A translation apparatus is provided which comprises: an inputting section for inputting a source document in a natural language; a layout analyzing section for analyzing layout information including cascade information, itemization information, numbered itemization information, labeled itemization information and separator line information in the source document inputted by the inputting section and specifying a translation range on the basis of the layout information; a translation processing section for translating a source document text in the specified translation range into a second language; and an outputting section for outputting a translated text provided by the translation processing section.

Automated Planning: Theory and Practice.

Introduction to Geometry. By H. S. M. Coxeter. Pp. xiv, 443. 1961. (John Wiley)

This paper introduces GEOS, the first automated system to solve unaltered SAT geometry questions by combining text understanding and diagram interpretation. We model the problem of understanding geometry questions as submodular optimization, and identify a formal problem description likely to be compatible with both the question text and diagram. GEOS then feeds the description to a geometric solver that attempts to determine the correct answer. In our experiments, GEOS achieves a 49% score on official SAT questions, and a score of 61% on practice questions. 1 Finally, we show that by integrating textual and visual information, GEOS boosts the accuracy of dependency and semantic parsing of the question text.

/pdf/solving-geometry-problems-combining-text-and-diagram-2n008284av.pdf

Solving Geometry Problems: Combining Text and Diagram Interpretation

The efficiency of drug development defined as a number of successfully launched new pharmaceuticals normalized by financial investments has significantly declined. Nonetheless, recent advances in high-throughput experimental techniques and computational modeling promise reductions in the costs and development times required to bring new drugs to market. The prediction of toxicity of drug candidates is one of the important components of modern drug discovery. In this work, we describe eToxPred, a new approach to reliably estimate the toxicity and synthetic accessibility of small organic compounds. eToxPred employs machine learning algorithms trained on molecular fingerprints to evaluate drug candidates. The performance is assessed against multiple datasets containing known drugs, potentially hazardous chemicals, natural products, and synthetic bioactive compounds. Encouragingly, eToxPred predicts the synthetic accessibility with the mean square error of only 4% and the toxicity with the accuracy of as high as 72%. eToxPred can be incorporated into protocols to construct custom libraries for virtual screening in order to filter out those drug candidates that are potentially toxic or would be difficult to synthesize. It is freely available as a stand-alone software at https://github.com/pulimeng/etoxpred
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/pdf/etoxpred-a-machine-learning-based-approach-to-estimate-the-nuexb89frv.pdf

eToxPred: a machine learning-based approach to estimate the toxicity of drug candidates.

The potential number of drug like small molecules is estimated to be between 10^23 and 10^60 while current databases of known compounds are orders of magnitude smaller with approximately 10^8 compounds. This discrepancy has led to an interest in generating virtual libraries using hand crafted chemical rules and fragment based methods to cover a larger area of chemical space and generate chemical libraries for use in in silico drug discovery endeavors. Here it is explored to what extent a recurrent neural network with long short term memory cells can figure out sensible chemical rules and generate synthesizable molecules by being trained on existing compounds encoded as SMILES. The networks can to a high extent generate novel, but chemically sensible molecules. The properties of the molecules are tuned by training on two different datasets consisting of fragment like molecules and drug like molecules. The produced molecules and the training databases have very similar distributions of molar weight, predicted logP, number of hydrogen bond acceptors and donors, number of rotatable bonds and topological polar surface area when compared to their respective training sets. The compounds are for the most cases synthesizable as assessed with SA score and Wiley ChemPlanner.

Molecular Generation with Recurrent Neural Networks (RNNs)

This paper presents a semi-automated methodology for generating geometric proof problems of the kind found in a highschool curriculum. We formalize the notion of a geometry proof problem and describe an algorithm for generating such problems over a user-provided figure. Our experimental results indicate that our problem generation algorithm can effectively generate proof problems in elementary geometry. On a corpus of 110 figures taken from popular geometry textbooks, our system generated an average of about 443 problems per figure in an average time of 4.7 seconds per figure.

/pdf/synthesis-of-geometry-proof-problems-5e5am9vu1s.pdf

Synthesis of geometry proof problems

Constructing high-quality libraries of molecular building blocks is essential for successful fragment-based drug discovery. In this communication, we describe eMolFrag, a new open-source software to decompose organic compounds into nonredundant fragments retaining molecular connectivity information. Given a collection of molecules, eMolFrag generates a set of unique fragments comprising larger moieties, bricks, and smaller linkers connecting bricks. These building blocks can subsequently be used to construct virtual screening libraries for targeted drug discovery. The robustness and computational performance of eMolFrag is assessed against the Directory of Useful Decoys, Enhanced database conducted in serial and parallel modes with up to 16 computing cores. Further, the application of eMolFrag in de novo drug design is illustrated using the adenosine receptor. eMolFrag is implemented in Python, and it is available as stand-alone software and a web server at www.brylinski.org/emolfrag and https://github.co...

Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with eMolFrag.

Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in widely used screening libraries, such as the ZINC database, will have a very low probability to exhibit the desired bioactivity for a given protein. Although combinatorial chemistry methods can be used to augment existing compound libraries with novel drug-like compounds, the broad chemical space is often too large to be explored. Consequently, the trend in library design has shifted to produce screening collections specifically tailored to modulate the function of a particular target or a protein family.
 Assuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. On this account, we developed eSynth, an exhaustive graph-based search algorithm to computationally synthesize new compounds by reconnecting these building blocks following their connectivity patterns. We conducted a series of benchmarking calculations against the Directory of Useful Decoys, Enhanced database. First, in a self-benchmarking test, the correctness of the algorithm is validated with the objective to recover a molecule from its building blocks. Encouragingly, eSynth can efficiently rebuild more than 80 % of active molecules from their fragment components. Next, the capability to discover novel scaffolds is assessed in a cross-benchmarking test, where eSynth successfully reconstructed 40 % of the target molecules using fragments extracted from chemically distinct compounds. Despite an enormous chemical space to be explored, eSynth is computationally efficient; half of the molecules are rebuilt in less than a second, whereas 90 % take only about a minute to be generated. eSynth can successfully reconstruct chemically feasible molecules from molecular fragments.
 Furthermore, in a procedure mimicking the real application, where one expects to discover novel compounds based on a small set of already developed bioactives, eSynth is capable of generating diverse collections of molecules with the desired activity profiles. Thus, we are very optimistic that our effort will contribute to targeted drug discovery. eSynth is freely available to the academic community at www.brylinski.org/content/molecular-synthesis
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/pdf/a-graph-based-approach-to-construct-target-focused-libraries-1rk82w5n8q.pdf

A graph-based approach to construct target-focused libraries for virtual screening.

A shaded area problem in high school geometry consists of a figure annotated with facts such as lengths of line segments or angle measures, and asks to compute the area of a shaded portion of the figure. We describe a technique to generate fresh figures for these problems. Given a figure, we describe a technique to automatically synthesize shaded area problems. We demonstrate the efficacy of our synthesis techniques by synthesizing problems from fresh figures as well as figures from a corpus of problems from high-school geometry textbooks.

Chris Alvin

Papers

Synthesis of geometry proof problems

Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with eMolFrag.

A graph-based approach to construct target-focused libraries for virtual screening.

Synthesis of Problems for Shaded Area Geometry Reasoning

Synthesis of Solutions for Shaded Area Geometry Problems