相关论文: A path-deformation framework for determining weigh…

Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…

The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…

Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…

We present an algorithmic approach to the conjugacy problems in monoids, using rewriting systems. We extend the classical theory of rewriting developed by Knuth and Bendix to a rewriting that takes into account the cyclic conjugates.

We investigate approaches to regularisation during fine-tuning of deep neural networks. First we provide a neural network generalisation bound based on Rademacher complexity that uses the distance the weights have moved from their initial…

This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…

We propose methods to train convolutional neural networks (CNNs) with both binarized weights and activations, leading to quantized models that are specifically friendly to mobile devices with limited power capacity and computation…

We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…

In Soda'06, Chaudhuri, Chen, Mihaescu and Rao study algorithmic properties of the tandem duplication - random loss model of genome rearrangement, well-known in evolutionary biology. In their model, the cost of one step of duplication-loss…

A common goal in observational research is to estimate marginal causal effects in the presence of confounding variables. One solution to this problem is to use the covariate distribution to weight the outcomes such that the data appear…

In this paper, we propose to train convolutional neural networks (CNNs) with both binarized weights and activations, leading to quantized models specifically} for mobile devices with limited power capacity and computation resources.…

Foundation models have achieved remarkable results in medical image analysis. However, its large network architecture and high computational complexity significantly impact inference speed, limiting its application on terminal medical…

In the context of the genome rearrangement problem, we analyze two well known models, namely the reversal and the prefix reversal models, by exploiting the connection with the notion of permutation pattern. More specifically, for any $k$,…

Prediction of protein-ligand complexes for flexible proteins remains still a challenging problem in computational structural biology and drug design. Here we present two novel deep neural network approaches with significant improvement in…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…

We address the problem of computing distances between rankings that take into account similarities between candidates. The need for evaluating such distances is governed by applications as diverse as rank aggregation, bioinformatics, social…

Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…

We develop a general framework for reasoning about distances between transition systems with quantitative information. Taking as starting point an arbitrary distance on system traces, we show how this leads to natural definitions of a…

Deformed generalized gauge groups, whch were created from physical considerations and made it possible to clarify some long-standing problems in physics, such as the problem of motion and the problem of the energy of the gravitational…