Belief-Propagation for Weighted b-Matchings on Arbitrary Graphs and its Relation to Linear Programs with Integer Solutions

We consider the general problem of finding the minimum weight \bm-matching on arbitrary graphs. We prove that, whenever the linear programming (LP) relaxation of the problem has no fractional solutions, then the belief propagation (BP) algorithm converges to the correct solution. We also show that when the LP relaxation has a fractional solution then the BP algorithm can be used to solve the LP relaxation. Our proof is based on the notion of graph covers and extends the analysis of (Bayati-Shah-Sharma 2005 and Huang-Jebara 2007}. These results are notable in the following regards: (1) It is one of a very small number of proofs showing correctness of BP without any constraint on the graph structure. (2) Variants of the proof work for both synchronous and asynchronous BP; it is the first proof of convergence and correctness of an asynchronous BP algorithm for a combinatorial optimization problem.Comment: 28 pages, 2 figures. Submitted to SIAM journal on Discrete Mathematics on March 19, 2009; accepted for publication (in revised form) August 30, 2010; published electronically July 1, 201

Shaped by Changing Space: Exploring Gender and the Discourse of Empowerment in Sikles, Nepal

Development work as it relates to women in Nepal is an ongoing topic of debate and discussion that may never have a concrete end. In the late 1970’s Indian women took a stand in defending their livelihood against commercial logging operations with authorities. This event was known as the Chipko movement and is often cited within the history of women and development as it caused people to “engage the question of gender and gendered livelihoods in the Himalayas” (Gurarani and Berry, 2015). It was women who served as the backbone of this movement in organizing nonviolent demonstrations against commercial deforestation. This movement also illuminated the unique burden women faced in the context of environmental degradation. Since then, many academic works and development projects have sought to analyze, “a politics of gendered exclusion that has resulted from the overlay of development discourses on state-led resource management endeavors” (Gurarani et al., 2015). In Nepal, specifically, projects devoted to women’s empowerment are prevalent and have emerged with their own set of discourse. There remains debate as to whether or not this often participatory approach is effective in achieving its intended goals

Parallelisation and application of AD3 as a method for solving large scale combinatorial auctions

Auctions, and combinatorial auctions (CAs), have been successfully employed to solve coordination problems in a wide range of application domains. However, the scale of CAs that can be optimally solved is small because of the complexity of the winner determination problem (WDP), namely of finding the bids that maximise the auctioneer’s revenue. A way of approximating the solution of a WDP is to solve its linear programming relaxation. The recently proposed Alternate Direction Dual Decomposition algorithm (AD3) has been shown to ef- ficiently solve large-scale LP relaxations. Hence, in this paper we show how to encode the WDP so that it can be approximated by means of AD3. Moreover, we present PAR-AD3, the first parallel implementation of AD3. PAR-AD3 shows to be up to 12.4 times faster than CPLEX in a single-thread execution, and up to 23 times faster than parallel CPLEX in an 8-core architecture. Therefore PAR- AD3 becomes the algorithm of choice to solve large-scale WDP LP relaxations for hard instances. Furthermore, PAR-AD3 has potential when considering large- scale coordination problems that must be solved as optimisation problems.Research supported by MICINN projects TIN2011-28689-C02-01, TIN2013-45732-C4-4-P and TIN2012-38876-C02-01Peer reviewe

A computational framework to empower probabilistic protein design

Motivation: The task of engineering a protein to perform a target biological function is known as protein design. A commonly used paradigm casts this functional design problem as a structural one, assuming a fixed backbone. In probabilistic protein design, positional amino acid probabilities are used to create a random library of sequences to be simultaneously screened for biological activity. Clearly, certain choices of probability distributions will be more successful in yielding functional sequences. However, since the number of sequences is exponential in protein length, computational optimization of the distribution is difficult

An Exact Algorithm for Side-Chain Placement in Protein Design

Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting overall energy is minimum. The choice of the side-chain then also determines the amino acid for this position. Many algorithms for this NP-hard problem have been proposed in the context of homology modeling, which, however, reach their limits when faced with large protein design instances. In this paper, we propose a new exact method for the side-chain placement problem that works well even for large instance sizes as they appear in protein design. Our main contribution is a dedicated branch-and-bound algorithm that combines tight upper and lower bounds resulting from a novel Lagrangian relaxation approach for side-chain placement. Our experimental results show that our method outperforms alternative state-of-the art exact approaches and makes it possible to optimally solve large protein design instances routinely

Survey propagation at finite temperature: application to a Sourlas code as a toy model

In this paper we investigate a finite temperature generalization of survey propagation, by applying it to the problem of finite temperature decoding of a biased finite connectivity Sourlas code for temperatures lower than the Nishimori temperature. We observe that the result is a shift of the location of the dynamical critical channel noise to larger values than the corresponding dynamical transition for belief propagation, as suggested recently by Migliorini and Saad for LDPC codes. We show how the finite temperature 1-RSB SP gives accurate results in the regime where competing approaches fail to converge or fail to recover the retrieval state

A family resource on prereading skills: Phonemic awareness

Phonemic awareness is an important prereading skill. Although taught in elementary school, prior exposure leads to stronger readers and lack of it is acknowledged as a major contributor to poor reading performance. As parents are often a child's first teacher, accurate and complete information in an easily accessible format is needed to expose phonemic awareness to their child. While access to this information is available through the Internet, it is not collected on a single website. This paper investigates the value and components of phonemic awareness, and whether free, "parent-friendly," complete, and accurate information is easily accessible through the Internet. It also provides a Phonemic Awareness Family Resource Handout directing the user to free websites.Includes bibliographical references (leaves 52-65)California State University, Northridge. Department of Education