Related papers: biobambam: tools for read pair collation based alg…
Background: Computational analysis of next-generation sequencing data is outpaced by data generation in many cases. In one such case, paired-end reads can be produced from the Illumina sequencing method faster than they can be overlapped by…
This paper introduces an Enhanced Boolean version of the Correlation Matrix Memory (CMM), which is useful to work with binary memories. A novel Boolean Orthonormalization Process (BOP) is presented to convert a non-orthonormal Boolean…
Hashmaps are widely utilized data structures in many applications to perform a probe on key-value pairs. However, their performance tends to degrade with the increase in the dataset size, which leads to expensive off-chip memory accesses to…
Bundle adjustment (BA) is a fundamental optimization technique used in many crucial applications, including 3D scene reconstruction, robotic localization, camera calibration, autonomous driving, space exploration, street view map generation…
Existed echocardiography segmentation methods often suffer from anatomical inconsistency challenge caused by shape variation, partial observation and region ambiguity with similar intensity across 2D echocardiographic sequences, resulting…
With the growing scale of big data, probabilistic structures receive increasing popularity for efficient approximate storage and query processing. For example, Bloom filters (BF) can achieve satisfactory performance for approximate…
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…
This paper presents new alternatives to the well-known Bloom filter data structure. The Bloom filter, a compact data structure supporting set insertion and membership queries, has found wide application in databases, storage systems, and…
As genome sequencing is finding utility in a wide variety of domains beyond the confines of traditional medical settings, its computational pipeline faces two significant challenges. First, the creation of up to 0.5 GB of data per minute…
We apply bio-inspired methods for the analysis of different dynamic bibliometric networks (linking papers by citation, authors, and keywords, respectively). Biological species are clusters of individuals defined by widely different criteria…
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.…
Applications involving telecommunication call data records, web pages, online transactions, medical records, stock markets, climate warning systems, etc., necessitate efficient management and processing of such massively exponential amount…
Next generation communication systems require accurate beam alignment to counteract the impairments that characterize propagation in high-frequency bands. The overhead of the pilot sequences required to select the best beam pair is…
Image-based localization (IBL) aims to estimate the 6DOF camera pose for a given query image. The camera pose can be computed from 2D-3D matches between a query image and Structure-from-Motion (SfM) models. Despite recent advances in IBL,…
Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…
System identification is normally involved in augmenting time series data by time shifting and nonlinearisation (e.g., polynomial basis), both of which introduce redundancy in features and samples. Many research works focus on reducing…
One common way to speed up the find operation within a set of text files involves a trigram index. This structure is merely a map from a trigram (sequence consisting of three characters) to a set of files which contain it. When searching…
We aim at advancing blind image quality assessment (BIQA), which predicts the human perception of image quality without any reference information. We develop a general and automated multitask learning scheme for BIQA to exploit auxiliary…
Millimeter-wave communications rely on narrow-beam transmissions to cope with the strong signal attenuation at these frequencies, thus demanding precise alignment between transmitter and receiver. However, the beam-alignment procedure may…
Many powerful machine learning models are based on the composition of multiple processing layers, such as deep nets, which gives rise to nonconvex objective functions. A general, recent approach to optimise such "nested" functions is the…