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Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…

Random forests are a machine learning method used to automatically classify datasets and consist of a multitude of decision trees. While these random forests often have higher performance and generalize better than a single decision tree,…

Motivation: The study of diverse enzyme superfamilies can provide important insight into the relationships between protein sequence, structure and function. It is often challenging, however, to discover these relationships across a large…

We present an approach to model-based hierarchical clustering by formulating an objective function based on a Bayesian analysis. This model organizes the data into a cluster hierarchy while specifying a complex feature-set partitioning that…

Spatial mapping of biodiversity is crucial to investigate spatial variations in natural communities. Several indices have been proposed in the literature to represent biodiversity as a single statistic. However, these indices only provide…

Clustering is a class of unsupervised learning methods that has been extensively applied and studied in computer vision. Little work has been done to adapt it to the end-to-end training of visual features on large scale datasets. In this…

Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…

Process discovery algorithms automatically extract process models from event logs, but high variability often results in complex and hard-to-understand models. To mitigate this issue, trace clustering techniques group process executions…

A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…

Pattern comparison represents a fundamental and crucial aspect of scientific modeling, artificial intelligence, and pattern recognition. Three main approaches have typically been applied for pattern comparison: (i) distances; (ii)…

Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…

Load shapes derived from smart meter data are frequently employed to analyze daily energy consumption patterns, particularly in the context of applications like Demand Response (DR). Nevertheless, one of the most important challenges to…

We attempt to set a mathematical foundation of immunology and amino acid chains. To measure the similarities of these chains, a kernel on strings is defined using only the sequence of the chains and a good amino acid substitution matrix…

The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets. A novel method that…

Similarity plays a fundamental role in many areas, including data mining, machine learning, statistics and various applied domains. Inspired by the success of ensemble methods and the flexibility of trees, we propose to learn a similarity…

Patchwork learning arises as a new and challenging data collection paradigm where both samples and features are observed in fragmented subsets. Due to technological limits, measurement expense, or multimodal data integration, such patchwork…

Purpose: This study aimed to enhance protein sequence classification using natural language processing (NLP) techniques while addressing the impact of sequence similarity on model performance. We compared various machine learning and deep…

Clustering of proteins is of interest in cancer cell biology. This article proposes a hierarchical Bayesian model for protein (variable) clustering hinging on correlation structure. Starting from a multivariate normal likelihood, we enforce…

State-of-the-art clustering algorithms use heuristics to partition the feature space and provide little insight into the rationale for cluster membership, limiting their interpretability. In healthcare applications, the latter poses a…

While modern biotechnologies allow synthesizing new proteins and function measurements at scale, efficiently exploring a protein sequence space and engineering it remains a daunting task due to the vast sequence space of any given protein.…