TASK DEFINITION: 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.
PROBLEM: There are already quite a few tools for solving the Satisfiability Modulo Theories (SMT) problems. In this paper, we present VolCE, a tool for counting the solutions of SMT constraints, or in other words, for computing the volume of the solution space. Its input is essentially a set of Boolean combinations of linear constraints, where the numeric variables are either all integers or all reals, and each variable is bounded. The tool extends SMT solving with integer solution counting and volume computation/estimation for convex polytopes. Effective heuristics are adopted, which enable the tool to deal with high-dimensional problem instances efficiently and accurately.

SOLUTION: A Tool for Computing and Estimating the Volume of the Solution Space of SMT(LA) Constraints

PROBLEM: Formal languages for probabilistic modeling enable re-use, modularity, and descriptive clarity, and can foster generic inference techniques. We introduce Church, a universal language for describing stochastic generative processes. Church is based on the Lisp model of lambda calculus, containing a pure Lisp as its deterministic subset. The semantics of Church is defined in terms of evaluation histories and conditional distributions on such histories. Church also includes a novel language construct, the stochastic memoizer, which enables simple description of many complex non-parametric models. We illustrate language features through several examples, including: a generalized Bayes net in which parameters cluster over trials, infinite PCFGs, planning by inference, and various non-parametric clustering models. Finally, we show how to implement query on any Church program, exactly and approximately, using Monte Carlo techniques.

SOLUTION: Church: a language for generative models

PROBLEM: 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.

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