Related papers: SPRINT: A fast, new software tool for reconstructi…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
Polyploidization, whereby an organism inherits multiple copies of the genome of their parents, is an important evolutionary event that has been observed in plants and animals. One way to study such events is in terms of the ploidy number of…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
Polyploidy is an important speciation mechanism, particularly in land plants. Allopolyploid species are formed after hybridization between otherwise intersterile parental species. Recent theoretical progress has led to successful…
We present FLINT (learning-based FLow estimation and temporal INTerpolation), a novel deep learning-based approach to estimate flow fields for 2D+time and 3D+time scientific ensemble data. FLINT can flexibly handle different types of…
Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods…
Traditionally, sparse retrieval systems relied on lexical representations to retrieve documents, such as BM25, dominated information retrieval tasks. With the onset of pre-trained transformer models such as BERT, neural sparse retrieval has…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
SLiM is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale. The program can incorporate complex scenarios of demography and population substructure,…
Real-world systems must continuously adapt to novel concepts from limited data without forgetting previously acquired knowledge. While Few-Shot Class-Incremental Learning (FSCIL) is established in computer vision, its application to tabular…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Table Structure Recognition (TSR) is vital for various downstream tasks like information retrieval, table reconstruction, and document understanding. While most state-of-the-art (SOTA) research predominantly focuses on TSR in English…
Detecting the source model of AI-generated images is a growing accountability problem. AI fingerprinting techniques address this by detecting imperceptible patterns in the images that are unique to each model, achieving high detection…
A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing…
Model customization necessitates high-quality and diverse datasets, but acquiring such data remains time-consuming and labor-intensive. Despite the great potential of large language models (LLMs) for data synthesis, current approaches are…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
We introduce SciWING, an open-source software toolkit which provides access to pre-trained models for scientific document processing tasks, inclusive of citation string parsing and logical structure recovery. SciWING enables researchers to…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…