相关论文: Exemplar or Matching: Modeling DCJ Problems with U…

Neural networks (NNs) have gained significant attention across various engineering disciplines, particularly in design optimization, where they are used to build surrogate models for high-dimensional regression problems. Despite their power…

In this work, we study linear error-correcting codes against adversarial insertion-deletion (indel) errors. While most constructions for the indel model are nonlinear, linear codes offer compact representations, efficient encoding, and…

Low-dimensional embeddings for data from disparate sources play critical roles in multi-modal machine learning, multimedia information retrieval, and bioinformatics. In this paper, we propose a supervised dimensionality reduction method…

Testing for the equality of two high-dimensional distributions is a challenging problem, and this becomes even more challenging when the sample size is small. Over the last few decades, several graph-based two-sample tests have been…

Graph edit distance / similarity is widely used in many tasks, such as graph similarity search, binary function analysis, and graph clustering. However, computing the exact graph edit distance (GED) or maximum common subgraph (MCS) between…

In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…

Mutation testing is vital for ensuring software quality. However, the presence of equivalent mutants is known to introduce redundant cost and bias issues, hindering the effectiveness of mutation testing in practical use. Although numerous…

The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work…

Comparing two (large) language models (LMs) side-by-side and pinpointing their prediction similarities and differences on the same set of inputs are crucial in many real-world scenarios, e.g., one can test if a licensed model was…

Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…

Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…

Distance metric learning (DML) approaches learn a transformation to a representation space where distance is in correspondence with a predefined notion of similarity. While such models offer a number of compelling benefits, it has been…

Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…

The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…

The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…

The problem of distance metric learning is mostly considered from the perspective of learning an embedding space, where the distances between pairs of examples are in correspondence with a similarity metric. With the rise and success of…

In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…

We introduce genetic algorithms as a means to estimate the accuracy required to discriminate among different models using experimental observables. We exemplify the technique in the context of the minimal supersymmetric standard model. If…

Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic…

As a highlighting research topic in the multimedia area, cross-media retrieval aims to capture the complex correlations among multiple media types. Learning better shared representation and distance metric for multimedia data is important…