In this task, you are given a part of an article. Your task is to generate headline (title) for this text. Preferred headlines are under fifteen words.
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Question: Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on high level of sequence identity, however, most of the existing alignment-free methods do not employ true full information content of sequences and thus can not accurately reveal similarities and differences among DNA sequences. We present a novel alignment-free computational method for sequence analysis based on Ramanujan-Fourier transform (RFT), in which complete information of DNA sequences is retained. We represent DNA sequences as four binary indicator sequences and apply RFT on the indicator sequences to convert them into frequency domain. The Euclidean distance of the complete RFT coefficients of DNA sequences are used as similarity measure. To address the different lengths in Euclidean space of RFT coefficients, we pad zeros to short DNA binary sequences so that the binary sequences equal the longest length in the comparison sequence data. Thus, the DNA sequences are compared in the same dimensional frequency space without information loss. We demonstrate the usefulness of the proposed method by presenting experimental results on hierarchical clustering of genes and genomes. The proposed method opens a new channel to biological sequence analysis, classification, and structural module identification.

Answer: A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform

Question: Independent Component Analysis (ICA) is the problem of learning a square matrix A, given samples of X = AS, where S is a random vector with independent coordinates. Most existing algorithms are provably efficient only when each Si has finite and moderately valued fourth moment. However, there are practical applications where this assumption need not be true, such as speech and finance. Algorithms have been proposed for heavy-tailed ICA, but they are not practical, using random walks and the full power of the ellipsoid algorithm multiple times. The main contributions of this paper are: (1) A practical algorithm for heavy-tailed ICA that we call HTICA. We provide theoretical guarantees and show that it outperforms other algorithms in some heavy-tailed regimes, both on real and synthetic data. Like the current state-of-the-art, the new algorithm is based on the centroid body (a first moment analogue of the covariance matrix). Unlike the state-of-the-art, our algorithm is practically efficient. To achieve this, we use explicit analytic representations of the centroid body, which bypasses the use of the ellipsoid method and random walks. (2) We study how heavy tails affect different ICA algorithms, including HTICA. Somewhat surprisingly, we show that some algorithms that use the covariance matrix or higher moments can successfully solve a range of ICA instances with infinite second moment. We study this theoretically and experimentally, with both synthetic and real-world heavy-tailed data.

Answer: Heavy-Tailed Analogues of the Covariance Matrix for ICA

Question: We introduce Deep Neural Programs (DNP), a novel programming paradigm for writing adaptive controllers for cyber-physical systems (CPS). DNP replace if and while statements, whose discontinuity is responsible for undecidability in CPS analysis, intractability in CPS design, and frailness in CPS implementation, with their smooth, neural nif and nwhile counterparts. This not only makes CPS analysis decidable and CPS design tractable, but also allows to write robust and adaptive CPS code. In DNP the connection between the sigmoidal guards of the nif and nwhile statements has to be given as a Gaussian Bayesian network, which reflects the partial knowledge, the CPS program has about its environment. To the best of our knowledge, DNP are the first approach linking neural networks to programs, in a way that makes explicit the meaning of the network. In order to prove and validate the usefulness of DNP, we use them to write and learn an adaptive CPS controller for the parallel parking of the Pioneer rovers available in our CPS lab.

Answer:
Deep Neural Programs for Adaptive Control in Cyber-Physical Systems