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Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it.…
In material science, models are derived to predict emergent material properties (e.g. elasticity, strength, conductivity) and their relations to processing conditions. A major drawback is the calibration of model parameters that depend on…
Exploring how genetic sequences shape phenotypes is a fundamental challenge in biology and a key step toward scalable, hypothesis-driven experimentation. The task is complicated by the large modality gap between sequences and phenotypes, as…
Motivation: MicroRNAs (miRNAs) play pivotal roles in gene expression regulation by binding to target sites of messenger RNAs (mRNAs). While identifying functional targets of miRNAs is of utmost importance, their prediction remains a great…
Recent randomised clinical trials have shown that patients with ischaemic stroke {due to occlusion of a large intracranial blood vessel} benefit from endovascular thrombectomy. However, predicting outcome of treatment in an individual…
Deep neural networks have amply demonstrated their prowess but estimating the reliability of their predictions remains challenging. Deep Ensembles are widely considered as being one of the best methods for generating uncertainty estimates…
Automated machine learning (AutoML) streamlines the creation of ML models. While most methods select the "best" model based on predictive quality, it's crucial to acknowledge other aspects, such as interpretability and resource consumption.…
Sequential models like recurrent neural networks and transformers have become standard for probabilistic multivariate time series forecasting across various domains. Despite their strengths, they struggle with capturing high-dimensional…
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…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially,…
A deep neural network model is a powerful framework for learning representations. Usually, it is used to learn the relation $x \to y$ by exploiting the regularities in the input $x$. In structured output prediction problems, $y$ is…
High-throughput RNA sequencing (RNA-seq) has emerged as a revolutionary and powerful technology for expression profiling. Most proposed methods for detecting differentially expressed (DE) genes from RNA-seq are based on statistics that…
This study introduces a surrogate modeling framework merging proper orthogonal decomposition, long short-term memory networks, and multi-task learning, to accurately predict elastoplastic deformations in real-time. Superior to single-task…
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…
Microarray gene expression data-based tumor classification is an active and challenging issue. In this paper, an integrated tumor classification framework is presented, which aims to exploit information in existing available samples, and…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a gene editing technology that has revolutionized the fields of biology and medicine. However, one of the challenges of using CRISPR is predicting the on-target efficacy…
Accurately measuring protein-RNA binding affinity is crucial in many biological processes and drug design. Previous computational methods for protein-RNA binding affinity prediction rely on either sequence or structure features, unable to…
MicroRNAs (miRNAs) are short sequences of ribonucleic acids that control the expression of target messenger RNAs (mRNAs) by binding them. Robust prediction of miRNA-mRNA pairs is of utmost importance in deciphering gene regulations but has…