Related papers: Nucleotide String Indexing using Range Matching
Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene…
Automotive radar provides reliable environmental perception in all-weather conditions with affordable cost, but it hardly supplies semantic and geometry information due to the sparsity of radar detection points. With the development of…
Automotive radar systems face the challenge of managing high sampling rates and large data bandwidth while complying with stringent real-time and energy efficiency requirements. The growing complexity of autonomous vehicles further…
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
LEarning TO Rank (LETOR) is a research area in the field of Information Retrieval (IR) where machine learning models are employed to rank a set of items. In the past few years, neural LETOR approaches have become a competitive alternative…
With powerful and integrative large language models (LLMs), medical AI agents have demonstrated unique advantages in providing personalized medical consultations, continuous health monitoring, and precise treatment plans.…
Background: Short sequence substrings of a fixed length k, called k-mers, are a ubiquitous computational primitive in bioinformatics, used across sequence indexing, read mapping, genome assembly, metagenomic classification, and comparative…
The Neural Tangent Kernel (NTK) characterizes how a model's state evolves over Gradient Descent. Computing the full NTK matrix is often infeasible, especially for recurrent architectures. Here, we introduce a matrix-free perspective, using…
To increase the computational efficiency of interest-point based object retrieval, researchers have put remarkable research efforts into improving the efficiency of kNN-based feature matching, pursuing to match thousands of features against…
In recent work, we have shown that NVIDIA's raytracing cores on RTX video cards can be exploited to realize hardware-accelerated lookups for GPU-resident database indexes. On a high level, the concept materializes all keys as triangles in a…
Supercomputers are equipped with an increasingly large number of cores to use computational power as a way of solving problems that are otherwise intractable. Unfortunately, getting serial algorithms to run in parallel to take advantage of…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
This paper studies the consistency of the kernel-based neural ranking model K-NRM, a recent state-of-the-art neural IR model, which is important for reproducible research and deployment in the industry. We find that K-NRM has low variance…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
Range Minimum Query (RMQ) is an important building brick of many compressed data structures and string matching algorithms. Although this problem is essentially solved in theory, with sophisticated data structures allowing for constant time…