Related papers: GRIM-Filter: Fast Seed Location Filtering in DNA R…
In-DRAM Processing-In-Memory (DRAM-PIM) has emerged as a promising approach to accelerate memory-intensive workloads by mitigating data transfer overhead between DRAM and the host processor. Bit-serial DRAM-PIM architectures, further…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Modern key-value stores rely heavily on Log-Structured Merge (LSM) trees for write optimization, but this design introduces significant read amplification. Auxiliary structures like Bloom filters help, but impose memory costs that scale…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
Graph Neural Networks (GNNs) are emerging ML models to analyze graph-structure data. Graph Neural Network (GNN) execution involves both compute-intensive and memory-intensive kernels, the latter dominates the total time, being significantly…
It is appealing but challenging to achieve real-time deep neural network (DNN) inference on mobile devices because even the powerful modern mobile devices are considered as ``resource-constrained'' when executing large-scale DNNs. It…
The initial location of data in DRAMs is determined and controlled by the 'address-mapping' and even modern memory controllers use a fixed and run-time-agnostic address mapping. On the other hand, the memory access pattern seen at the…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
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…
Processing-using-DRAM has been proposed for a limited set of basic operations (i.e., logic operations, addition). However, in order to enable full adoption of processing-using-DRAM, it is necessary to provide support for more complex…
This paper proposes an iterative algorithm for choosing gradient directions use to reconstruct white matter fibers in the brain. The present study is not focusing on data acquisition where scanning is performed. The Adaptive Gradient…
DL inference queries play an important role in diverse internet services and a large fraction of datacenter cycles are spent on processing DL inference queries. Specifically, the matrix-matrix multiplication (GEMM) operations of…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
The process of screening molecules for desirable properties is a key step in several applications, ranging from drug discovery to material design. During the process of drug discovery specifically, protein-ligand docking, or chemical…
In this paper we develop the Greedy Recombination Interpolation Method (GRIM) for finding sparse approximations of functions initially given as linear combinations of some (large) number of simpler functions. In a similar spirit to the…
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…
Image matching, which establishes correspondences between two-view images to recover 3D structure and camera geometry, serves as a cornerstone in computer vision and underpins a wide range of applications, including visual localization, 3D…
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 sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…