Related papers: Multiple Sequence Alignment is not a Solved Proble…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to…
We present a new multi-layer peeling technique to cluster points in a metric space. A well-known non-parametric objective is to embed the metric space into a simpler structured metric space such as a line (i.e., Linear Arrangement) or a…
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in…
Hypergraph matching has recently become a popular approach for solving correspondence problems in computer vision as it allows to integrate higher-order geometric information. Hypergraph matching can be formulated as a third-order…
Equilibrium logic is an approach to nonmonotonic reasoning that extends the stable-model and answer-set semantics for logic programs. In particular, it includes the general case of nested logic programs, where arbitrary Boolean combinations…
Practical optimization problems may contain different kinds of difficulties that are often not tractable if one relies on a particular optimization method. Different optimization approaches offer different strengths that are good at…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…
AI alignment is often framed as the task of ensuring that an AI system follows a set of stated principles or human preferences, but general principles rarely determine their own application in concrete cases. When principles conflict, when…
Finding correspondences between shapes is a fundamental problem in computer vision and graphics, which is relevant for many applications, including 3D reconstruction, object tracking, and style transfer. The vast majority of correspondence…
Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and…
A coreset is a subset of the training set, using which a machine learning algorithm obtains performances similar to what it would deliver if trained over the whole original data. Coreset discovery is an active and open line of research as…
In this work we study permutation synchronisation for the challenging case of partial permutations, which plays an important role for the problem of matching multiple objects (e.g. images or shapes). The term synchronisation refers to the…
In a multiobjective optimization problem a solution is called Pareto-optimal if no criterion can be improved without deteriorating at least one of the other criteria. Computing the set of all Pareto-optimal solutions is a common task in…
The subject of this paper is to study conformance checking for timed models, that is, process models that consider both the sequence of events in a process as well as the timestamps at which each event is recorded. Time-aware process mining…
Network alignment (NA) aims to find a node mapping between molecular networks of different species that identifies topologically or functionally similar network regions. Analogous to genomic sequence alignment, NA can be used to transfer…
Progressive methods offer efficient and reasonably good solutions to the multiple sequence alignment problem. However, resulting alignments are biased by guide-trees, especially for relatively distant sequences. We propose MSARC, a new…
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…
Single-cell data integration can provide a comprehensive molecular view of cells, and many algorithms have been developed to remove unwanted technical or biological variations and integrate heterogeneous single-cell datasets. Despite their…