Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure

<p>Abstract</p> <p>Background</p> <p>Protein secondary structure prediction provides insight into protein function and is a valuable preliminary step for predicting the 3D structure of a protein. Dynamic Bayesian networks (DBNs) and support vector machines (SVMs) have been shown to provide state-of-the-art performance in secondary structure prediction. As the size of the protein database grows, it becomes feasible to use a richer model in an effort to capture subtle correlations among the amino acids and the predicted labels. In this context, it is beneficial to derive sparse models that discourage over-fitting and provide biological insight.</p> <p>Results</p> <p>In this paper, we first show that we are able to obtain accurate secondary structure predictions. Our per-residue accuracy on a well established and difficult benchmark (CB513) is 80.3%, which is comparable to the state-of-the-art evaluated on this dataset. We then introduce an algorithm for sparsifying the parameters of a DBN. Using this algorithm, we can automatically remove up to 70-95% of the parameters of a DBN while maintaining the same level of predictive accuracy on the SD576 set. At 90% sparsity, we are able to compute predictions three times faster than a fully dense model evaluated on the SD576 set. We also demonstrate, using simulated data, that the algorithm is able to recover true sparse structures with high accuracy, and using real data, that the sparse model identifies known correlation structure (local and non-local) related to different classes of secondary structure elements.</p> <p>Conclusions</p> <p>We present a secondary structure prediction method that employs dynamic Bayesian networks and support vector machines. We also introduce an algorithm for sparsifying the parameters of the dynamic Bayesian network. The sparsification approach yields a significant speed-up in generating predictions, and we demonstrate that the amino acid correlations identified by the algorithm correspond to several known features of protein secondary structure. Datasets and source code used in this study are available at <url>http://noble.gs.washington.edu/proj/pssp</url>.</p

MMPosE: Movie-induced multi-label positive emotion classification through EEG signals

Emotional information plays an important role in various multimedia applications. Movies, as a widely available form of multimedia content, can induce multiple positive emotions and stimulate people's pursuit of a better life. Different from negative emotions, positive emotions are highly correlated and difficult to distinguish in the emotional space. Since different positive emotions are often induced simultaneously by movies, traditional single-target or multi-class methods are not suitable for the classification of movie-induced positive emotions. In this paper, we propose TransEEG, a model for multi-label positive emotion classification from a viewer's brain activities when watching emotional movies. The key features of TransEEG include (1) explicitly modeling the spatial correlation and temporal dependencies of multi-channel EEG signals using the Transformer structure based model, which effectively addresses long-distance dependencies, (2) exploiting the label-label correlations to guide the discriminative EEG representation learning, for that we design an Inter-Emotion Mask for guiding the Multi-Head Attention to learn the inter-emotion correlations, and (3) constructing an attention score vector from the representation-label correlation matrix to refine emotion-relevant EEG features. To evaluate the ability of our model for multi-label positive emotion classification, we demonstrate our model on a state-of-the-art positive emotion database CPED. Extensive experimental results show that our proposed method achieves superior performance over the competitive approaches

Ensemble deep learning: A review

Ensemble learning combines several individual models to obtain better generalization performance. Currently, deep learning models with multilayer processing architecture is showing better performance as compared to the shallow or traditional classification models. Deep ensemble learning models combine the advantages of both the deep learning models as well as the ensemble learning such that the final model has better generalization performance. This paper reviews the state-of-art deep ensemble models and hence serves as an extensive summary for the researchers. The ensemble models are broadly categorised into ensemble models like bagging, boosting and stacking, negative correlation based deep ensemble models, explicit/implicit ensembles, homogeneous /heterogeneous ensemble, decision fusion strategies, unsupervised, semi-supervised, reinforcement learning and online/incremental, multilabel based deep ensemble models. Application of deep ensemble models in different domains is also briefly discussed. Finally, we conclude this paper with some future recommendations and research directions

Data Mining in Smart Grids

Effective smart grid operation requires rapid decisions in a data-rich, but information-limited, environment. In this context, grid sensor data-streaming cannot provide the system operators with the necessary information to act on in the time frames necessary to minimize the impact of the disturbances. Even if there are fast models that can convert the data into information, the smart grid operator must deal with the challenge of not having a full understanding of the context of the information, and, therefore, the information content cannot be used with any high degree of confidence. To address this issue, data mining has been recognized as the most promising enabling technology for improving decision-making processes, providing the right information at the right moment to the right decision-maker. This Special Issue is focused on emerging methodologies for data mining in smart grids. In this area, it addresses many relevant topics, ranging from methods for uncertainty management, to advanced dispatching. This Special Issue not only focuses on methodological breakthroughs and roadmaps in implementing the methodology, but also presents the much-needed sharing of the best practices. Topics include, but are not limited to, the following: Fuzziness in smart grids computing Emerging techniques for renewable energy forecasting Robust and proactive solution of optimal smart grids operation Fuzzy-based smart grids monitoring and control frameworks Granular computing for uncertainty management in smart grids Self-organizing and decentralized paradigms for information processin

Automatic recognition of multiparty human interactions using dynamic Bayesian networks

Relating statistical machine learning approaches to the automatic analysis of multiparty communicative events, such as meetings, is an ambitious research area. We have investigated automatic meeting segmentation both in terms of “Meeting Actions” and “Dialogue Acts”. Dialogue acts model the discourse structure at a fine grained level highlighting individual speaker intentions. Group meeting actions describe the same process at a coarse level, highlighting interactions between different meeting participants and showing overall group intentions. A framework based on probabilistic graphical models such as dynamic Bayesian networks (DBNs) has been investigated for both tasks. Our first set of experiments is concerned with the segmentation and structuring of meetings (recorded using multiple cameras and microphones) into sequences of group meeting actions such as monologue, discussion and presentation. We outline four families of multimodal features based on speaker turns, lexical transcription, prosody, and visual motion that are extracted from the raw audio and video recordings. We relate these lowlevel multimodal features to complex group behaviours proposing a multistreammodelling framework based on dynamic Bayesian networks. Later experiments are concerned with the automatic recognition of Dialogue Acts (DAs) in multiparty conversational speech. We present a joint generative approach based on a switching DBN for DA recognition in which segmentation and classification of DAs are carried out in parallel. This approach models a set of features, related to lexical content and prosody, and incorporates a weighted interpolated factored language model. In conjunction with this joint generative model, we have also investigated the use of a discriminative approach, based on conditional random fields, to perform a reclassification of the segmented DAs. The DBN based approach yielded significant improvements when applied both to the meeting action and the dialogue act recognition task. On both tasks, the DBN framework provided an effective factorisation of the state-space and a flexible infrastructure able to integrate a heterogeneous set of resources such as continuous and discrete multimodal features, and statistical language models. Although our experiments have been principally targeted on multiparty meetings; features, models, and methodologies developed in this thesis can be employed for a wide range of applications. Moreover both group meeting actions and DAs offer valuable insights about the current conversational context providing valuable cues and features for several related research areas such as speaker addressing and focus of attention modelling, automatic speech recognition and understanding, topic and decision detection

Automatic analysis of facial actions: a survey

As one of the most comprehensive and objective ways to describe facial expressions, the Facial Action Coding System (FACS) has recently received significant attention. Over the past 30 years, extensive research has been conducted by psychologists and neuroscientists on various aspects of facial expression analysis using FACS. Automating FACS coding would make this research faster and more widely applicable, opening up new avenues to understanding how we communicate through facial expressions. Such an automated process can also potentially increase the reliability, precision and temporal resolution of coding. This paper provides a comprehensive survey of research into machine analysis of facial actions. We systematically review all components of such systems: pre-processing, feature extraction and machine coding of facial actions. In addition, the existing FACS-coded facial expression databases are summarised. Finally, challenges that have to be addressed to make automatic facial action analysis applicable in real-life situations are extensively discussed. There are two underlying motivations for us to write this survey paper: the first is to provide an up-to-date review of the existing literature, and the second is to offer some insights into the future of machine recognition of facial actions: what are the challenges and opportunities that researchers in the field face

Network Architecture of Unsupervised Boltzmann Machines

Our thesis wants to illustrate recent developments in ANN, and study the topological properties of a specific type of ANN using tools from graph theory. The work is divided in two main parts. First, it presents useful concepts and models. We then focus on understanding the mode of operation of a Deep Belief Network (DBN), a multi-layer neural network that works under the unsupervised learning framework. The second part of this work analyzes a trained DBN (qualified on reading digits images from the popular MNIST database ADD REF) from a network perspective. We inspect the topological properties of the DBN, making use of graph theory. The goal of this unprecedented analysis is to seek a deeper knowledge of the topological modifications that the DBN experiences during the training