Word Embeddings for Entity-annotated Texts

Learned vector representations of words are useful tools for many information retrieval and natural language processing tasks due to their ability to capture lexical semantics. However, while many such tasks involve or even rely on named entities as central components, popular word embedding models have so far failed to include entities as first-class citizens. While it seems intuitive that annotating named entities in the training corpus should result in more intelligent word features for downstream tasks, performance issues arise when popular embedding approaches are naively applied to entity annotated corpora. Not only are the resulting entity embeddings less useful than expected, but one also finds that the performance of the non-entity word embeddings degrades in comparison to those trained on the raw, unannotated corpus. In this paper, we investigate approaches to jointly train word and entity embeddings on a large corpus with automatically annotated and linked entities. We discuss two distinct approaches to the generation of such embeddings, namely the training of state-of-the-art embeddings on raw-text and annotated versions of the corpus, as well as node embeddings of a co-occurrence graph representation of the annotated corpus. We compare the performance of annotated embeddings and classical word embeddings on a variety of word similarity, analogy, and clustering evaluation tasks, and investigate their performance in entity-specific tasks. Our findings show that it takes more than training popular word embedding models on an annotated corpus to create entity embeddings with acceptable performance on common test cases. Based on these results, we discuss how and when node embeddings of the co-occurrence graph representation of the text can restore the performance.Comment: This paper is accepted in 41st European Conference on Information Retrieva

Tadpole renormalization and relativistic corrections in lattice NRQCD

We make a comparison of two tadpole renormalization schemes in the context of the quarkonium hyperfine splittings in lattice NRQCD. Improved gauge-field and NRQCD actions are analyzed using the mean-link $u_{0,L}$ in Landau gauge, and using the fourth root of the average plaquette $u_{0,P}$. Simulations are done for $c\bar c$, $b\bar c$, and $b\bar b$ systems. The hyperfine splittings are computed both at leading and at next-to-leading order in the relativistic expansion. Results are obtained at lattice spacings in the range of about 0.14~fm to 0.38~fm. A number of features emerge, all of which favor tadpole renormalization using $u_{0,L}$. This includes much better scaling behavior of the hyperfine splittings in the three quarkonium systems when $u_{0,L}$ is used. We also find that relativistic corrections to the spin splittings are smaller when $u_{0,L}$ is used, particularly for the $c\bar c$ and $b\bar c$ systems. We also see signs of a breakdown in the NRQCD expansion when the bare quark mass falls below about one in lattice units. Simulations with $u_{0,L}$ also appear to be better behaved in this context: the bare quark masses turn out to be larger when $u_{0,L}$ is used, compared to when $u_{0,P}$ is used on lattices with comparable spacings. These results also demonstrate the need to go beyond tree-level tadpole improvement for precision simulations.Comment: 14 pages, 7 figures (minor changes to some phraseology and references

Analysis of a Large Sample of Neutrino-Induced Muons with the ArgoNeuT Detector

ArgoNeuT, or Argon Neutrino Test, is a 170 liter liquid argon time projection chamber designed to collect neutrino interactions from the NuMI beam at Fermi National Accelerator Laboratory. ArgoNeuT operated in the NuMI low-energy beam line directly upstream of the MINOS Near Detector from September 2009 to February 2010, during which thousands of neutrino and antineutrino events were collected. The MINOS Near Detector was used to measure muons downstream of ArgoNeuT. Though ArgoNeuT is primarily an R&D project, the data collected provide a unique opportunity to measure neutrino cross sections in the 0.1-10 GeV energy range. Fully reconstructing the muon from these interactions is imperative for these measurements. This paper focuses on the complete kinematic reconstruction of neutrino-induced through-going muons tracks. Analysis of this high statistics sample of minimum ionizing tracks demonstrates the reliability of the geometric and calorimetric reconstruction in the ArgoNeuT detector

ArgoNeuT and the Neutrino-Argon Charged Current Quasi-Elastic Cross Section

ArgoNeuT, a Liquid Argon Time Projection Chamber in the NuMI beamline at Fermilab, has recently collected thousands of neutrino and anti-neutrino events between 0.1 and 10 GeV. The experiment will, among other things, measure the cross section of the neutrino and anti-neutrino Charged Current Quasi-Elastic interaction and analyze the vertex activity associated with such events. These topics are discussed along with ArgoNeuT's automated reconstruction software, currently capable of fully reconstructing the muon and finding the event vertex in neutrino interactions.Comment: 6 pages, 4 figures, presented at the International Nuclear Physics Conference, Vancouver, Canada, July 4-9, 2010, to be published in Journal of Physics: Conference Series (JPCS

A phenomenological approach to the simulation of metabolism and proliferation dynamics of large tumour cell populations

A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a simplified model of cell metabolism, growth and proliferation, suitable for inclusion in a multicell simulator, now under development (Chignola R and Milotti E 2004 Physica A 338 261-6). Nutrients regulate the proliferation dynamics of tumor cells which adapt their behaviour to respond to changes in the biochemical composition of the environment. This modeling of nutrient metabolism and cell cycle at a mesoscopic scale level leads to a continuous flow of information between the two disparate spatiotemporal scales of molecular and cellular dynamics that can be simulated with modern computers and tested experimentally.Comment: 58 pages, 7 figures, 3 tables, pdf onl

First Measurement of Monoenergetic Muon Neutrino Charged Current Interactions

We report the first measurement of monoenergetic muon neutrino charged current interactions. MiniBooNE has isolated 236 MeV muon neutrino events originating from charged kaon decay at rest ($K^+ \rightarrow \mu^+ \nu_\mu$) at the NuMI beamline absorber. These signal $\nu_\mu$-carbon events are distinguished from primarily pion decay in flight $\nu_\mu$ and $\overline{\nu}_\mu$ backgrounds produced at the target station and decay pipe using their arrival time and reconstructed muon energy. The significance of the signal observation is at the 3.9$\sigma$ level. The muon kinetic energy, neutrino-nucleus energy transfer ($\omega=E_\nu-E_\mu$), and total cross section for these events is extracted. This result is the first known-energy, weak-interaction-only probe of the nucleus to yield a measurement of $\omega$ using neutrinos, a quantity thus far only accessible through electron scattering.Comment: 6 pages, 4 figure