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The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

Populations and Evolution · Quantitative Biology 2025-12-08 Yun Deng , Shing H. Zhan , Yulin Zhang , Chao Zhang , Bingjie Chen

We use reinforcement learning to learn tree-structured neural networks for computing representations of natural language sentences. In contrast with prior work on tree-structured models in which the trees are either provided as input or…

Computation and Language · Computer Science 2016-11-29 Dani Yogatama , Phil Blunsom , Chris Dyer , Edward Grefenstette , Wang Ling

Deep research agents, which synthesize information across diverse sources, are significantly constrained by the sequential nature of reasoning. This bottleneck results in high latency, poor runtime adaptability, and inefficient resource…

Distributed, Parallel, and Cluster Computing · Computer Science 2026-03-31 Lunyiu Nie , Nedim Lipka , Ryan A. Rossi , Swarat Chaudhuri

We address the problem of representing dynamic graphs using $k^2$-trees. The $k^2$-tree data structure is one of the succinct data structures proposed for representing static graphs, and binary relations in general. It relies on compact…

Data Structures and Algorithms · Computer Science 2019-12-09 Miguel E. Coimbra , Alexandre P. Francisco , Luís M. S. Russo , Guillermo de Bernardo , Susana Ladra , Gonzalo Navarro

Decision trees and random forest remain highly competitive for classification on medium-sized, standard datasets due to their robustness, minimal preprocessing requirements, and interpretability. However, a single tree suffers from high…

Machine Learning · Statistics 2025-12-02 Cencheng Shen , Yuexiao Dong , Carey E. Priebe

Tree-based data structures are ubiquitous across applications. Therefore, a multitude of different tree implementations exist. However, while these implementations are diverse, they share a tree structure as the underlying data structure.…

Hardware Architecture · Computer Science 2025-01-30 Daniel Biebert , Christian Hakert , Jian-Jia Chen

Property graphs often contain tree-shaped substructures, yet they are not captured by existing proposals for graph schemas; likewise, query languages and query engines offer little-to-no native support for managing them systematically. As a…

The next-generation non-volatile memory (NVM) is striding into computer systems as a new tier as it incorporates both DRAM's byte-addressability and disk's persistency. Researchers and practitioners have considered building persistent…

Data Structures and Algorithms · Computer Science 2021-06-02 Chongnan Ye , Chundong Wang

In this paper, we propose and investigate a novel memory architecture for neural networks called Hierarchical Attentive Memory (HAM). It is based on a binary tree with leaves corresponding to memory cells. This allows HAM to perform memory…

Machine Learning · Computer Science 2016-02-24 Marcin Andrychowicz , Karol Kurach

Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…

Data Structures and Algorithms · Computer Science 2026-02-05 Lorraine A. K. Ayad , Gabriele Fici , Ragnar Groot Koerkamp , Grigorios Loukides , Rob Patro , Giulio Ermanno Pibiri , Solon P. Pissis

A decision tree looks like a simple directed acyclic computational graph, where only the leaf nodes specify the output values and the non-terminals specify their tests or split conditions. From the numerical perspective, we express decision…

Machine Learning · Computer Science 2024-11-07 Jinxiong Zhang

Suffix trees and suffix arrays are two of the most widely used data structures for text indexing. Each uses linear space and can be constructed in linear time for polynomially sized alphabets. However, when it comes to answering queries…

Data Structures and Algorithms · Computer Science 2013-11-08 Richard Cole , Tsvi Kopelowitz , Moshe Lewenstein

Database research can help machine learning performance in many ways. One way is to design better data structures. This paper combines the use of incremental computation and sequential and probabilistic filtering to enable "forgetful"…

Machine Learning · Computer Science 2022-12-16 Zhehu Yuan , Yinqi Sun , Dennis Shasha

This paper studies the performances of BERT combined with tree structure in short sentence ranking task. In retrieval-based question answering system, we retrieve the most similar question of the query question by ranking all the questions…

Computation and Language · Computer Science 2019-09-09 Tong Guo , Huilin Gao

We introduce a data structure that allows for efficient (probabilistic) presence proofs and non-probabilistic absence proofs in a bandwidth efficient and secure way. The Bloom tree combines the idea of Bloom filters with that of Merkle…

Data Structures and Algorithms · Computer Science 2020-02-20 Lum Ramabaja , Arber Avdullahu

In hierarchical text classification, we perform a sequence of inference steps to predict the category of a document from top to bottom of a given class taxonomy. Most of the studies have focused on developing novels neural network…

Computation and Language · Computer Science 2020-05-25 Kervy Rivas Rojas , Gina Bustamante , Arturo Oncevay , Marco A. Sobrevilla Cabezudo

The era of Big Data has spawned unprecedented interests in developing hashing algorithms for efficient storage and fast nearest neighbor search. Most existing work learn hash functions that are numeric quantizations of feature values in…

Machine Learning · Computer Science 2015-03-23 Kai Li , Guojun Qi , Jun Ye , Kien A. Hua

Learning discriminative global features plays a vital role in semantic segmentation. And most of the existing methods adopt stacks of local convolutions or non-local blocks to capture long-range context. However, due to the absence of…

Computer Vision and Pattern Recognition · Computer Science 2019-09-30 Lin Song , Yanwei Li , Zeming Li , Gang Yu , Hongbin Sun , Jian Sun , Nanning Zheng

Recently proposed budding tree is a decision tree algorithm in which every node is part internal node and part leaf. This allows representing every decision tree in a continuous parameter space, and therefore a budding tree can be jointly…

Machine Learning · Computer Science 2014-12-22 Ozan İrsoy , Ethem Alpaydın

We revisit the classical problem of computing the \emph{contour tree} of a scalar field $f:\mathbb{M} \to \mathbb{R}$, where $\mathbb{M}$ is a triangulated simplicial mesh in $\mathbb{R}^d$. The contour tree is a fundamental topological…

Computational Geometry · Computer Science 2015-12-11 Benjamin Raichel , C. Seshadhri