Decoding Hidden Markov Models Faster Than Viterbi Via Online Matrix-Vector (max, +)-Multiplication

In this paper, we present a novel algorithm for the maximum a posteriori decoding (MAPD) of time-homogeneous Hidden Markov Models (HMM), improving the worst-case running time of the classical Viterbi algorithm by a logarithmic factor. In our approach, we interpret the Viterbi algorithm as a repeated computation of matrix-vector $(\max, +)$-multiplications. On time-homogeneous HMMs, this computation is online: a matrix, known in advance, has to be multiplied with several vectors revealed one at a time. Our main contribution is an algorithm solving this version of matrix-vector $(\max,+)$-multiplication in subquadratic time, by performing a polynomial preprocessing of the matrix. Employing this fast multiplication algorithm, we solve the MAPD problem in $O(mn^2/ \log n)$ time for any time-homogeneous HMM of size $n$ and observation sequence of length $m$, with an extra polynomial preprocessing cost negligible for $m > n$. To the best of our knowledge, this is the first algorithm for the MAPD problem requiring subquadratic time per observation, under the only assumption -- usually verified in practice -- that the transition probability matrix does not change with time.Comment: AAAI 2016, to appea

Effects of Nostalgia on Responses to Negative Feedback

Nostalgia is a bittersweet emotion evoked by memories of cherished personal experiences. Though nostalgia is a self-focused emotion, it has many interpersonal effects as well. Feeling nostalgia increases feelings of social connectedness and self esteem, and may protect against negative effects of existential threat (Wildschut et al., 2006). However, less is known about the extent to which nostalgia relates to anger and aggression. We hypothesized that nostalgia would buffer against the effect of negative feedback on feelings of anger and motivation to aggress. Undergraduate students wrote about a nostalgic or objective memory, and then received negative feedback about another personal writing project. Participants reported their feelings of anger, then had the opportunity to punish the individual who gave them negative feedback by administering loud noise blasts in a competitive game. We discuss the results and real-world implications of these findings.https://scholarscompass.vcu.edu/uresposters/1283/thumbnail.jp

How Charts Lie: What You Design Is Not What People See

Visualizations such as charts, maps and infographics are ubiquitous nowadays. They are useful because they can reveal patterns and trends in data. Good visualizations make us smarter - if we know how to read them. However, visualizations can also deceive us by displaying incomplete or inaccurate data, suggesting misleading patterns, and concealing uncertainty. They are also frequently misunderstood. Many of us are ill-equipped to interpret the visuals that politicians, journalists, advertisers and even our employers present each day. We are in need of expanding the notion of literacy to include numeracy (numerical literacy) and graphicacy (graphical literacy)

HEBI SANI: MENTAL WELL BEING AMONG THE WORKING CLASS AFRO-SURINAMESE IN PARAMARIBO, SURINAME

This dissertation describes the results of a two year anthropological investigation into the concept of mental well being among the working class Afro-Surinamese population in Paramaribo, Suriname. More specifically, the research investigated how working class Afro-Surinamese in Paramaribo, Suriname define and maintain their sense of mental well-being, given their unique ethnic identity within a multi-ethnic and multicultural society, and given that their environment is heavily compromised by negative globalizing forces Over the course of two years a total of 62 people contributed information through group and individual interviews, which was supplemented by information obtained through participant observation. Findings show a highly complex system of mental well being that consists of a number of interlocking and interdependent factors, which, when kept in a harmonious relationship with each other, are presumed to bring mental well being. There are unique Afro-Surinamese measures available for strengthening mental well being based in rich and historical cultural traditions that are currently under-utilized, but have the potential to be revived and introduced for the benefit of peoples mental well being. Suriname was selected as a Caribbean country that struggles in a marginalized political and economic position in regards to the rest of the Caribbean, and in relation to the world powers. Suriname is also a Dutch Caribbean country about which little academic information has been published. This research aimed to bring forth a story of a globally marginalized people, and particularly of a population of African descent. It aimed to bring attention to the concept of mental well being among African Diaspora people, and to use the story of a small population as a starting point to connect with and look at other populations, Diaspora based or otherwise. Theoretical viewpoints of African Diaspora, Globalization, and a combination of Black Feminist/Third World Feminist/Caribbean Feminist theories were used to guide and shape this research. Lastly, an attempt was made to introduce the concept of Spirituality as a new and complementary aspect of ethnographic methodology

Studies in SEOP Hyperpolarized 3He: Measuring Ko and the Spatial Dependence of Alkali Polarization

3He is an isotope of helium whose nucleus is composed of two protons and one neutron. The proportion of atoms whose spins are pointed along the same direction in a volume of 3He gas is known as the polarization. This study entails two experiments in the field of 3He polarimetry concerned with measuring the polarization of a 3He cell and reducing the uncertainty associated with it. 3He cells are full of gaseous 3He, along with alkali metal vapors, K and Rb in our case. The polarization of a 3He cell can be measured using an electron paramagnetic resonance (EPR) frequency shift. The EPR frequency is related to the 3He polarization through a constant, Ko. The first experiment in this study involves isolating Ko by varying the geometry of the magnetic field generated by the polarized 3He. The spatial dependence of the polarization is also of interest. To measure this, we use Faraday rotation. For a 3He cell, the amount of rotation is determined by the polarization of the alkali gas. The second experiment in the study involves inferring the polarization of a path through a cell using Faraday rotation measurements. This will establish a spatial mapping of polarization in the cell that will help improve our understanding of its overall polarization

Expression and refolding of the protective antigen of Bacillus anthracis: A model for high-throughput screening of antigenic recombinant protein refolding

Bacillus anthracis protective antigen (PA) is a well known and relevant immunogenicprotein that is the basis for both anthrax vaccines and diagnostic methods. Properly foldedantigenic PA is necessary for these applications. In this study a high level of PA was obtained inrecombinant Escherichia coli. The protein was initially accumulated in inclusion bodies, whichfacilitated its efficient purification by simple washing steps; however, it could not be recognizedby specific antibodies. Refolding conditions were subsequently analyzed in a high-throughputmanner that enabled nearly a hundred different conditions to be tested simultaneously. Therecovery of the ability of PA to be recognized by antibodies was screened by dot blot usinga coefficient that provided a measure of properly refolded protein levels with a high degreeof discrimination. The best refolding conditions resulted in a tenfold increase in the intensityof the dot blot compared to the control. The only refolding additive that consistently yieldedgood results was L-arginine. The statistical analysis identified both cooperative and negativeinteractions between the different refolding additives. The high-throughput approach describedin this study that enabled overproduction, purification and refolding of PA in a simple andstraightforward manner, can be potentially useful for the rapid screening of adequate refoldingconditions for other overexpressed antigenic proteins.Fil: Pavan, María Elisa. Biochemiq; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Pavan, Esteban E.. Politecnico di Milano; ItaliaFil: Cairo, Fabian Martin. Biochemiq; ArgentinaFil: Pettinari, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentin

The Promyelocytic Leukaemia gene product PML interacts with Myc and influences the expression of Myc target genes

c-myc is a well-known proto-oncogene encoding a transcription factor that needs to be tightly regulated in order to preserve cell homeostasis. The Promyelocytic Leukaemia gene product PML plays an important role in cell growth and survival, and resides in discrete sub-nuclear structures called Nuclear Bodies (NB). PML is largely involved in gene regulation via recruitment of several transcription factors and co factors to the NB. In this report, I show that Myc partially localizes to the NB and physically interacts with PML, and I demonstrate that PML over-expression affects Myc-mediated transcription of a reporter gene. Comparative analysis of the expression of 40 Myc target genes and of Myc binding to their regulatory regions in wild type and PML knockout mouse embryo fibroblasts was performed. The data show that if PML is absent, although Myc binding to the DNA regulatory sequences is unchanged, the expression profile of several Myc target genes is altered. As deregulation of both activated and repressed Myc target genes occurs, I propose that PML influences Myc transcriptional activity through a mechanism that involves the control of Myc post-translational modifications