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We describe the development of a multi-purpose software for Bayesian statistical inference, BAT.jl, written in the Julia language. The major design considerations and implemented algorithms are summarized here, together with a test suite…

The importance of computers is continually increasing in radiotherapy. Efficient algorithms, implementations and the ability to leverage advancements in computer science are crucial to improve cancer care even further and deliver the best…

Given a set of data, biclustering aims at finding simultaneous partitions in biclusters of its samples and of the features which are used for representing the samples. Consistent biclusterings allow to obtain correct classifications of the…

Biclustering, also called co-clustering, block clustering, or two-way clustering, involves the simultaneous clustering of both the rows and columns of a data matrix into distinct groups, such that the rows and columns within a group display…

We present StochasticPrograms.jl, a user-friendly and powerful open-source framework for stochastic programming written in the Julia language. The framework includes both modeling tools and structure-exploiting optimization algorithms.…

Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…

Biological systems with intertwined feedback loops pose a challenge to mathematical modeling efforts. Moreover, rare events, such as mutation and extinction, complicate system dynamics. Stochastic simulation algorithms are useful in…

In this paper we present BilevelJuMP, a new Julia package to support bilevel optimization within the JuMP framework. The package is a Julia library that enables the user to describe both upper and lower-level optimization problems using the…

To understand complex biological systems, the research community has produced huge corpus of gene expression data. A large number of clustering approaches have been proposed for the analysis of gene expression data. However, extracting…

Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes…

When measuring a range of different genomic, epigenomic, transcriptomic and other variables, an integrative approach to analysis can strengthen inference and give new insights. This is also the case when clustering patient samples, and…

Biclustering numerical data became a popular data-mining task in the beginning of 2000's, especially for analysing gene expression data. A bicluster reflects a strong association between a subset of objects and a subset of attributes in a…

Biclustering, also known as co-clustering or two-way clustering, simultaneously partitions the rows and columns of a data matrix to reveal submatrices with coherent patterns. Incorporating background knowledge into clustering to enhance…

Biclustering algorithms play a central role in the biotechnological and biomedical domains. The knowledge extracted supports the extraction of putative regulatory modules, essential to understanding diseases, aiding therapy research, and…

Data matrix having different sets of entities in its rows and columns are known as two mode data or affiliation data. Many practical problems require to find relationships between the two modes by simultaneously clustering the rows and…

In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying…

Biclustering has gained interest in gene expression data analysis due to its ability to identify groups of samples that exhibit similar behaviour in specific subsets of genes (or vice versa), in contrast to traditional clustering methods…

Medical image segmentation is a cornerstone of computer-assisted diagnosis and treatment planning. While recent multimodal vision-language models have shown promise in enhancing semantic understanding through textual descriptions, their…

Proprietary closed-source software is still the norm in advanced process control. Transparency and reproducibility are key aspects of scientific research. Free and open-source toolkit can contribute to the development, sharing and…

Connectivity across landscapes influences a wide range of conservation-relevant ecological processes, including species movements, gene flow, and the spread of wildfire, pests, and diseases. Recent improvements in remote sensing data…