A Deep Embedding Model for Co-occurrence Learning

Co-occurrence Data is a common and important information source in many areas, such as the word co-occurrence in the sentences, friends co-occurrence in social networks and products co-occurrence in commercial transaction data, etc, which contains rich correlation and clustering information about the items. In this paper, we study co-occurrence data using a general energy-based probabilistic model, and we analyze three different categories of energy-based model, namely, the $L_1$, $L_2$ and $L_k$ models, which are able to capture different levels of dependency in the co-occurrence data. We also discuss how several typical existing models are related to these three types of energy models, including the Fully Visible Boltzmann Machine (FVBM) ($L_2$), Matrix Factorization ($L_2$), Log-BiLinear (LBL) models ($L_2$), and the Restricted Boltzmann Machine (RBM) model ($L_k$). Then, we propose a Deep Embedding Model (DEM) (an $L_k$ model) from the energy model in a \emph{principled} manner. Furthermore, motivated by the observation that the partition function in the energy model is intractable and the fact that the major objective of modeling the co-occurrence data is to predict using the conditional probability, we apply the \emph{maximum pseudo-likelihood} method to learn DEM. In consequence, the developed model and its learning method naturally avoid the above difficulties and can be easily used to compute the conditional probability in prediction. Interestingly, our method is equivalent to learning a special structured deep neural network using back-propagation and a special sampling strategy, which makes it scalable on large-scale datasets. Finally, in the experiments, we show that the DEM can achieve comparable or better results than state-of-the-art methods on datasets across several application domains

Preference Networks: Probabilistic Models for Recommendation Systems

Recommender systems are important to help users select relevant and personalised information over massive amounts of data available. We propose an unified framework called Preference Network (PN) that jointly models various types of domain knowledge for the task of recommendation. The PN is a probabilistic model that systematically combines both content-based filtering and collaborative filtering into a single conditional Markov random field. Once estimated, it serves as a probabilistic database that supports various useful queries such as rating prediction and top-$N$ recommendation. To handle the challenging problem of learning large networks of users and items, we employ a simple but effective pseudo-likelihood with regularisation. Experiments on the movie rating data demonstrate the merits of the PN.Comment: In Proc. of 6th Australasian Data Mining Conference (AusDM), Gold Coast, Australia, pages 195--202, 200

COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl