Related papers: GRIM-filter: fast seed filtering in read mapping u…
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for…
Deep Generative Models (DGMs) are versatile tools for learning data representations while adequately incorporating domain knowledge such as the specification of conditional probability distributions. Recently proposed DGMs tackle the…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Background: Regarding the importance of right diagnosis in medical applications, various methods have been exploited for processing medical images solar. The method of segmentation is used to analyze anal to miscall structures in medical…
Entity alignment aims to use pre-aligned seed pairs to find other equivalent entities from different knowledge graphs (KGs) and is widely used in graph fusion-related fields. However, as the scale of KGs increases, manually annotating…
Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the…
Image Registration (IR) is the process of aligning two (or more) images of the same scene taken at different times, different viewpoints and/or by different sensors. It is an important, crucial step in various image analysis tasks where…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
Processing-in-memory (PIM), as a novel computing paradigm, provides significant performance benefits from the aspect of effective data movement reduction. SRAM-based PIM has been demonstrated as one of the most promising candidates due to…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Spurred by widening gap between data processing speed and data communication speed in Von-Neumann computing architectures, some bioinformatic applications have harnessed the computational power of Processing-in-Memory (PIM) platforms.…
Retrieval-Augmented Generation (RAG) enhances large language models (LLMs) by integrating external knowledge retrieval but faces challenges on edge devices due to high storage, energy, and latency demands. Computing-in-Memory (CIM) offers a…
Neural network models of real-world systems, such as industrial processes, made from sensor data must often rely on incomplete data. System states may not all be known, sensor data may be biased or noisy, and it is not often known which…
Generative recommendation (GR) is an emerging paradigm that represents each item via a tokenizer as an n-digit semantic ID (SID) and predicts the next item by autoregressively generating its SID conditioned on the user's history. However,…
Sorting is fundamental and ubiquitous in modern computing systems. Hardware sorting systems are built based on comparison operations with Von Neumann architecture, but their performance are limited by the bandwidth between memory and…
Regularization is essential in deep learning to enhance generalization and mitigate overfitting. However, conventional techniques often rely on heuristics, making them less reliable or effective across diverse settings. We propose Self…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream…
Gene prioritization (identifying genes potentially associated with a biological process) is increasingly tackled with Artificial Intelligence. However, existing methods struggle with the high dimensionality and incomplete labelling of…
The inverse design of RNA three-dimensional (3D) structures is crucial for engineering functional RNAs in synthetic biology and therapeutics. While recent deep learning approaches have advanced this field, they are typically optimized and…