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Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, motif finding algorithms of increasingly high performance are required to process the big…

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…

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.…

Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…

We present an automated approach for identifying and annotating motifs and domains in protein sequences, using pretrained Protein Language Models (PLMs) and Concept Activation Vectors (CAVs), adapted from interpretability research in…

We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…

Link prediction plays an important role in network analysis and applications. Recently, approaches for link prediction have evolved from traditional similarity-based algorithms into embedding-based algorithms. However, most existing…

Over the past decade, neural networks have been successful at making predictions from biological sequences, especially in the context of regulatory genomics. As in other fields of deep learning, tools have been devised to extract features…

Time series motifs play an important role in the time series analysis. The motif-based time series clustering is used for the discovery of higher-order patterns or structures in time series data. Inspired by the convolutional neural network…

Data science projects often involve various machine learning (ML) methods that depend on data, code, and models. One of the key activities in these projects is the selection of a model or algorithm that is appropriate for the data analysis…

Attribute reconstruction is used to predict node or edge features in the pre-training of graph neural networks. Given a large number of molecules, they learn to capture structural knowledge, which is transferable for various downstream…

Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a…

Motif counting plays a crucial role in understanding the structural properties of networks. By computing motif frequencies, researchers can draw key insights into the structural properties of the underlying network. As networks become…

Motif finding is an important step for the detection of rare events occurring in a set of DNA or protein sequences. Extraction of information about these rare events can lead to new biological discoveries. Motifs are some important patterns…

Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using…

Community detection for unweighted networks has been widely studied in network analysis, but the case of weighted networks remains a challenge. This paper proposes a general Distribution-Free Model (DFM) for weighted networks in which nodes…

This paper is the first to explore an automatic way to detect bias in deep convolutional neural networks by simply looking at their weights. Furthermore, it is also a step towards understanding neural networks and how they work. We show…

Mass spectra, which are agglomerations of ionized fragments from targeted molecules, play a crucial role across various fields for the identification of molecular structures. A prevalent analysis method involves spectral library…

Flow matching models generate high-fidelity molecular geometries but incur significant computational costs during inference, requiring hundreds of network evaluations. This inference overhead becomes the primary bottleneck when such models…

Network motif provides a way to uncover the basic building blocks of most complex networks. This task usually demands high computer processing, specially for motif with 5 or more vertices. This paper presents an extended methodology with…