Inferring Effective Connectivity Networks From fMRI Time Series With a Temporal Entropy-Score.

Inferring brain-effective connectivity networks from neuroimaging data has become a very hot topic in neuroinformatics and bioinformatics. In recent years, the search methods based on Bayesian network score have been greatly developed and become an emerging method for inferring effective connectivity. However, the previous score functions ignore the temporal information from functional magnetic resonance imaging (fMRI) series data and may not be able to determine all orientations in some cases. In this article, we propose a novel score function for inferring effective connectivity from fMRI data based on the conditional entropy and transfer entropy (TE) between brain regions. The new score employs the TE to capture the temporal information and can effectively infer connection directions between brain regions. Experimental results on both simulated and real-world data demonstrate the efficacy of our proposed score function.

Continual representation learning for evolving biomedical bipartite networks.

MOTIVATION: Many real-world biomedical interactions such as 'gene-disease', 'disease-symptom' and 'drug-target' are modeled as a bipartite network structure. Learning meaningful representations for such networks is a fundamental problem in the research area of Network Representation Learning (NRL). NRL approaches aim to translate the network structure into low-dimensional vector representations that are useful to a variety of biomedical applications. Despite significant advances, the existing approaches still have certain limitations. First, a majority of these approaches do not model the unique topological properties of bipartite networks. Consequently, their straightforward application to the bipartite graphs yields unsatisfactory results. Second, the existing approaches typically learn representations from static networks. This is limiting for the biomedical bipartite networks that evolve at a rapid pace, and thus necessitate the development of approaches that can update the representations in an online fashion. RESULTS: In this research, we propose a novel representation learning approach that accurately preserves the intricate bipartite structure, and efficiently updates the node representations. Specifically, we design a customized autoencoder that captures the proximity relationship between nodes participating in the bipartite bicliques (2 × 2 sub-graph), while preserving both the global and local structures. Moreover, the proposed structure-preserving technique is carefully interleaved with the central tenets of continual machine learning to design an incremental learning strategy that updates the node representations in an online manner. Taken together, the proposed approach produces meaningful representations with high fidelity and computational efficiency. Extensive experiments conducted on several biomedical bipartite networks validate the effectiveness and rationality of the proposed approach.

A hybrid self-attention deep learning framework for multivariate sleep stage classification.

BACKGROUND: Sleep is a complex and dynamic biological process characterized by different sleep patterns. Comprehensive sleep monitoring and analysis using multivariate polysomnography (PSG) records has achieved significant efforts to prevent sleep-related disorders. To alleviate the time consumption caused by manual visual inspection of PSG, automatic multivariate sleep stage classification has become an important research topic in medical and bioinformatics. RESULTS: We present a unified hybrid self-attention deep learning framework, namely HybridAtt, to automatically classify sleep stages by capturing channel and temporal correlations from multivariate PSG records. We construct a new multi-view convolutional representation module to learn channel-specific and global view features from the heterogeneous PSG inputs. The hybrid attention mechanism is designed to further fuse the multi-view features by inferring their dependencies without any additional supervision. The learned attentional representation is subsequently fed through a softmax layer to train an end-to-end deep learning model. CONCLUSIONS: We empirically evaluate our proposed HybridAtt model on a benchmark PSG dataset in two feature domains, referred to as the time and frequency domains. Experimental results show that HybridAtt consistently outperforms ten baseline methods in both feature spaces, demonstrating the effectiveness of HybridAtt in the task of sleep stage classification.

MeSHProbeNet: a self-attentive probe net for MeSH indexing.

MOTIVATION: MEDLINE is the primary bibliographic database maintained by National Library of Medicine (NLM). MEDLINE citations are indexed with Medical Subject Headings (MeSH), which is a controlled vocabulary curated by the NLM experts. This greatly facilitates the applications of biomedical research and knowledge discovery. Currently, MeSH indexing is manually performed by human experts. To reduce the time and monetary cost associated with manual annotation, many automatic MeSH indexing systems have been proposed to assist manual annotation, including DeepMeSH and NLM's official model Medical Text Indexer (MTI). However, the existing models usually rely on the intermediate results of other models and suffer from efficiency issues. We propose an end-to-end framework, MeSHProbeNet (formerly named as xgx), which utilizes deep learning and self-attentive MeSH probes to index MeSH terms. Each MeSH probe enables the model to extract one specific aspect of biomedical knowledge from an input article, thus comprehensive biomedical information can be extracted with different MeSH probes and interpretability can be achieved at word level. MeSH terms are finally recommended with a unified classifier, making MeSHProbeNet both time efficient and space efficient. RESULTS: MeSHProbeNet won the first place in the latest batch of Task A in the 2018 BioASQ challenge. The result on the last test set of the challenge is reported in this paper. Compared with other state-of-the-art models, such as MTI and DeepMeSH, MeSHProbeNet achieves the highest scores in all the F-measures, including Example Based F-Measure, Macro F-Measure, Micro F-Measure, Hierarchical F-Measure and Lowest Common Ancestor F-measure. We also intuitively show how MeSHProbeNet is able to extract comprehensive biomedical knowledge from an input article.

A Multi-View Deep Learning Framework for EEG Seizure Detection.

The recent advances in pervasive sensing technologies have enabled us to monitor and analyze the multi-channel electroencephalogram (EEG) signals of epilepsy patients to prevent serious outcomes caused by epileptic seizures. To avoid manual visual inspection from long-term EEG readings, automatic EEG seizure detection has garnered increasing attention among researchers. In this paper, we present a unified multi-view deep learning framework to capture brain abnormalities associated with seizures based on multi-channel scalp EEG signals. The proposed approach is an end-to-end model that is able to jointly learn multi-view features from both unsupervised multi-channel EEG reconstruction and supervised seizure detection via spectrogram representation. We construct a new autoencoder-based multi-view learning model by incorporating both inter and intra correlations of EEG channels to unleash the power of multi-channel information. By adding a channel-wise competition mechanism in the training phase, we propose a channel-aware seizure detection module to guide our multi-view structure to focus on important and relevant EEG channels. To validate the effectiveness of the proposed framework, extensive experiments against nine baselines, including both traditional handcrafted feature extraction and conventional deep learning methods, are carried out on a benchmark scalp EEG dataset. Experimental results show that the proposed model is able to achieve higher average accuracy and f1-score at 94.37% and 85.34%, respectively, using 5-fold subject-independent cross validation, demonstrating a powerful and effective method in the task of EEG seizure detection.

A multi-context learning approach for EEG epileptic seizure detection.

BACKGROUND: Epilepsy is a neurological disease characterized by unprovoked seizures in the brain. The recent advances in sensor technologies allow researchers to analyze the collected biological records to improve the treatment of epilepsy. Electroencephalogram (EEG) is the most commonly used biological measurement to effectively capture the abnormalities of different brain areas during the EEG seizures. To avoid manual visual inspection from long-term EEG readings, automatic epileptic EEG seizure detection has become an important research issue in bioinformatics. RESULTS: We present a multi-context learning approach to automatically detect EEG seizures by incorporating a feature fusion strategy. We generate EEG scalogram sequences from the EEG records by utilizing waveform transform to describe the frequency content over time. We propose a multi-stage unsupervised model that integrates the features extracted from the global handcrafted engineering, channel-wise deep learning, and EEG embeddings, respectively. The learned multi-context features are subsequently merged to train a seizure detector. CONCLUSIONS: To validate the effectiveness of the proposed approach, extensive experiments against several baseline methods are carried out on two benchmark biological datasets. The experimental results demonstrate that the representative context features from multiple perspectives can be learned by the proposed model, and further improve the performance for the task of EEG seizure detection.

Towards self-learning based hypotheses generation in biomedical text domain.

Motivation: The overwhelming amount of research articles in the domain of bio-medicine might cause important connections to remain unnoticed. Literature Based Discovery is a sub-field within biomedical text mining that peruses these articles to formulate high confident hypotheses on possible connections between medical concepts. Although many alternate methodologies have been proposed over the last decade, they still suffer from scalability issues. The primary reason, apart from the dense inter-connections between biological concepts, is the absence of information on the factors that lead to the edge-formation. In this work, we formulate this problem as a collaborative filtering task and leverage a relatively new concept of word-vectors to learn and mimic the implicit edge-formation process. Along with single-class classifier, we prune the search-space of redundant and irrelevant hypotheses to increase the efficiency of the system and at the same time maintaining and in some cases even boosting the overall accuracy. Results: We show that our proposed framework is able to prune up to 90% of the hypotheses while still retaining high recall in top-K results. This level of efficiency enables the discovery algorithm to look for higher-order hypotheses, something that was infeasible until now. Furthermore, the generic formulation allows our approach to be agile to perform both open and closed discovery. We also experimentally validate that the core data-structures upon which the system bases its decision has a high concordance with the opinion of the experts.This coupled with the ability to understand the edge formation process provides us with interpretable results without any manual intervention. Availability and implementation: The relevant JAVA codes are available at: https://github.com/vishrawas/Medline-Code_v2. Supplementary information: Supplementary data are available at Bioinformatics online.

Detecting epileptic seizures with electroencephalogram via a context-learning model.

BACKGROUND: Epileptic seizure is a serious health problem in the world and there is a huge population suffering from it every year. If an algorithm could automatically detect seizures and deliver the patient therapy or notify the hospital, that would be of great assistance. Analyzing the scalp electroencephalogram (EEG) is the most common way to detect the onset of a seizure. In this paper, we proposed the context-learning based EEG analysis for seizure detection (Context-EEG) algorithm. METHODS: The proposed method aims at extracting both the hidden inherent features within EEG fragments and the temporal features from EEG contexts. First, we segment the EEG signals into EEG fragments of fixed length. Second, we learn the hidden inherent features from each fragment with a sparse auto-encoder and thus the dimensionality of the original data is reduced. Third, we translate each EEG fragment to an EEG word so that a continuous EEG signal is converted to a sequence of EEG words. Fourth, by analyzing the context information of EEG words, we learn the temporal features for EEG signals. And finally, we concatenate the hidden features and the temporal features together to train a binary classifier which can be used to detect the onset of an epileptic sezure. RESULTS: 4302 EEG fragments from four different patients are used to train and test our model. An error rate of 22.93 % is achieved by our model as a general, non-patient specific seizure detector. The error rate of our model is averagely 16.7 % lower than the other baseline models. Receiver operating characteristics (ROC curve) and area under curve (AUC) confirm the effectiveness of our model. Furthermore, we discuss the extracted features and how to reconstruct the original data based on the extracted features, as well as the parameter sensitivity. CONCLUSIONS: Given a EEG fragment, by extracting high-quality features (the hidden inherent features and temporal features) from the EEG signals, our Context-EEG model is able to detect the onset of a seizure with high accuracy in real time.