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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.…

Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…

De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…

The Real-Time Systems Engineering Department of the Scientific Computing Division at Fermilab has deployed set of customizations to our Off-The-Shelf Data Acquisition solution (otsdaq) at the Fermilab Test Beam Facility (FTBF) to read out…

The recent amalgamation of transformer and convolutional designs has led to steady improvements in accuracy and efficiency of the models. In this work, we introduce FastViT, a hybrid vision transformer architecture that obtains the…

Large language models (LLMs) are often used for infilling tasks, which involve predicting or generating missing information in a given text. These tasks typically require multiple interactions with similar context. To reduce the computation…

In the field of digital signal processing, the fast Fourier transform (FFT) is a fundamental algorithm, with its processors being implemented using either the pipelined architecture, well-known for high-throughput applications but weak in…

Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…

To effectively implement quantum algorithms on noisy intermediate-scale quantum (NISQ) processors is a central task in modern quantum technology. NISQ processors feature tens to a few hundreds of noisy qubits with limited coherence times…

In recent years, federated learning (FL) has emerged as a promising technique for training machine learning models in a decentralized manner while also preserving data privacy. The non-independent and identically distributed (non-i.i.d.)…

The exponential growth of Internet of Things (IoT) applications has intensified the demand for efficient, high-throughput, and energy-efficient data processing at the edge. Conventional CPU-centric encryption methods suffer from performance…

Assembly code search is vital for reducing the burden on reverse engineers, allowing them to quickly identify specific functions using natural language within vast binary programs. Despite its significance, this critical task is impeded by…

Recent research in federated large language models (LLMs) has primarily focused on enabling clients to fine-tune their locally deployed homogeneous LLMs collaboratively or on transferring knowledge from server-based LLMs to small language…

Communication overhead is one of the major challenges in Federated Learning(FL). A few classical schemes assume the server can extract the auxiliary information about training data of the participants from the local models to construct a…

Variant calling, the problem of estimating whether a position in a DNA sequence differs from a reference sequence, given noisy, redundant, overlapping short sequences that cover that position, is fundamental to genomics. We propose a deep…

Efficient deployment of large language models (LLMs) requires extreme quantization, forcing a critical trade-off between low-bit efficiency and performance. Residual binarization enables hardware-friendly, matmul-free inference by stacking…

Weight-only quantization has emerged as a promising solution to the deployment challenges of large language models (LLMs). However, it necessitates FP-INT operations, which make implementation on general-purpose hardware like GPUs…

SimRank is a similarity measure for graph nodes that has numerous applications in practice. Scalable SimRank computation has been the subject of extensive research for more than a decade, and yet, none of the existing solutions can…

LLM inference for enterprise applications, such as summarization, RAG, and code-generation, typically observe much longer prompt than generations, leading to high prefill cost and response latency. We present SwiftKV, a novel model…

Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…