Haplotype Assembly: An Information Theoretic View

This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the corresponding positions on the other chromosome in a homologous pair. Information about the order of bases in a genome is readily inferred using short reads provided by high-throughput DNA sequencing technologies. In this paper, the recovery of the target pair of haplotype sequences using short reads is rephrased as a joint source-channel coding problem. Two messages, representing haplotypes and chromosome memberships of reads, are encoded and transmitted over a channel with erasures and errors, where the channel model reflects salient features of high-throughput sequencing. The focus of this paper is on the required number of reads for reliable haplotype reconstruction, and both the necessary and sufficient conditions are presented with order-wise optimal bounds.Comment: 30 pages, 5 figures, 1 tabel, journa

Coding mechanisms for communication and compression : analysis of wireless channels and DNA sequencing

textThis thesis comprises of two related but distinct components: Coding arguments for communication channels and information-theoretic analysis for haplotype assembly. The common thread for both problems is utilizing information and coding theoretic principles in understanding their underlying mechanisms. For the first class of problems, I study two practical challenges that prevent optimal discrete codes utilizing in real communication and compression systems, namely, coding over analog alphabet and fading. In particular, I use an expansion coding scheme to convert the original analog channel coding and source coding problems into a set of independent discrete subproblems. By adopting optimal discrete codes over the expanded levels, this low-complexity coding scheme can approach Shannon limit perfectly or in ratio. Meanwhile, I design a polar coding scheme to deal with the unstable state of fading channels. This novel coding mechanism of hierarchically utilizing different types of polar codes has been proved to be ergodic capacity achievable for several fading systems, without channel state information known at the transmitter. For the second class of problems, I build an information-theoretic view for haplotype assembly. More precisely, the recovery of the target pair of haplotype sequences using short reads is rephrased as the joint source-channel coding problem. Two binary messages, representing haplotypes and chromosome memberships of reads, are encoded and transmitted over a channel with erasures and errors, where the channel model reflects salient features of highthroughput sequencing. The focus is on determining the required number of reads for reliable haplotype reconstruction.Electrical and Computer Engineerin

Polar Coding for Fading Channels

A polar coding scheme for fading channels is proposed in this paper. More specifically, the focus is Gaussian fading channel with a BPSK modulation technique, where the equivalent channel could be modeled as a binary symmetric channel with varying cross-over probabilities. To deal with variable channel states, a coding scheme of hierarchically utilizing polar codes is proposed. In particular, by observing the polarization of different binary symmetric channels over different fading blocks, each channel use corresponding to a different polarization is modeled as a binary erasure channel such that polar codes could be adopted to encode over blocks. It is shown that the proposed coding scheme, without instantaneous channel state information at the transmitter, achieves the capacity of the corresponding fading binary symmetric channel, which is constructed from the underlying fading AWGN channel through the modulation scheme.Comment: 6 pages, 4 figures, conferenc

Lossy Compression of Exponential and Laplacian Sources using Expansion Coding

A general method of source coding over expansion is proposed in this paper, which enables one to reduce the problem of compressing an analog (continuous-valued source) to a set of much simpler problems, compressing discrete sources. Specifically, the focus is on lossy compression of exponential and Laplacian sources, which is subsequently expanded using a finite alphabet prior to being quantized. Due to decomposability property of such sources, the resulting random variables post expansion are independent and discrete. Thus, each of the expanded levels corresponds to an independent discrete source coding problem, and the original problem is reduced to coding over these parallel sources with a total distortion constraint. Any feasible solution to the optimization problem is an achievable rate distortion pair of the original continuous-valued source compression problem. Although finding the solution to this optimization problem at every distortion is hard, we show that our expansion coding scheme presents a good solution in the low distrotion regime. Further, by adopting low-complexity codes designed for discrete source coding, the total coding complexity can be tractable in practice.Comment: 8 pages, 3 figure

Multi-Scenario Ranking with Adaptive Feature Learning

Recently, Multi-Scenario Learning (MSL) is widely used in recommendation and retrieval systems in the industry because it facilitates transfer learning from different scenarios, mitigating data sparsity and reducing maintenance cost. These efforts produce different MSL paradigms by searching more optimal network structure, such as Auxiliary Network, Expert Network, and Multi-Tower Network. It is intuitive that different scenarios could hold their specific characteristics, activating the user's intents quite differently. In other words, different kinds of auxiliary features would bear varying importance under different scenarios. With more discriminative feature representations refined in a scenario-aware manner, better ranking performance could be easily obtained without expensive search for the optimal network structure. Unfortunately, this simple idea is mainly overlooked but much desired in real-world systems.Further analysis also validates the rationality of adaptive feature learning under a multi-scenario scheme. Moreover, our A/B test results on the Alibaba search advertising platform also demonstrate that Maria is superior in production environments.Comment: 10 pages