Related papers: FMtree: A fast locating algorithm of FM-indexes fo…
Recent advancements in tree search algorithms guided by verifiers have significantly enhanced the reasoning capabilities of large language models (LLMs), but at the cost of increased computational resources. In this work, we identify two…
Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and…
Tree-based machine learning techniques, such as Decision Trees and Random Forests, are top performers in several domains as they do well with limited training datasets and offer improved interpretability compared to Deep Neural Networks…
Data intensive applications on clusters often require requests quickly be sent to the node managing the desired data. In many applications, one must look through a sorted tree structure to determine the responsible node for accessing or…
With the rapid development of mobile computing and Web services, a huge amount of data with spatial and temporal information have been collected everyday by smart mobile terminals, in which an object is described by its spatial information…
In the presence of dynamic insertions and deletions into a partially reconfigurable FPGA, fragmentation is unavoidable. This poses the challenge of developing efficient approaches to dynamic defragmentation and reallocation. One key aspect…
Modern pattern recognition tasks use complex algorithms that take advantage of large datasets to make more accurate predictions than traditional algorithms such as decision trees or k-nearest-neighbor better suited to describe simple…
Given a binary string $\omega$ over the alphabet $\{0, 1\}$, a vector $(a, b)$ is a Parikh vector if and only if a factor of $\omega$ contains exactly $a$ occurrences of $0$ and $b$ occurrences of $1$. Answering whether a vector is a Parikh…
Spatial data is ubiquitous. Massive amounts of data are generated every day from billions of GPS-enabled devices such as cell phones, cars, sensors, and various consumer-based applications such as Uber, Tinder, location-tagged posts in…
A central task in string processing is text indexing, where the goal is to preprocess a text (a string of length $n$) into an efficient index (a data structure) supporting queries about the text. Cole, Gottlieb, and Lewenstein (STOC 2004)…
Decision tree learning is a widely used approach in machine learning, favoured in applications that require concise and interpretable models. Heuristic methods are traditionally used to quickly produce models with reasonably high accuracy.…
Decision trees, owing to their interpretability, are attractive as control policies for (dynamical) systems. Unfortunately, constructing, or synthesising, such policies is a challenging task. Previous approaches do so by imitating a…
CVTree is an alignment-free methodology for inferring species phylogeny and taxonomy. This method allows for the efficient and accurate resolution of evolutionary relationships among large numbers of species based on whole-genome sequence…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
Fully Homomorphic Encryption (FHE) allows for computation directly on encrypted data and enables privacy-preserving neural inference in the cloud. Prior work has focused on models with dense inputs (e.g., CNNs), with less attention given to…
Recently a deterministic method, frequent directions (FD) is proposed to solve the high dimensional low rank approximation problem. It works well in practice, but experiences high computational cost. In this paper, we establish a fast…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Information retrieval is a core component of many intelligent systems as it enables conditioning of outputs on new and large-scale datasets. While effective, the standard practice of encoding data into high-dimensional representations for…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Mining frequent tree patterns has many applications in different areas such as XML data, bioinformatics and World Wide Web. The crucial step in frequent pattern mining is frequency counting, which involves a matching operator to find…