Dyson-Schwinger equations in the theory of computation

Following Manin's approach to renormalization in the theory of computation, we investigate Dyson-Schwinger equations on Hopf algebras, operads and properads of flow charts, as a way of encoding self-similarity structures in the theory of algorithms computing primitive and partial recursive functions and in the halting problem.Comment: 26 pages, LaTeX, final version, in "Feynman Amplitudes, Periods and Motives", Contemporary Mathematics, AMS 201

Neo: A Learned Query Optimizer

Query optimization is one of the most challenging problems in database systems. Despite the progress made over the past decades, query optimizers remain extremely complex components that require a great deal of hand-tuning for specific workloads and datasets. Motivated by this shortcoming and inspired by recent advances in applying machine learning to data management challenges, we introduce Neo (Neural Optimizer), a novel learning-based query optimizer that relies on deep neural networks to generate query executions plans. Neo bootstraps its query optimization model from existing optimizers and continues to learn from incoming queries, building upon its successes and learning from its failures. Furthermore, Neo naturally adapts to underlying data patterns and is robust to estimation errors. Experimental results demonstrate that Neo, even when bootstrapped from a simple optimizer like PostgreSQL, can learn a model that offers similar performance to state-of-the-art commercial optimizers, and in some cases even surpass them

Subpath Queries on Compressed Graphs: A Survey

Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text T, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in T in time proportional to the query’s length. The earliest optimal-time solution to the problem, the suffix tree, dates back to 1973 and requires up to two orders of magnitude more space than the plain text just to be stored. In the year 2000, two breakthrough works showed that efficient queries can be achieved without this space overhead: a fast index be stored in a space proportional to the text’s entropy. These contributions had an enormous impact in bioinformatics: today, virtually any DNA aligner employs compressed indexes. Recent trends considered more powerful compression schemes (dictionary compressors) and generalizations of the problem to labeled graphs: after all, texts can be viewed as labeled directed paths. In turn, since finite state automata can be considered as a particular case of labeled graphs, these findings created a bridge between the fields of compressed indexing and regular language theory, ultimately allowing to index regular languages and promising to shed new light on problems, such as regular expression matching. This survey is a gentle introduction to the main landmarks of the fascinating journey that took us from suffix trees to today’s compressed indexes for labeled graphs and regular languages

Tolerating Correlated Failures in Massively Parallel Stream Processing Engines

Fault-tolerance techniques for stream processing engines can be categorized into passive and active approaches. A typical passive approach periodically checkpoints a processing task's runtime states and can recover a failed task by restoring its runtime state using its latest checkpoint. On the other hand, an active approach usually employs backup nodes to run replicated tasks. Upon failure, the active replica can take over the processing of the failed task with minimal latency. However, both approaches have their own inadequacies in Massively Parallel Stream Processing Engines (MPSPE). The passive approach incurs a long recovery latency especially when a number of correlated nodes fail simultaneously, while the active approach requires extra replication resources. In this paper, we propose a new fault-tolerance framework, which is Passive and Partially Active (PPA). In a PPA scheme, the passive approach is applied to all tasks while only a selected set of tasks will be actively replicated. The number of actively replicated tasks depends on the available resources. If tasks without active replicas fail, tentative outputs will be generated before the completion of the recovery process. We also propose effective and efficient algorithms to optimize a partially active replication plan to maximize the quality of tentative outputs. We implemented PPA on top of Storm, an open-source MPSPE and conducted extensive experiments using both real and synthetic datasets to verify the effectiveness of our approach

Multiple sequence alignment based on set covers

We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches

Noun phrase recognition with tree patterns

This paper offers a method for the noun phrase recognition of Hungarian natural language texts based on machine learning methods. The approach learns noun phrase tree patterns described by regular expressions from an annotated corpus. The tree patterns are completed with probability values using error statistics. The noun phrase recognition parser tries to find the best-fitting trees for a sentence using backtracking technique. The results are used in an information extraction toolchain

Root-Weighted Tree Automata and their Applications to Tree Kernels

In this paper, we define a new kind of weighted tree automata where the weights are only supported by final states. We show that these automata are sequentializable and we study their closures under classical regular and algebraic operations. We then use these automata to compute the subtree kernel of two finite tree languages in an efficient way. Finally, we present some perspectives involving the root-weighted tree automata