MOTIVATION: Simulation is an essential technique for generating biomolecular data with a 'known' history for use in validating phylogenetic inference and other evolutionary methods. On longer time scales, simulation supports investigations of equilibrium behavior and provides a formal framework for testing competing evolutionary hypotheses. Twenty years of molecular evolution research have produced a rich repertoire of simulation methods. However, current models do not capture the stringent constraints acting on the domain insertions, duplications, and deletions by which multidomain architectures evolve. Although these processes have the potential to generate any combination of domains, only a tiny fraction of possible domain combinations are observed in nature. Modeling these stringent constraints on domain order and co-occurrence is a fundamental challenge in domain architecture simulation that does not arise with sequence and gene family simulation. RESULTS: Here, we introduce a stochastic model of domain architecture evolution to simulate evolutionary trajectories that reflect the constraints on domain order and co-occurrence observed in nature. This framework is implemented in a novel domain architecture simulator, DomArchov, using the Metropolis-Hastings algorithm with data-driven transition probabilities. The use of a data-driven event module enables quick and easy redeployment of the simulator for use in different taxonomic and protein function contexts. Using empirical evaluation with metazoan datasets, we demonstrate that domain architectures simulated by DomArchov recapitulate properties of genuine domain architectures that reflect the constraints on domain order and adjacency seen in nature. This work expands the realm of evolutionary processes that are amenable to simulation. AVAILABILITY AND IMPLEMENTATION: DomArchov is written in Python 3 and is available at http://www.cs.cmu.edu/~durand/DomArchov. The data underlying this article are available via the same link. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Despite the advent of deep learning in computer vision, the general handwriting recognition problem is far from solved. Most existing approaches focus on handwriting datasets that have clearly written text and carefully segmented labels. In this paper, we instead focus on learning handwritten characters from maintenance logs, a constrained setting where data is very limited and noisy. We break the problem into two consecutive stages of word segmentation and word recognition respectively, and utilize data augmentation techniques to train both stages. Extensive comparisons with popular baselines for scene-text detection and word recognition show that our system achieves a lower error rate and is more suited to handle noisy and difficult documents.

Software frameworks which support integration and scaling of text analysis algorithms make it possible to build complex, high performance information systems for information extraction, information retrieval, and question answering; IBM's Watson is a prominent example. As the complexity and scaling of information systems become ever greater, it is much more challenging to effectively and efficiently determine which toolkits, algorithms, knowledge bases or other resources should be integrated into an information system in order to achieve a desired or optimal level of performance on a given task. This paper presents a formal representation of the space of possible system configurations, given a set of information processing components and their parameters (configuration space) and discusses algorithmic approaches to determine the optimal configuration within a given configuration space (configuration space exploration or CSE). We introduce the CSE framework, an extension to the UIMA framework which provides a general distributed solution for building and exploring configuration spaces for information systems. The CSE framework was used to implement biomedical information systems in case studies involving over a trillion different configuration combinations of components and parameter values operating on question answering tasks from the TREC Genomics. The framework automatically and efficiently evaluated different system configurations, and identified configurations that achieved better results than prior published results.