相关论文: Digital search trees and chaos game representation

Reverse search is a convenient method for enumerating structured objects, that can be used both to address theoretical issues and to solve data mining problems. This method has already been successfully developed to handle unordered trees.…

DNA sequences are fundamental for encoding genetic information. The genetic information may not only be understood by symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed…

A novel graph-to-tree conversion mechanism called the deep-tree generation (DTG) algorithm is first proposed to predict text data represented by graphs. The DTG method can generate a richer and more accurate representation for nodes (or…

Retrieval-Augmented Generation (RAG) mitigates the hallucination problem of Large Language Models (LLMs) by incorporating external knowledge. Recursive summarization constructs a hierarchical summary tree by clustering text chunks,…

The chaos game representation (CGR) is an interesting method to visualize one-dimensional sequences. In this paper, we show how to construct a chaos game representation. The applications mentioned here are biological, in which CGR was able…

Given a string $T$, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with $e_T$ arcs, taking overall $O(e_T+e_{{\overline{T}}})$ words of space, where ${\overline{T}}$ is the reverse…

This paper establishes formal mathematical foundations linking Chaos Game Representations (CGR) of DNA sequences to their underlying $k$-mer frequencies. We prove that the Frequency CGR (FCGR) of order $k$ is mathematically equivalent to a…

This study proposes CGRclust, a novel combination of unsupervised twin contrastive clustering of Chaos Game Representations (CGR) of DNA sequences, with convolutional neural networks (CNNs). To the best of our knowledge, CGRclust is the…

This thesis develops computational methods in similarity-preserving hashing, classification, and cancer genomics. Standard space partitioning-based hashing relies on Binary Search Trees (BSTs), but their exponential growth and sparsity…

The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…

Tackling simulation optimization problems with non-convex objective functions remains a fundamental challenge in operations research. In this paper, we propose a class of random search algorithms, called Regular Tree Search, which…

In this paper, we propose an explicit, non-strict representation of search trees in constraint-logic object-oriented programming. Our search tree representation includes both the non-deterministic and deterministic behaviour during…

Recent studies have shown that Dense Retrieval (DR) techniques can significantly improve the performance of first-stage retrieval in IR systems. Despite its empirical effectiveness, the application of DR is still limited. In contrast to…

Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…

Generative retrieval constitutes an innovative approach in information retrieval, leveraging generative language models (LM) to generate a ranked list of document identifiers (docid) for a given query. It simplifies the retrieval pipeline…

Binary search trees (BST) are a popular type of data structure when dealing with ordered data. Indeed, they enable one to access and modify data efficiently, with their height corresponding to the worst retrieval time. From a probabilistic…

DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…

Given a text, rank and select queries return the number of occurrences of a character up to a position (rank) or the position of a character with a given rank (select). These queries have applications in, e.g., compression, computational…

Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…

We introduce the lazy search tree data structure. The lazy search tree is a comparison-based data structure on the pointer machine that supports order-based operations such as rank, select, membership, predecessor, successor, minimum, and…