Related papers: TripNet: A Method for Constructing Phylogenetic Ne…

Accurately modeling the relationship between perturbations, transcriptional responses, and phenotypic changes is essential for building an AI Virtual Cell (AIVC). However, existing methods typically constrained to modeling direct…

In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…

Deep learning has proven itself as a successful set of models for learning useful semantic representations of data. These, however, are mostly implicitly learned as part of a classification task. In this paper we propose the triplet network…

In this paper, we propose a novel method for the prior-art search task. We fine-tune SciBERT transformer model using Triplet Network approach, allowing us to represent each patent with a fixed-size vector. This also enables us to conduct…

Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…

A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…

Background: Networks in different domains are characterized by similar global characteristics while differing in local structures. To further extend this concept, we investigated network regularities on a fine scale in order to examine the…

We showed in this paper that similarity network can be used as an powerful tools to study the relationship of tRNA genes. We constructed a network of 3719 tRNA gene sequences using simplest alignment and studied its topology, degree…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…

Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…

A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…

A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…

Due to the scarcity of large-scale in-the-wild triplet data and the improper use of masks, the performance of video virtual try-on models remains limited. In this paper, we first introduce **TripVVT-10K**, the largest and most diverse…

We introduce "TriMap"; a dimensionality reduction technique based on triplet constraints, which preserves the global structure of the data better than the other commonly used methods such as t-SNE, LargeVis, and UMAP. To quantify the global…

While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…

As networking systems become increasingly complex, achieving disruptive innovation grows more challenging. At the same time, recent progress in Large Language Models (LLMs) has shown strong potential for scientific hypothesis formation and…

Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…