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

Category Theoretic Analysis of Hierarchical Protein Materials and Social Networks

Materials in biology span all the scales from Angstroms to meters and typically consist of complex hierarchical assemblies of simple building blocks. Here we describe an application of category theory to describe structural and resulting functional properties of biological protein materials by developing so-called ologs. An olog is like a “concept web” or “semantic network” except that it follows a rigorous mathematical formulation based on category theory. This key difference ensures that an olog is unambiguous, highly adaptable to evolution and change, and suitable for sharing concepts with other olog. We consider simple cases of beta-helical and amyloid-like protein filaments subjected to axial extension and develop an olog representation of their structural and resulting mechanical properties. We also construct a representation of a social network in which people send text-messages to their nearest neighbors and act as a team to perform a task. We show that the olog for the protein and the olog for the social network feature identical category-theoretic representations, and we proceed to precisely explicate the analogy or isomorphism between them. The examples presented here demonstrate that the intrinsic nature of a complex system, which in particular includes a precise relationship between structure and function at different hierarchical levels, can be effectively represented by an olog. This, in turn, allows for comparative studies between disparate materials or fields of application, and results in novel approaches to derive functionality in the design of de novo hierarchical systems. We discuss opportunities and challenges associated with the description of complex biological materials by using ologs as a powerful tool for analysis and design in the context of materiomics, and we present the potential impact of this approach for engineering, life sciences, and medicine.Presidential Early Career Award for Scientists and Engineers (N000141010562)United States. Army Research Office. Multidisciplinary University Research Initiative (W911NF0910541)United States. Office of Naval Research (grant N000141010841)Massachusetts Institute of Technology. Dept. of MathematicsStudienstiftung des deutschen VolkesClark BarwickJacob Luri

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