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Recent advances in machine learning and neuro-inspired systems enabled the increased interest in efficient pattern recognition at the edge. A wide variety of applications, such as near-sensor classification, require fast and low-power…
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.…
Resistive Random Access Memory (RRAM) is an emerging device for processing-in-memory (PIM) architecture to accelerate convolutional neural network (CNN). However, due to the highly coupled crossbar structure in the RRAM array, it is…
Binary neural networks (BNNs) that use 1-bit weights and activations have garnered interest as extreme quantization provides low power dissipation. By implementing BNNs as computing-in-memory (CIM), which computes multiplication and…
Processing-in-memory (PIM) architectures bring computation closer to data, reducing the processor-memory transfer bottleneck in traditional processor-centric designs. Novel hardware solutions, such as UPMEM's in-memory processing…
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm…
The performance of traditional compressive sensing-based MRI (CS-MRI) reconstruction is affected by its slow iterative procedure and noise-induced artefacts. Although many deep learning-based CS-MRI methods have been proposed to mitigate…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
The Transformer architecture, underpinned by the self-attention mechanism, has become the de facto standard for sequence modeling tasks. However, its core computational primitive scales quadratically with sequence length (O(N^2)), creating…
We propose a novel recurrent network-based HDR deghosting method for fusing arbitrary length dynamic sequences. The proposed method uses convolutional and recurrent architectures to generate visually pleasing, ghosting-free HDR images. We…
Compressed Sensing MRI (CS-MRI) has provided theoretical foundations upon which the time-consuming MRI acquisition process can be accelerated. However, it primarily relies on iterative numerical solvers which still hinders their adaptation…
Processing-in-memory (PIM) has emerged as the go to solution for addressing the von Neumann bottleneck in edge AI accelerators. However, state-of-the-art (SoTA) digital PIM approaches suffer from low compute density, primarily due to the…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
Neural architecture search (NAS) in expressive search spaces is a computationally hard problem, but it also holds the potential to automatically discover completely novel and performant architectures. To achieve this we need effective…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…
Medical image reconstruction with pre-trained score-based generative models (SGMs) has advantages over other existing state-of-the-art deep-learned reconstruction methods, including improved resilience to different scanner setups and…
Structured illumination microscopy (SIM) improves resolution by down-modulating high-frequency information of an object to fit within the passband of the optical system. Generally, the reconstruction process requires prior knowledge of the…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
A large class of traditional graph and data mining algorithms can be concisely expressed in Datalog, and other Logic-based languages, once aggregates are allowed in recursion. In fact, for most BigData algorithms, the difficult semantic…