Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions.

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Abstract-A new signal classification approach is presented that is based upon modeling the dynamics of a system as they are captured in a reconstructed phase space. The modeling is done using full covariance Gaussian Mixture Models of time domain signatures, in contrast with current and previous work in signal classification that is typically focused on either linear systems analysis using frequency content or simple nonlinear machine learning models such as artificial neural networks. The proposed approach has strong theoretical foundations based on dynamical systems and topological theorems, resulting in a signal reconstruction, which is asymptotically guaranteed to be a complete representation of the underlying system, given properly chosen parameters. The algorithm automatically calculates these parameters to form appropriate reconstructed phase spaces, requiring only the number of mixtures, the signals, and their class labels as input. Three separate data sets are used for validation, including motor current simulations, electrocardiogram recordings, and speech waveforms. The results show that the proposed method is robust across these diverse domains, significantly outperforming the time delay neural network used as a baseline.

This paper introduces a novel approach to the analysis and classification of time series signals using statistical models of reconstructed phase spaces. With sufficient dimension, such reconstructed phase spaces are, with probability one, guaranteed to be topologically equivalent to the state dynamics of the generating system, and, therefore, may contain information that is absent in analysis and classification methods rooted in linear assumptions. Parametric and nonparametric distributions are introduced as statistical representations over the multidimensional reconstructed phase space, with classification accomplished through methods such as Bayes maximum likelihood and artificial neural networks (ANNs). The technique is demonstrated on heart arrhythmia classification and speech recognition. This new approach is shown to be a viable and effective alternative to traditional signal classification approaches, particularly for signals with strong nonlinear characteristics.

Deep neural networks are proposed for short-term natural gas load forecasting. Deep learning has proven to be a powerful tool for many classification problems seeing significant use in machine learning fields such as image recognition and speech processing. We provide an overview of natural gas forecasting. Next, the deep learning method, contrastive divergence is explained. We compare our proposed deep neural network method to a linear regression model and a traditional artificial neural network on 62 operating areas, each of which has at least 10 years of data. The proposed deep network outperforms traditional artificial neural networks by 9.83% weighted mean absolute percent error (WMAPE).

Background Near infrared spectroscopy (NIRS) is currently complementing techniques to age-grade mosquitoes. NIRS classifies lab-reared and semi-field raised mosquitoes into < or ≥ 7 days old with an average accuracy of 80%, achieved by training a regression model using partial least squares (PLS) and interpreted as a binary classifier. Methods and findings We explore whether using an artificial neural network (ANN) analysis instead of PLS regression improves the current accuracy of NIRS models for age-grading malaria transmitting mosquitoes. We also explore if directly training a binary classifier instead of training a regression model and interpreting it as a binary classifier improves the accuracy. A total of 786 and 870 NIR spectra collected from laboratory reared An . gambiae and An . arabiensis , respectively, were used and pre-processed according to previously published protocols. The ANN regression model scored root mean squared error (RMSE) of 1.6 ± 0.2 for An . gambiae and 2.8 ± 0.2 for An . arabiensis ; whereas the PLS regression model scored RMSE of 3.7 ± 0.2 for An . gambiae , and 4.5 ± 0.1 for An . arabiensis . When we interpreted regression models as binary classifiers, the accuracy of the ANN regression model was 93.7 ± 1.0% for An . gambiae , and 90.2 ± 1.7% for An . arabiensis ; while PLS regression model scored the accuracy of 83.9 ± 2.3% for An . gambiae , and 80.3 ± 2.1% for An . arabiensis . We also find that a directly trained binary classifier yields higher age estimation accuracy than a regression model interpreted as a binary classifier. A directly trained ANN binary classifier scored an accuracy of 99.4 ± 1.0 for An . gambiae and 99.0 ± 0.6% for An . arabiensis ; while a directly trained PLS binary classifier scored 93.6 ± 1.2% for An . gambiae and 88.7 ± 1.1% for An . arabiensis . We further tested the reproducibility of these results on different independent mosquito datasets. ANNs scored higher estimation accuracies than when the same age models are trained using PLS. Regardless of the model architecture, directly trained binary classifiers scored higher accuracies on classifying age of mosquitoes than regression models translated as binary classifiers. Conclusion We ...

Abstract. The novel Time Series Data Mining (TSDM) framework is applied to analyzing financial time series. The TSDM framework adapts and innovates data mining concepts to analyzing time series data. In particular, it creates a set of methods that reveal hidden temporal patterns that are characteristic and predictive of time series events. This contrasts with other time series analysis techniques, which typically characterize and predict all observations. The TSDM framework and concepts are reviewed, and the applicable TSDM method is discussed. Finally, the TSDM method is applied to time series generated by a basket of financial securities. The results show that statistically significant temporal patterns that are both characteristic and predictive of events in financial time series can be identified.