Related papers: Large-scale compression of genomic sequence databa…
Convolution neural network demonstrates great capability for multiple tasks, such as image classification and many others. However, much resource is required to train a network. Hence much effort has been made to accelerate neural network…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
This article shows that any type of binary data can be defined as a collection from codewords of variable length. This feature helps us to define an Injective and surjective function from the suggested codewords to the required codewords.…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Chain-of-Thought (CoT) reasoning successfully enhances the reasoning capabilities of Large Language Models (LLMs), yet it incurs substantial computational overhead for inference. Existing CoT compression methods often suffer from a critical…
In recent years, deep neural networks have achieved great success in the field of computer vision. However, it is still a big challenge to deploy these deep models on resource-constrained embedded devices such as mobile robots, smart phones…
Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts…
The Burrows Wheeler transform has applications in data compression as well as full text indexing. Despite its important applications and various existing algorithmic approaches the construction of the transform for large data sets is still…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Emerging sonography techniques often imply increasing in the number of transducer elements involved in the imaging process. Consequently, larger amounts of data must be acquired and processed by the beamformer. The significant growth in the…
This article describes lossless compression algorithms for multisets of sequences, taking advantage of the multiset's unordered structure. Multisets are a generalisation of sets where members are allowed to occur multiple times. A multiset…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
Model compression is essential for serving large deep neural nets on devices with limited resources or applications that require real-time responses. As a case study, a state-of-the-art neural language model usually consists of one or more…
Data compression is a well-studied (and well-solved) problem in the setup of long coding blocks. But important emerging applications need to compress data to memory words of small fixed widths. This new setup is the subject of this paper.…
Deep convolutional neural networks (CNNs) with a large number of parameters require intensive computational resources, and thus are hard to be deployed in resource-constrained platforms. Decomposition-based methods, therefore, have been…
We introduce the concept of compressed convolution, a technique to convolve a given data set with a large number of non-orthogonal kernels. In typical applications our technique drastically reduces the effective number of computations. The…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
Compression algorithms reduce the redundancy in data representation to decrease the storage required for that data. Data compression offers an attractive approach to reducing communication costs by using available bandwidth effectively.…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…