Serially-regulated biological networks fully realize a constrained set of functions

We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an environmental input on a target species depends only on the direct path from the input to the target, even when there is a feedback loop allowing for multiple interaction pathways. Using a stochastic model for a set of small transcriptional regulatory networks that have been studied experimentally, we further find that all networks can achieve all functions permitted by this constraint under reasonable settings of biochemical parameters. This underscores the functional versatility of the networks.Comment: 9 pages, 3 figure

Faster subsequence recognition in compressed strings

Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to Lempel--Ziv compression. For an SLP-compressed text of length $\bar m$, and an uncompressed pattern of length $n$, C{\'e}gielski et al. gave an algorithm for local subsequence recognition running in time $O(\bar mn^2 \log n)$. We improve the running time to $O(\bar mn^{1.5})$. Our algorithm can also be used to compute the longest common subsequence between a compressed text and an uncompressed pattern in time $O(\bar mn^{1.5})$; the same problem with a compressed pattern is known to be NP-hard

RLZAP: Relative Lempel-Ziv with Adaptive Pointers

Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s (SPIRE 2010) original implementation, a reference genome is selected and then the other genomes are greedily parsed into phrases exactly matching substrings of the reference. Deorowicz and Grabowski (Bioinformatics, 2011) pointed out that letting each phrase end with a mismatch character usually gives better compression because many of the differences between individuals' genomes are single-nucleotide substitutions. Ferrada et al. (SPIRE 2014) then pointed out that also using relative pointers and run-length compressing them usually gives even better compression. In this paper we generalize Ferrada et al.'s idea to handle well also short insertions, deletions and multi-character substitutions. We show experimentally that our generalization achieves better compression than Ferrada et al.'s implementation with comparable random-access times

Who Chooses Open-Source Software?

Economists and legal scholars have debated the reasons people adopt opensource software, and accordingly whether and to what extent the open-source model can scale, replacing proprietary rights as a primary means of production. In this Article, we use the release by a biotechnology company of similar software under both proprietary and open-source licenses to investigate who uses open-source software and why. We find that academic users are somewhat more likely to adopt open-source software than private firms. We find only modest differences in the willingness of open-source users to modify or improve existing programs. And we find that users of open-source software often make business decisions that seem indifferent to the norms of opensource distribution. Our findings cast some doubt on the penetration of the open-source ethos beyond traditional software markets

Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known complexities for both problems. In particular, we significantly improve the space bounds, which in practical applications are likely to be a bottleneck

Information in Infinite Ensembles of Infinitely-Wide Neural Networks

In this preliminary work, we study the generalization properties of infinite ensembles of infinitely-wide neural networks. Amazingly, this model family admits tractable calculations for many information-theoretic quantities. We report analytical and empirical investigations in the search for signals that correlate with generalization.Comment: 2nd Symposium on Advances in Approximate Bayesian Inference, 201

Optimizing XML Compression

The eXtensible Markup Language (XML) provides a powerful and flexible means of encoding and exchanging data. As it turns out, its main advantage as an encoding format (namely, its requirement that all open and close markup tags are present and properly balanced) yield also one of its main disadvantages: verbosity. XML-conscious compression techniques seek to overcome this drawback. Many of these techniques first separate XML structure from the document content, and then compress each independently. Further compression gains can be realized by identifying and compressing together document content that is highly similar, thereby amortizing the storage costs of auxiliary information required by the chosen compression algorithm. Additionally, the proper choice of compression algorithm is an important factor not only for the achievable compression gain, but also for access performance. Hence, choosing a compression configuration that optimizes compression gain requires one to determine (1) a partitioning strategy for document content, and (2) the best available compression algorithm to apply to each set within this partition. In this paper, we show that finding an optimal compression configuration with respect to compression gain is an NP-hard optimization problem. This problem remains intractable even if one considers a single compression algorithm for all content. We also describe an approximation algorithm for selecting a partitioning strategy for document content based on the branch-and-bound paradigm.Comment: 16 pages, extended version of paper accepted for XSym 200

Efficient LZ78 factorization of grammar compressed text

We present an efficient algorithm for computing the LZ78 factorization of a text, where the text is represented as a straight line program (SLP), which is a context free grammar in the Chomsky normal form that generates a single string. Given an SLP of size $n$ representing a text $S$ of length $N$, our algorithm computes the LZ78 factorization of $T$ in $O(n\sqrt{N}+m\log N)$ time and $O(n\sqrt{N}+m)$ space, where $m$ is the number of resulting LZ78 factors. We also show how to improve the algorithm so that the $n\sqrt{N}$ term in the time and space complexities becomes either $nL$, where $L$ is the length of the longest LZ78 factor, or $(N - \alpha)$ where $\alpha \geq 0$ is a quantity which depends on the amount of redundancy that the SLP captures with respect to substrings of $S$ of a certain length. Since $m = O(N/\log_\sigma N)$ where $\sigma$ is the alphabet size, the latter is asymptotically at least as fast as a linear time algorithm which runs on the uncompressed string when $\sigma$ is constant, and can be more efficient when the text is compressible, i.e. when $m$ and $n$ are small.Comment: SPIRE 201

Protein-DNA computation by stochastic assembly cascade

The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan DNA sequence through a cascade of random nucleation and disassembly events that is mechanistically similar to the dynamic instability of microtubules. This iterative cascade is a multistage kinetic proofreading process that amplifies minute differences, even a single base change. Our measurements suggest that this stochastic Turing-like machine can compute certain integral transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/ http://www.pnas.org/content/99/18/11589.abstrac