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Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We…
Nanobodies are small antibody fragments derived from camelids that selectively bind to antigens. These proteins have marked physicochemical properties that support advanced therapeutics, including treatments for SARS-CoV-2. To realize their…
Understanding the intertwined contributions of amino acid sequence and spatial structure is essential to explain protein behaviour. Here, we introduce INFUSSE (Integrated Network Framework Unifying Structure and Sequence Embeddings), a deep…
This paper studies the problem of, given the structure of a linear-time invariant system and a set of possible inputs, finding the smallest subset of input vectors that ensures system's structural controllability. We refer to this problem…
Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…
Current open-source prompt-injection detectors converge on two architectural choices: regular-expression pattern matching and fine-tuned transformer classifiers. Both share failure modes that recent work has made concrete. Regular…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…
Understanding sub-cellular protein localisation is an essential component to analyse context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
We introduce constraints necessary for type checking a higher-order concurrent constraint language, and solve them with an incremental algorithm. Our constraint system extends rational unification by constraints x$\subseteq$ y saying that…
Accurate localization of proteins from fluorescence microscopy images is challenging due to the inter-class similarities and intra-class disparities introducing grave concerns in addressing multi-class classification problems. Conventional…
We present in this paper a way to transform a constrained statistical inference problem into an unconstrained one in order to be able to use modern computational methods, such as those based on automatic differentiation, GPU computing,…
This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including…
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…
High-dimensional biomedical studies require models that are simultaneously accurate, sparse, and interpretable, yet exact best subset selection for generalized linear models is computationally intractable. We develop a scalable method that…
Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for elucidating them and their phenotypic effects. Especially…
Machine learning has been successfully applied in developing malware detection systems, with a primary focus on accuracy, and increasing attention to reducing computational overhead and improving model interpretability. However, an…
Semi-supervised learning (SSL) for medical image segmentation is a challenging yet highly practical task, which reduces reliance on large-scale labeled dataset by leveraging unlabeled samples. Among SSL techniques, the weak-to-strong…