Abraham Heifets

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This paper describes an experimental system in which customized high performance XML parsers are prepared using parser generation and compilation techniques. Parsing is integrated with Schema-based validation and deserialization, and the resulting validating processors are shown to be as fast as or in many cases significantly faster than traditional(More)
XML, as a data interchange technology, delivers key advantages in interoperability due to its flexibility, expressiveness, and platform-neutrality. The broad range of applications and growing base of users for XML technologies has driven the development of common tooling, providing a consistent, robust infrastructure on which to build applications. These(More)
E. Perkins M. Matsa M. G. Kostoulas A. Heifets N. Mendelsohn With the widespread adoption of SOAP and Web services, XML-based processing, and parsing of XML documents in particular, is becoming a performance-critical aspect of business computing. In such scenarios, XML is often constrained by an XML Schema grammar, which can be used during parsing to(More)
Deep convolutional neural networks comprise a subclass of deep neural networks (DNN) with a constrained architecture that leverages the spatial and temporal structure of the domain they model. Convolutional networks achieve the best predictive performance in areas such as speech and image recognition by hierarchically composing simple local features into(More)
Ligand-based active site alignment is a widely adopted technique for the structural analysis of protein-ligand complexes. However, existing tools for ligand alignment treat the ligands as rigid objects even though most biological ligands are flexible. We present LigAlign, an automated system for flexible ligand alignment and analysis. When performing rigid(More)
XML delivers key advantages in interoperability due to its flexibility, expressiveness, and platform-neutrality. As XML has become a performance-critical aspect of the next generation of business computing infrastructure, however, it has become increasingly clear that XML parsing often carries a heavy performance penalty, and that current, widely-used(More)
The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives,(More)
Automated Synthetic Feasibility Assessment: A Data-driven Derivation of Computational Tools for Medicinal Chemistry Abraham Heifets Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2014 The planning of organic syntheses, a critical problem in chemistry, can be directly modeled as resourceconstrained branching plans in a(More)