A Topic Modeling Toolbox Using Belief Propagation

Latent Dirichlet allocation (LDA) is an important hierarchical Bayesian model for probabilistic topic modeling, which attracts worldwide interests and touches on many important applications in text mining, computer vision and computational biology. This paper introduces a topic modeling toolbox (TMBP) based on the belief propagation (BP) algorithms. TMBP toolbox is implemented by MEX C++/Matlab/Octave for either Windows 7 or Linux. Compared with existing topic modeling packages, the novelty of this toolbox lies in the BP algorithms for learning LDA-based topic models. The current version includes BP algorithms for latent Dirichlet allocation (LDA), author-topic models (ATM), relational topic models (RTM), and labeled LDA (LaLDA). This toolbox is an ongoing project and more BP-based algorithms for various topic models will be added in the near future. Interested users may also extend BP algorithms for learning more complicated topic models. The source codes are freely available under the GNU General Public Licence, Version 1.0 at https://mloss.org/software/view/399/.Comment: 4 page

Memory-Efficient Topic Modeling

As one of the simplest probabilistic topic modeling techniques, latent Dirichlet allocation (LDA) has found many important applications in text mining, computer vision and computational biology. Recent training algorithms for LDA can be interpreted within a unified message passing framework. However, message passing requires storing previous messages with a large amount of memory space, increasing linearly with the number of documents or the number of topics. Therefore, the high memory usage is often a major problem for topic modeling of massive corpora containing a large number of topics. To reduce the space complexity, we propose a novel algorithm without storing previous messages for training LDA: tiny belief propagation (TBP). The basic idea of TBP relates the message passing algorithms with the non-negative matrix factorization (NMF) algorithms, which absorb the message updating into the message passing process, and thus avoid storing previous messages. Experimental results on four large data sets confirm that TBP performs comparably well or even better than current state-of-the-art training algorithms for LDA but with a much less memory consumption. TBP can do topic modeling when massive corpora cannot fit in the computer memory, for example, extracting thematic topics from 7 GB PUBMED corpora on a common desktop computer with 2GB memory.Comment: 20 pages, 7 figure

A Study of Molecular Adsorption and Transport at Cell Membrane and Biologically Relevant Surfaces by Second Harmonic Generation

Most of the biological processes in living systems involve molecular adsorption and transport at biomembranes. It is highly desired to study the time-resolved transport kinetics through living cell membranes. In this thesis, an experimental means based on a nonlinear optical phenomenon, Second Harmonic Generation (SHG) has been demonstrated to detect the molecular adsorption and transport through living cell membranes in real time and to evaluate the salt ion effects on adsorption processes in biologically relevant colloidal systems. In the case of gram-negative bacteria, E.coli, a hydrophobic cation, Malachite Green (MG) has been observed to adsorb onto the cell surface and then sequentially transport across the double bilayer structures, the bacterial outer membrane and the cytoplasmic membrane. The adsorption characteristics as well as the transport rate constant at each of the membranes have been determined. In contrast to the prokaryotic E.coli cell, the molecular ion can adsorb onto the eukaryotic Murine Erythroleukemia (MEL) cell but cannot penetrate its membrane which has no hydrophobic ion permeable channels and is more tightly packed. MG cation has been used as a SHG indicator to probe the effects of solvent ionic strength and ion specificity on molecular adsorption at model protein systems. Polystyrene sulfate (PSS) microspheres and polystyrene carboxyl (PSC) microspheres have been examined. The electrostatic force dominated molecule-surface interaction between MG cations and the sulfate terminations at PSS surface is largely affected by the ionic strength of the solution but is not sensitive to the ion identity. On the other hand, the hydrophobic force dominated molecule-surface interaction between hydrophobic regions of the MG dye and PSC microsphere shows pronounced specific ion effects but is less affected by ionic strength of the solution

Interferon-induced and Constitutive Expression of Immunity-related GTPases (IRG) in Mouse Tissues

Immunity-related GTPases (IRG) are essential, interferon-inducible resistant factors in mice that are actively against a broad spectrum of important intracellular pathogens. IRGs are represented by 25 genes in the mouse and also in almost all mammals and many other vertebrates, but surprisingly not in human. Structurally IRGs all share canonical GTP-binding domains and the crystal structure of one representative family member, Irga6, possesses an H-Ras-1-like GTP-binding domain. The biochemical properties of Irga6 are reminiscent of dynamins. Though the resistance mechanisms are still obscure, there is growing evidence supporting the role of IRG proteins as cell-autonomous resistant factors most probably through their direct targeting to intracellular pathogen-containing membrane compartments. IRGs are expressed under the tight regulation of IFNs. We found in this work unexpectedly that IRG proteins do have significant constitutive as well as IFN-induced expression in vivo. In liver at least for one member of IRG, Irga6, this differential expression is achieved by alternative activation of a liver-specific promoter and an IFN-inducible promoter. The constitutively expressed Irga6 in the presence of other constitutively expressed IRG proteins in primary hepatocytes is able to launch a similar anti-T.gondii program as IFN-induced protein, implying the role of IRG proteins as sentinel in the resistance against intracellular pathogens in liver that is an organ of immune privilege. Peculiar Irga6 focal expression in liver as well as in kidney is also observed and proved to be induced by local production of IFNs. This production of IFN-γ that induces Irga6 focal expression in liver surprisingly represents the local activation of NKT cells even in the absence of microbial environment (germ-free mice). Even though the causes of this NKT cell activation are still elusive, we speculate that this stimulation of NKT cells may stand for an ongoing process required for the maintenance of the effector status for peripheral NKT cells

A New Approach to Speeding Up Topic Modeling

Latent Dirichlet allocation (LDA) is a widely-used probabilistic topic modeling paradigm, and recently finds many applications in computer vision and computational biology. In this paper, we propose a fast and accurate batch algorithm, active belief propagation (ABP), for training LDA. Usually batch LDA algorithms require repeated scanning of the entire corpus and searching the complete topic space. To process massive corpora having a large number of topics, the training iteration of batch LDA algorithms is often inefficient and time-consuming. To accelerate the training speed, ABP actively scans the subset of corpus and searches the subset of topic space for topic modeling, therefore saves enormous training time in each iteration. To ensure accuracy, ABP selects only those documents and topics that contribute to the largest residuals within the residual belief propagation (RBP) framework. On four real-world corpora, ABP performs around $10$ to $100$ times faster than state-of-the-art batch LDA algorithms with a comparable topic modeling accuracy.Comment: 14 pages, 12 figure

A Review of Alexander Broadie's A History of Scottish Philosophy

Scottish philosophy and intellectual history have become the increasingly fashionable fields of academic studies. Alexander Broadie, one of the pioneers and an accomplished scholar of the Scottish Enlightenment, returns to the basic question, namely, “what is Scottish philosophy?”, and presents a comprehensive work on the history of Scottish philosophy. Broadie successfully elucidates the nature and significance of Scottish philosophy both historically and philosophically. He argues that Scottish philosophy must be studied in its historical context, for it is not only a philosophical enterprise but also a persistent tradition which has united the Scottish nation for centuries. The advancements in science, literature, politics, and culture in Scotland would be extremely unlikely, if not impossible, without such an intellectual culture established by thinkers in that tradition. This article is intended as a review of Broadie’s A History of Scottish Philosophy in the background of his shifting academic interests from philosophy to history while he holds the professorship in University of Glasgow. His commitment to Scottish philosophical culture deserves the attention of contemporary historians and philosophers, for his work opens up a space for dialogue between intellectual history and history of philosophy, an issue addressed at the end of this paper

Challenges of Primary Frequency Control and Benefits of Primary Frequency Response Support from Electric Vehicles

As the integration of wind generation displaces conventional plants, system inertia provided by rotating mass declines, causing concerns over system frequency stability. This paper implements an advanced stochastic scheduling model with inertia-dependent fast frequency response requirements to investigate the challenges on the primary frequency control in the future Great Britain electricity system. The results suggest that the required volume and the associated cost of primary frequency response increase significantly along with the increased capacity of wind plants. Alternative measures (e.g. electric vehicles) have been proposed to alleviate these concerns. Therefore, this paper also analyses the benefits of primary frequency response support from electric vehicles in reducing system operation cost, wind curtailment and carbon emissions