Related papers: biobambam: tools for read pair collation based alg…
Let $[q\rangle$ denote the integer set $\{0,1,\ldots,...,q-1\}$ and let $\mathbb{B}=\{0,1\}$. The problem of implementing functions $[q\rangle\rightarrow\mathbb{B}$ on content-addressable memories (CAMs) is considered. CAMs can be…
Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of…
Modern mobile applications include instrumentation that sample internal application metrics at regular intervals. Following a crash, sample metrics are collected and can potentially be valuable for root-causing difficult to diagnose…
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…
Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work…
Many modern programming languages are shifting toward a functional style for collection interfaces such as sets, maps, and sequences. Functional interfaces offer many advantages, including being safe for parallelism and providing simple and…
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…
Large language models (LLMs) excel in generating coherent text, but they often struggle with context awareness, leading to inaccuracies in tasks requiring faithful adherence to provided information. We introduce FastMem, a novel method…
Beamforming-capable antenna arrays overcome the high free-space path loss at higher carrier frequencies. However, the beams must be properly aligned to ensure that the highest power is radiated towards (and received by) the user equipment…
For early breast cancer detection, regular screening with mammography imaging is recommended. Routinary examinations result in datasets with a predominant amount of negative samples. A potential solution to such class-imbalance is joining…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
Our formulation reveals that the reduction across the sequence axis can be efficiently computed in parallel through a tree reduction. Our algorithm, called Tree Attention, for parallelizing exact attention computation across multiple GPUs…
Deep clustering - joint representation learning and latent space clustering - is a well studied problem especially in computer vision and text processing under the deep learning framework. While the representation learning is generally…
The manual migration between different third-party libraries represents a challenge for software developers. Developers typically need to explore both libraries Application Programming Interfaces, along with reading their documentation, in…
Humans can learn concepts or recognize items from just a handful of examples, while machines require many more samples to perform the same task. In this paper, we build a computational model to investigate the possibility of this kind of…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Often, machine learning applications have to cope with dynamic environments where data are collected in the form of continuous data streams with potentially infinite length and transient behavior. Compared to traditional (batch) data…
Analyzing the relation between a set of biological sequences can help to identify and understand the evolutionary history of these sequences and the functional relations among them. Multiple Sequence Alignment (MSA) is the main obstacle to…
Bit-serial Processing-In-Memory (PIM) is an attractive paradigm for accelerator architectures, for parallel workloads such as Deep Learning (DL), because of its capability to achieve massive data parallelism at a low area overhead and…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…