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This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
This paper deals with two main issues regarding the short polar codes: the potential of FEC-assisted decoding and optimal code concatenation strategies under various design scenarios. Code concatenation and FEC-assisted decoding are…
Reconstructing DNA sequences without a reference, known as de novo assembly, is a complex computational task involving the alignment of overlapping fragments. To address this problem, a usual strategy is to map the assembly to a Quadratic…
Convolutional codes are constructed, designed and analysed using row and/or block structures of unit algebraic schemes. Infinite series of such codes and of codes with specific properties are derived. Properties are shown algebraically and…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Sorting operation is one of the main bottlenecks for the successive-cancellation list (SCL) decoding. This paper introduces an improvement to the SCL decoding for polar and pre-transformed polar codes that reduces the number of sorting…
Our formal understanding of the inductive bias that drives the success of convolutional networks on computer vision tasks is limited. In particular, it is unclear what makes hypotheses spaces born from convolution and pooling operations so…
Our work aims to reproduce the set of findings published in "Network Deconvolution" by Ye et al. (2020)[1]. That paper proposes an optimization technique for model training in convolutional neural networks. The proposed technique "network…
Cell imaging and analysis are fundamental to biomedical research because cells are the basic functional units of life. Among different cell-related analysis, cell counting and detection are widely used. In this paper, we focus on one common…
We propose a new framework for constructing polar codes (i.e., selecting the frozen bit positions) for arbitrary channels, and tailored to a given decoding algorithm, rather than based on the (not necessarily optimal) assumption of…
From the perspective of tree, we design a length-flexible coding scheme. For an arbitrary code length, we first construct a balanced binary tree (BBT) where the root node represents a transmitted codeword, the leaf nodes represent either…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
Sampling-based decoding underlies complex reasoning in large language models (LLMs), where decoding strategies critically shape model behavior. Temperature- and truncation-based methods reshape the next-token distribution through global…
In the Shannon lecture at the 2019 International Symposium on Information Theory (ISIT), Ar{\i}kan proposed to employ a one-to-one convolutional transform as a pre-coding step before the polar transform. The resulting codes of this…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Biological sequence comparison is a key step in inferring the relatedness of various organisms and the functional similarity of their components. Thanks to the Next Generation Sequencing efforts, an abundance of sequence data is now…
Polarization-adjusted convolutional (PAC) codes combine the polar and convolutional transformations to enhance the distance properties of polar codes. They offer a performance very close to the finite length information-theoretic bounds for…
In this paper, we propose binary sparse convolutional networks called BSC-Net for efficient point cloud analysis. We empirically observe that sparse convolution operation causes larger quantization errors than standard convolution. However,…
Protein sequence design is a challenging problem in protein engineering, which aims to discover novel proteins with useful biological functions. Directed evolution is a widely-used approach for protein sequence design, which mimics the…