Efficient Correlated Topic Modeling with Topic Embedding

Correlated topic modeling has been limited to small model and problem sizes due to their high computational cost and poor scaling. In this paper, we propose a new model which learns compact topic embeddings and captures topic correlations through the closeness between the topic vectors. Our method enables efficient inference in the low-dimensional embedding space, reducing previous cubic or quadratic time complexity to linear w.r.t the topic size. We further speedup variational inference with a fast sampler to exploit sparsity of topic occurrence. Extensive experiments show that our approach is capable of handling model and data scales which are several orders of magnitude larger than existing correlation results, without sacrificing modeling quality by providing competitive or superior performance in document classification and retrieval.Comment: KDD 2017 oral. The first two authors contributed equall

Classifying Web Exploits with Topic Modeling

This short empirical paper investigates how well topic modeling and database meta-data characteristics can classify web and other proof-of-concept (PoC) exploits for publicly disclosed software vulnerabilities. By using a dataset comprised of over 36 thousand PoC exploits, near a 0.9 accuracy rate is obtained in the empirical experiment. Text mining and topic modeling are a significant boost factor behind this classification performance. In addition to these empirical results, the paper contributes to the research tradition of enhancing software vulnerability information with text mining, providing also a few scholarly observations about the potential for semi-automatic classification of exploits in the existing tracking infrastructures.Comment: Proceedings of the 2017 28th International Workshop on Database and Expert Systems Applications (DEXA). http://ieeexplore.ieee.org/abstract/document/8049693

Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices

Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale computational modeling efforts. Nonetheless, these research agendas have yet to prove decisively their value among the broader community of theoretical and experimental biologists. In this commentary, we examine a range of philosophical and practical issues relevant to understanding the potential of integrative simulations. We discuss the role of theory and modeling in different areas of physics and suggest that certain sub-disciplines of physics provide useful cultural analogies for imagining the future role of simulations in biological research. We examine philosophical issues related to modeling which consistently arise in discussions about integrative simulations and suggest a pragmatic viewpoint that balances a belief in philosophy with the recognition of the relative infancy of our state of philosophical understanding. Finally, we discuss community workflow and publication practices to allow research to be readily discoverable and amenable to incorporation into simulations. We argue that there are aligned incentives in widespread adoption of practices which will both advance the needs of integrative simulation efforts as well as other contemporary trends in the biological sciences, ranging from open science and data sharing to improving reproducibility.Comment: 10 page