Attending to characters in neural sequence labeling models

Sequence labeling architectures use word embeddings for capturing similarity, but suffer when handling previously unseen or rare words. We investigate character-level extensions to such models and propose a novel architecture for combining alternative word representations. By using an attention mechanism, the model is able to dynamically decide how much information to use from a word- or character-level component. We evaluated different architectures on a range of sequence labeling datasets, and character-level extensions were found to improve performance on every benchmark. In addition, the proposed attention-based architecture delivered the best results even with a smaller number of trainable parameters

Variable typing: Assigning meaning to variables in mathematical text

Information about the meaning of mathematical variables in text is useful in NLP/IR tasks such as symbol disambiguation, topic modeling and mathematical information retrieval (MIR). We introduce variable typing, the task of assigning one mathematical type (multi-word technical terms referring to mathematical concepts) to each variable in a sentence of mathematical text. As part of this work, we also introduce a new annotated data set composed of 33,524 data points extracted from scientific documents published on arXiv. Our intrinsic evaluation demonstrates that our data set is sufficient to successfully train and evaluate current classifiers from three different model architectures. The best performing model is evaluated on an extrinsic task: MIR, by producing a typed formula index. Our results show that the best performing MIR models make use of our typed index, compared to a formula index only containing raw symbols, thereby demonstrating the usefulness of variable typing

Assessment of a Large-Scale Unbiased Malignant Pleural Effusion Proteomics Study of a Real-Life Cohort

Background: Pleural effusion (PE) is common in advanced-stage lung cancer patients and is related to poor prognosis. Identification of cancer cells is the standard method for the diagnosis of a malignant PE (MPE). However, it only has moderate sensitivity. Thus, more sensitive diagnostic tools are urgently needed. Methods: The present study aimed to discover potential protein targets to distinguish malignant pleural effusion (MPE) from other non-malignant pathologies. We have collected PE from 97 patients to explore PE proteomes by applying state-of-the-art liquid chromatography-mass spectrometry (LC-MS) to identify potential biomarkers that correlate with immunohistochemistry assessment of tumor biopsy or with survival data. Functional analyses were performed to elucidate functional differences in PE proteins in malignant and benign samples. Results were integrated into a clinical risk prediction model to identify likely malignant cases. Sensitivity, specificity, and negative predictive value were calculated. Results: In total, 1689 individual proteins were identified by MS-based proteomics analysis of the 97 PE samples, of which 35 were diagnosed as malignant. A comparison between MPE and benign PE (BPE) identified 58 differential regulated proteins after correction of the p-values for multiple testing. Furthermore, functional analysis revealed an up-regulation of matrix intermediate filaments and cellular movement-related proteins. Additionally, gene ontology analysis identified the involvement of metabolic pathways such as glycolysis/gluconeogenesis, pyruvate metabolism and cysteine and methionine metabolism. Conclusion: This study demonstrated a partial least squares regression model with an area under the curve of 98 and an accuracy of 0.92 when evaluated on the holdout test data set. Furthermore, highly significant survival markers were identified (e.g., PSME1 with a log-rank of 1.68 × 10−6 ).info:eu-repo/semantics/publishedVersio

Discrete Painlevé equations from Y-systems

We consider T-systems and Y-systems arising from cluster mutations applied to quivers that have the property of being periodic under a sequence of mutations. The corresponding nonlinear recurrences for cluster variables (coefficient-free T-systems) were described in the work of Fordy and Marsh, who completely classified all such quivers in the case of period 1, and characterized them in terms of the skew-symmetric exchange matrix B that defines the quiver. A broader notion of periodicity in general cluster algebras was introduced by Nakanishi, who also described the corresponding Y-systems, and T-systems with coefficients. A result of Fomin and Zelevinsky says that the coefficient-free T-system provides a solution of the Y-system. In this paper, we show that in general there is a discrepancy between these two systems, in the sense that the solution of the former does not correspond to the general solution of the latter. This discrepancy is removed by introducing additional non-autonomous coefficients into the T-system. In particular, we focus on the period 1 case and show that, when the exchange matrix B is degenerate, discrete Painlev\'e equations can arise from this construction

Integrable structure of box-ball systems: crystal, Bethe ansatz, ultradiscretization and tropical geometry

The box-ball system is an integrable cellular automaton on one dimensional lattice. It arises from either quantum or classical integrable systems by the procedures called crystallization and ultradiscretization, respectively. The double origin of the integrability has endowed the box-ball system with a variety of aspects related to Yang-Baxter integrable models in statistical mechanics, crystal base theory in quantum groups, combinatorial Bethe ansatz, geometric crystals, classical theory of solitons, tau functions, inverse scattering method, action-angle variables and invariant tori in completely integrable systems, spectral curves, tropical geometry and so forth. In this review article, we demonstrate these integrable structures of the box-ball system and its generalizations based on the developments in the last two decades.Comment: 73 page

A tropical analogue of Fay's trisecant identity and the ultra-discrete periodic Toda lattice

We introduce a tropical analogue of Fay's trisecant identity for a special family of hyperelliptic tropical curves. We apply it to obtain the general solution of the ultra-discrete Toda lattice with periodic boundary conditions in terms of the tropical Riemann's theta function.Comment: 25 pages, 3 figure

Polaronic Signatures in Mid-Infrared Spectra: Prediction for LaMnO3 and CaMnO3

Hole-doped LaMnO3 and electron-doped CaMnO3 form self-trapped electronic states. The spectra of these states have been calculated using a two orbital (Mn eg Jahn-Teller) model, from which the non-adiabatic optical conductivity spectra are obtained. In both cases the optical spectrum contains weight in the gap region, whose observation will indicate the self-trapped nature of the carrier states. The predicted spectra are proportional to the concentration of the doped carriers in the dilute regime, with coefficients calculated with no further model parameters.Comment: 6 pages with 3 figures imbedde

Genipin-cross-linked collagen/chitosan biomimetic scaffolds for articular cartilage tissue engineering applications

This was the first study to use genipin to cross-link collagen and chitosan.In this study, genipin-cross-linked collagen/chitosan biodegradable porous scaffolds were prepared for articular cartilage regeneration. The influence of chitosan amount and genipin concentration on the scaffolds physicochemical properties was evaluated. The morphologies of the scaffolds were characterized by scanning electron microscope (SEM) and cross-linking degree was investigated by ninhydrin assay. Additionally, the mechanical properties of the scaffolds were assessed under dynamic compression. To study the swelling ratio and the biostability of the collagen/chitosan scaffold, in vitro tests were also carried out by immersion of the scaffolds in PBS solution or digestion in collagenase, respectively. The results showed that the morphologies of the scaffolds underwent a fiber-like to a sheet-like structural transition by increasing chitosan amount. Genipin cross-linking remarkably changed the morphologies and pore sizes of the scaffolds when chitosan amount was less than 25%. Either by increasing the chitosan ratio or performing cross-linking treatment, the swelling ratio of the scaffolds can be tailored. The ninhydrin assay demonstrated that the addition of chitosan could obviously increase the cross-linking efficiency. The degradation studies indicated that genipin cross-linking can effectively enhance the biostability of the scaffolds. The biocompatibility of the scaffolds was evaluated by culturing rabbit chondrocytes in vitro. This study demonstrated that a good viability of the chondrocytes seeded on the scaffold was achieved. The SEM analysis has revealed that the chondrocytes adhered well to the surface of the scaffolds and contacted each other. These results suggest that the genipin-cross-linked collagen/chitosan matrix may be a promising formulation for articular cartilage scaffolding.Key Projects in the National Science and Technology Pillar Program in the Eleventh Five-year Plan Period. Grant Number: 2006BA116B04Guangdong Natural Science Foundation. Grant Number: 07300602Natural Science Foundation Team Project of Guangdong. Grant Number: 4205786State Key Program of National Natural Science of China. Grant Number: 50732003National Basic Research Program of China. Grant Number: 2005CB62390