DutchHatTrick: semantic query modeling, ConText, section detection, and match score maximization

This report discusses the collaborative work of the ErasmusMC, University of Twente, and the University of Amsterdam on the TREC 2011 Medical track. Here, the task is to retrieve patient visits from the University of Pittsburgh NLP Repository for 35 topics. The repository consists of 101,711 patient reports, and a patient visit was recorded in one or more reports

An Extended Relevance Model for Session Search

The session search task aims at best serving the user's information need given her previous search behavior during the session. We propose an extended relevance model that captures the user's dynamic information need in the session. Our relevance modelling approach is directly driven by the user's query reformulation (change) decisions and the estimate of how much the user's search behavior affects such decisions. Overall, we demonstrate that, the proposed approach significantly boosts session search performance

The EU, the WTO and indirect land use change

Efforts to meet the European Union’s (EU) alternative energy targets have resulted in increased production of biofuels. This production has resulted in deforestation-related emissions through displacement of agricultural production, a problem known as indirect land-use change. The European Commission (EC) has proposed regulatory options to respond to this problem, but all risk not being in conformity with World Trade Organization (WTO) law.Trade law challenges result from the underlying methodological uncertainty, and the attempt to address a systemic problem on the level of individual producers.Yet, this does not necessarily indicate that the intent of these regulations is to protect EU markets.Thus, this is an instructive case study to examine the relationship between WTO law and complex, emerging environmental problems

Kolmogorov Complexity in perspective. Part II: Classification, Information Processing and Duality

We survey diverse approaches to the notion of information: from Shannon entropy to Kolmogorov complexity. Two of the main applications of Kolmogorov complexity are presented: randomness and classification. The survey is divided in two parts published in a same volume. Part II is dedicated to the relation between logic and information system, within the scope of Kolmogorov algorithmic information theory. We present a recent application of Kolmogorov complexity: classification using compression, an idea with provocative implementation by authors such as Bennett, Vitanyi and Cilibrasi. This stresses how Kolmogorov complexity, besides being a foundation to randomness, is also related to classification. Another approach to classification is also considered: the so-called "Google classification". It uses another original and attractive idea which is connected to the classification using compression and to Kolmogorov complexity from a conceptual point of view. We present and unify these different approaches to classification in terms of Bottom-Up versus Top-Down operational modes, of which we point the fundamental principles and the underlying duality. We look at the way these two dual modes are used in different approaches to information system, particularly the relational model for database introduced by Codd in the 70's. This allows to point out diverse forms of a fundamental duality. These operational modes are also reinterpreted in the context of the comprehension schema of axiomatic set theory ZF. This leads us to develop how Kolmogorov's complexity is linked to intensionality, abstraction, classification and information system.Comment: 43 page

Finding Cycles and Trees in Sublinear Time

We present sublinear-time (randomized) algorithms for finding simple cycles of length at least $k\geq 3$ and tree-minors in bounded-degree graphs. The complexity of these algorithms is related to the distance of the graph from being $C_k$-minor-free (resp., free from having the corresponding tree-minor). In particular, if the graph is far (i.e., $\Omega(1)$-far) {from} being cycle-free, i.e. if one has to delete a constant fraction of edges to make it cycle-free, then the algorithm finds a cycle of polylogarithmic length in time \tildeO(\sqrt{N}), where $N$ denotes the number of vertices. This time complexity is optimal up to polylogarithmic factors. The foregoing results are the outcome of our study of the complexity of {\em one-sided error} property testing algorithms in the bounded-degree graphs model. For example, we show that cycle-freeness of $N$-vertex graphs can be tested with one-sided error within time complexity \tildeO(\poly(1/\e)\cdot\sqrt{N}). This matches the known $\Omega(\sqrt{N})$ query lower bound, and contrasts with the fact that any minor-free property admits a {\em two-sided error} tester of query complexity that only depends on the proximity parameter \e. For any constant $k\geq3$, we extend this result to testing whether the input graph has a simple cycle of length at least $k$. On the other hand, for any fixed tree $T$, we show that $T$-minor-freeness has a one-sided error tester of query complexity that only depends on the proximity parameter \e. Our algorithm for finding cycles in bounded-degree graphs extends to general graphs, where distances are measured with respect to the actual number of edges. Such an extension is not possible with respect to finding tree-minors in $o(\sqrt{N})$ complexity.Comment: Keywords: Sublinear-Time Algorithms, Property Testing, Bounded-Degree Graphs, One-Sided vs Two-Sided Error Probability Updated versio

3D mapping of young stars in the solar neighbourhood with Gaia DR2

We study the three dimensional arrangement of young stars in the solar neighbourhood using the second release of the Gaia mission (Gaia DR2) and we provide a new, original view of the spatial configuration of the star forming regions within 500 pc from the Sun. By smoothing the star distribution through a gaussian filter, we construct three dimensional density maps for early-type stars (upper-main sequence, UMS) and pre-main sequence (PMS) sources. The PMS and the UMS samples are selected through a combination of photometric and astrometric criteria. A side product of the analysis is a three dimensional, G-band extinction map, which we use to correct our colour-magnitude diagram for extinction and reddening. Both density maps show three prominent structures, Scorpius-Centaurus, Orion, and Vela. The PMS map shows a plethora of lower mass star forming regions, such as Taurus, Perseus, Cepheus, Cassiopeia, and Lacerta, which are less visible in the UMS map, due to the lack of large numbers of bright, early-type stars. We report the finding of a candidate new open cluster towards $l, b \sim 218.5^{\circ}, -2^{\circ}$, which could be related to the Orion star forming complex. We estimate ages for the PMS sample and we study the distribution of PMS stars as a function of their age. We find that younger stars cluster in dense, compact clumps, and are surrounded by older sources, whose distribution is instead more diffuse. The youngest groups that we find are mainly located in Scorpius-Centaurus, Orion, Vela, and Taurus. Cepheus, Cassiopeia, and Lacerta are instead more evolved and less numerous. Finally, we find that the three dimensional density maps show no evidence for the existence of the ring-like structure which is usually referred to as the Gould Belt.Comment: 17 pages, 17 figures, 6 appendixes; accepted for publication in A&A; image quality decreased to comply with the arXiv.org rules on file siz

THE KINETIC CHARACTERIZATION OF TWO PUTATIVE GALACTOSIDASES, BT2857 AND SCO6594, AND THE PRELIMINARY ANALYSES OF SCO6595-97

Bacteroides thetaiotaomicron is a prolific bacterium found in the distal intestinal tract of humans that possesses the ability to breakdown complex polysaccharides through the release of carbohydrate-active enzymes (CAZymes). Overall, the saccharolytic prowess of B. thetaiotaomicron presents an intriguing model for understanding microbial-host nutrient exchange within the gut and to identify novel mechanisms for accessing carbohydrates. The successful expression, purification, and preliminary kinetic characterization of BT2857 are reported. BT2857 was found to be enzymatically active against the artificial substrate, 4-nitrophenyl β-D-galactopyranoside (pNP-Gal); suggesting its role as a putative β-galactosidase and allowed for the quantification of BT2857 activity by the determination of the Michaelis-Menten parameters kcat, KM, and Vmax. A combinatorial molecular modeling approach of genomic context predicted a two-domain structure formed primarily of beta-sheets and loops. Polysaccharide Utilization Loci (PUL) analysis revealed BT2851-55 collectively belonging to GH36, GH42, GH3 and GH2 providing insight on potential substrates downstream from BT2857. The natural substrate remains unknown despite experiments demonstrating the upregulation of this region of the B.thetaiotaomicron genome in the presence of varying carbohydrates. Crystallization of the truncations of BT2857 will be a key finding for structure and functional characterization. Streptomyces coelicolor is the representative species within its genus and predominantly found in soil with access to a diverse environment of carbohydrate sources. The main contribution of S. coelicolor is the metabolism of insoluble remains from plants ii and animals indicating positive improvements on plant growth and the rhizosphere. To date, the kinetic characterization of a putative galactosidase, SCO6594 has been explored including the determination of Michaelis-Menten parameters. Solubility screening of SCO6595-67 also display potential expression and characterization of this gene cluster will enable an understanding of protein regulation and carbohydrate interaction