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We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
Reliability is an important tool for evaluating the performance of modern networks. Currently, it is NP-hard and #P-hard to calculate the exact reliability of a binary-state network when the reliability of each component is assumed to be…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
Decision trees provide a rich family of highly non-linear but efficient models, due to which they continue to be the go-to family of predictive models by practitioners across domains. But learning trees is challenging due to their discrete…
Estimating a joint Highest Posterior Density credible set for a multivariate posterior density is challenging as dimension gets larger. Credible intervals for univariate marginals are usually presented for ease of computation and…
We consider exact enumerations and probabilistic properties of ranked trees when generated under the random coalescent process. Using a new approach, based on generating functions, we derive several statistics such as the exact probability…
Terrestrial laser scanning (TLS) can obtain tree point cloud with high precision and high density. Efficient classification of wood points and leaf points is essential to study tree structural parameters and ecological characteristics. By…
There have been many recent studies on sequential pattern mining. The sequential pattern mining on progressive databases is relatively very new, in which we progressively discover the sequential patterns in period of interest. Period of…
In high-dimensional generalized linear models, it is crucial to identify a sparse model that adequately accounts for response variation. Although the best subset section has been widely regarded as the Holy Grail of problems of this type,…
While speculative decoding has recently appeared as a promising direction for accelerating the inference of large language models (LLMs), the speedup and scalability are strongly bounded by the token acceptance rate. Prevalent methods…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
We propose a new measure of support (the number of occur- rences of a pattern), in which instances are more important if they occur with a certain frequency and close after each other in the stream of trans- actions. We will explain this…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
The study of Markov processes and broadcasting on trees has deep connections to a variety of areas including statistical physics, graphical models, phylogenetic reconstruction, Markov Chain Monte Carlo, and community detection in random…
Wood increment is critical information in forestry management. Previous studies used mathematics models to describe complex growing pattern of forest stand, in order to determine the dynamic status of growing forest stand in multiple…
While the analysis of airborne laser scanning (ALS) data often provides reliable estimates for certain forest stand attributes -- such as total volume or basal area -- there is still room for improvement, especially in estimating…
We compare different methods for sampling from discrete probability distributions and introduce a new algorithm which is especially efficient on massively parallel processors, such as GPUs. The scheme preserves the distribution properties…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Traditional Quartet Puzzling algorithms use maximum likelihood methods to reconstruct quartet trees, and a puzzling algorithm to combine these quartets into a tree for the full collection of $n$ taxa. We propose a variation of Quartet…