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A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify…
We propose ODTE, a new ensemble that uses oblique decision trees as base classifiers. Additionally, we introduce STree, the base algorithm for growing oblique decision trees, which leverages support vector machines to define hyperplanes…
The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered…
The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…
Bipartite learning is a machine learning task that aims to predict interactions between pairs of instances. It has been applied to various domains, including drug-target interactions, RNA-disease associations, and regulatory network…
Vine copulas are pair-copula constructions enabling multivariate dependence modeling in terms of bivariate building blocks. One of the main tasks of fitting a vine copula is the selection of a suitable tree structure. For this the prevalent…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
We propose a new approach to image segmentation, which exploits the advantages of both conditional random fields (CRFs) and decision trees. In the literature, the potential functions of CRFs are mostly defined as a linear combination of…
We propose a novel tree classification system called Treelogy, that fuses deep representations with hand-crafted features obtained from leaf images to perform leaf-based plant classification. Key to this system are segmentation of the leaf…
Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Compositional reasoning remains a persistent weakness of modern vision language models (VLMs): they often falter when a task hinges on understanding how multiple objects, attributes, and relations interact within an image. Multiple research…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
We present a multi-modal trajectory generation and selection algorithm for real-world mapless outdoor navigation in human-centered environments. Such environments contain rich features like crosswalks, grass, and curbs, which are easily…
This paper proposes a novel, node-splitting support vector machine (SVM) for creating survival trees. This approach is capable of non-linearly partitioning survival data which includes continuous, right-censored outcomes. Our method…
In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…
Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way…
High-quality text representations are crucial for natural language understanding (NLU), but low-resource languages like Vietnamese face challenges due to limited annotated data. While pre-trained models like PhoBERT and CafeBERT perform…