Related papers: Analyzing large-scale DNA Sequences on Multi-core …
Neural kernels have drastically increased performance on diverse and nonstandard data modalities but require significantly more compute, which previously limited their application to smaller datasets. In this work, we address this by…
Recent works have introduced task-based parallelization schemes to accelerate graph search and sparse data-structure traversal, where some solutions scale up to thousands of processing units (PUs) on a single chip. However parallelizing…
We study parallel algorithms for the minimization of Deterministic Finite Automata (DFAs). In particular, we implement four different massively parallel algorithms on Graphics Processing Units (GPUs). Our results confirm the expectations…
In the rapidly evolving domain of next generation sequencing and bioinformatics analysis, data generation is one aspect that is increasing at a concomitant rate. The burden associated with processing large amounts of sequencing data has…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
Recent progress on salient object detection mainly aims at exploiting how to effectively integrate multi-scale convolutional features in convolutional neural networks (CNNs). Many popular methods impose deep supervision to perform…
The Simplex tableau has been broadly used and investigated in the industry and academia. With the advent of the big data era, ever larger problems are posed to be solved in ever larger machines whose architecture type did not exist in the…
DBSCAN is a very classic algorithm for data clus- tering, which is widely used in many fields. However, with the data scale growing much more bigger than before, the traditional serial algorithm can not meet the performance requirement.…
Accurate automatic segmentation of brain anatomy from $T_1$-weighted~($T_1$-w) magnetic resonance images~(MRI) has been a computationally intensive bottleneck in neuroimaging pipelines, with state-of-the-art results obtained by unsupervised…
We investigate the problem of exact set similarity joins using a co-process CPU-GPU scheme. The state-of-the-art CPU solutions split the wok in two main phases. First, filtering and index building takes place to reduce the candidate sets to…
This paper describes a new asynchronous algorithm and implementation for the problem of k-mer counting (KC), which concerns quantifying the frequency of length k substrings in a DNA sequence. This operation is common to many computational…
The field of remote sensing is nowadays faced with huge amounts of data. While this offers a variety of exciting research opportunities, it also yields significant challenges regarding both computation time and space requirements. In…
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA…
Complex systems often exhibit unexpected faults that are difficult to handle. Such systems are desirable to be diagnosable, i.e. faults can be automatically detected as they occur (or shortly afterwards), enabling the system to handle the…
Nearest Neighbor Search (NNS) has recently drawn a rapid increase of interest due to its core role in managing high-dimensional vector data in data science and AI applications. The interest is fueled by the success of neural embedding,…
In the past few years, Differentiable Neural Architecture Search (DNAS) rapidly imposed itself as the trending approach to automate the discovery of deep neural network architectures. This rise is mainly due to the popularity of DARTS, one…
A distributed-memory parallelization strategy for the density matrix renormalization group is proposed for cases where correlation functions are required. This new strategy has substantial improvements with respect to previous works. A…
Real-world graphs often evolve over time, making community or cluster detection a crucial task. In this technical report, we extend three dynamic approaches - Naive-dynamic (ND), Delta-screening (DS), and Dynamic Frontier (DF) - to our…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Cycles are one of the fundamental subgraph patterns and being able to enumerate them in graphs enables important applications in a wide variety of fields, including finance, biology, chemistry, and network science. However, to enable cycle…