Related papers: Nucleotide String Indexing using Range Matching
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
As a language model that integrates traditional symbolic operations and flexible neural representations, recurrent neural network grammars (RNNGs) have attracted great attention from both scientific and engineering perspectives. However,…
Neural radiance fields (NeRF) have transformed 3D reconstruction and rendering, facilitating photorealistic image synthesis from sparse viewpoints. This work introduces an explicit data reuse neural rendering (EDR-NR) architecture, which…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
The range, segment and rectangle query problems are fundamental problems in computational geometry, and have extensive applications in many domains. Despite the significant theoretical work on these problems, efficient implementations can…
Regular pattern matching is used in numerous application domains, including text processing, bioinformatics, and network security. Patterns are typically expressed with an extended syntax of regular expressions that include the…
Content addressable memory (CAM) is widely used in associative search tasks for its highly parallel pattern matching capability. To accommodate the increasingly complex and data-intensive pattern matching tasks, it is critical to keep…
Analysis of large-scale sequential data has been one of the most crucial tasks in areas such as bioinformatics, text, and audio mining. Existing string kernels, however, either (i) rely on local features of short substructures in the…
We present memory-efficient and scalable algorithms for kernel methods used in machine learning. Using hierarchical matrix approximations for the kernel matrix the memory requirements, the number of floating point operations, and the…
Regular expression (regex) matching is fundamental in many applications, especially in web services. However, matching by backtracking -- preferred by most real-world implementations for its practical performance and backward compatibility…
The widely used retrieve-and-rerank pipeline faces two critical limitations: they are constrained by the initial retrieval quality of the top-k documents, and the growing computational demands of LLM-based rerankers restrict the number of…
Recommendation system has gained a large popularity for a variety of personalized suggestion tasks, but the ever-increasing number of user data makes real-time processing of recommendation systems difficult. NAND flash memory-based…
The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic sequencing and in turn the amount of data that needs to be processed, requiring highly efficient computation for its analysis. In this…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
Retrieval-Augmented Generation (RAG) couples a retriever with a large language model (LLM) to ground generated responses in external evidence. While this framework enhances factuality and domain adaptability, it faces a key bottleneck:…
Deep learning inference that needs to largely take place on the 'edge' is a highly computational and memory intensive workload, making it intractable for low-power, embedded platforms such as mobile nodes and remote security applications.…
In this paper, a new and novel data structure is proposed to dynamically insert and delete segments. Unlike the standard segment trees[3], the proposed data structure permits insertion of a segment with interval range beyond the interval…
We consider the problem of maintaining a dynamic set of integers and answering queries of the form: report a point (equivalently, all points) in a given interval. Range searching is a natural and fundamental variant of integer search, and…
The aggressive application of scalar replacement to array references substantially reduces the number of memory operations at the expense of a possibly very large number of registers. In this paper we describe a register allocation…
The Neural Tangent Kernel (NTK) has discovered connections between deep neural networks and kernel methods with insights of optimization and generalization. Motivated by this, recent works report that NTK can achieve better performances…