gene expression is a challenging one. Some of these motifs are known transcription factors, but sequence inspection often provides valuable clues, even discovery of novel motifs with uncharacterized…
Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…
Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…