Mix 'n Match: Integrating Text Matching and Product Substitutability within Product Search

Two products are substitutes if both can satisfy the same consumer need. Intrinsic incorporation of product substitutability - where substitutability is integrated within latent vector space models - is in contrast to the extrinsic re-ranking of result lists. The fusion of text matching and product substitutability objectives allows latent vector space models to mix and match regularities contained within text descriptions and substitution relations. We introduce a method for intrinsically incorporating product substitutability within latent vector space models for product search that are estimated using gradient descent; it integrates flawlessly with state-of-the-art vector space models. We compare our method to existing methods for incorporating structural entity relations, where product substitutability is incorporated extrinsically by re-ranking. Our method outperforms the best extrinsic method on four benchmarks. We investigate the effect of different levels of text matching and product similarity objectives, and provide an analysis of the effect of incorporating product substitutability on product search ranking diversity. Incorporating product substitutability information improves search relevance at the cost of diversity

The Apollo ATCA Platform

We have developed a novel and generic open-source platform - Apollo - which simplifies the design of custom Advanced Telecommunications Computing Architecture (ATCA) blades by factoring the design into generic infrastructure and application-specific parts. The Apollo "Service Module" provides the required ATCA Intelligent Platform Management Controller, power entry and conditioning, a powerful system-on-module (SoM) computer, and flexible clock and communications infrastructure. The Apollo "Command Module" is customized for each application and typically includes two large field-programmable gate arrays, several hundred optical fiber interfaces operating at speeds up to 28 Gbps, memories, and other supporting infrastructure. The command and service module boards can be operated together or independently on the bench without need for an ATCA shelf.Comment: Submitted to the Proceedings for TWEPP 201

So what do we really mean when we say that systems biology is holistic?

Background: An old debate has undergone a resurgence in systems biology: that of reductionism versus holism. At least 35 articles in the systems biology literature since 2003 have touched on this issue. The histories of holism and reductionism in the philosophy of biology are reviewed, and the current debate in systems biology is placed in context. Results: Inter-theoretic reductionism in the strict sense envisaged by its creators from the 1930s to the 1960s is largely impractical in biology, and was effectively abandoned by the early 1970s in favour of a more piecemeal approach using individual reductive explanations. Classical holism was a stillborn theory of the 1920s, but the term survived in several fields as a loose umbrella designation for various kinds of anti-reductionism which often differ markedly. Several of these different anti-reductionisms are on display in the holistic rhetoric of the recent systems biology literature. This debate also coincides with a time when interesting arguments are being proposed within the philosophy of biology for a new kind of reductionism. Conclusions: Engaging more deeply with these issues should sharpen our ideas concerning the philosophy of systems biology and its future best methodology. As with previous decisive moments in the history of biology, only those theories that immediately suggest relatively easy experiments will be winners

Integrative Network Biology: Graph Prototyping for Co-Expression Cancer Networks

Network-based analysis has been proven useful in biologically-oriented areas, e.g., to explore the dynamics and complexity of biological networks. Investigating a set of networks allows deriving general knowledge about the underlying topological and functional properties. The integrative analysis of networks typically combines networks from different studies that investigate the same or similar research questions. In order to perform an integrative analysis it is often necessary to compare the properties of matching edges across the data set. This identification of common edges is often burdensome and computational intensive. Here, we present an approach that is different from inferring a new network based on common features. Instead, we select one network as a graph prototype, which then represents a set of comparable network objects, as it has the least average distance to all other networks in the same set. We demonstrate the usefulness of the graph prototyping approach on a set of prostate cancer networks and a set of corresponding benign networks. We further show that the distances within the cancer group and the benign group are statistically different depending on the utilized distance measure