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: A pseudo independent (PI) model is a proba­ bilistic domain model (PDM) where proper subsets of a set of collectively dependent variables display marginal independence. PI models cannot be learned correctly by many algorithms that rely on a single link search. Earlier work on learning PI models has sug­ gested a straightforward multi-link search al­ gorithm. However, when a domain contains recursively embedded PI submodels, it may escape the detection of such an algorithm. In this paper, we propose an improved al­ gorithm that ensures the learning of all em­ bedded PI submodels whose sizes are upper bounded by a predetermined parameter. We show that this improved learning capability only increases the complexity slightly beyond that of the previous algorithm. The perfor­ mance of the new algorithm is demonstrated through experiment.

Answer: Learning Belief Networks in Domains with Recursively Embedded Pseudo Independent Submodels


Question: We present and analyze an agnostic active learning algorithm that works without keeping a version space. This is unlike all previous approaches where a restricted set of candidate hypotheses is maintained throughout learning, and only hypotheses from this set are ever returned. By avoiding this version space approach, our algorithm sheds the computational burden and brittleness associated with maintaining version spaces, yet still allows for substantial improvements over supervised learning for classification.

Answer:
Agnostic Active Learning Without Constraints