Proceedings. IEEE International Conference on Bioinformatics and Biomedicine最新文献

In acute ischemic stroke treatment, prediction of tissue survival outcome plays a fundamental role in the clinical decision-making process, as it can be used to assess the balance of risk vs. possible benefit when considering endovascular clot-retrieval intervention. For the first time, we construct a deep learning model of tissue fate based on randomly sampled local patches from the hypoperfusion (Tmax) feature observed in MRI immediately after symptom onset. We evaluate the model with respect to the ground truth established by an expert neurologist four days after intervention. Experiments on 19 acute stroke patients evaluated the accuracy of the model in predicting tissue fate. Results show the superiority of the proposed regional learning framework versus a single-voxel-based regression model.

Kidney cancer is of prominent concern in modern medicine. Predicting patient survival is critical to patient awareness and developing a proper treatment regimens. Previous prediction models built upon molecular feature analysis are limited to just gene expression data. In this study we investigate the difference in predicting five year survival between unimodal and multimodal analysis of RNA-seq data from gene, exon, junction, and isoform modalities. Our preliminary findings report higher predictive accuracy-as measured by area under the ROC curve (AUC)-for multimodal learning when compared to unimodal learning with both support vector machine (SVM) and k-nearest neighbor (KNN) methods. The results of this study justify further research on the use of multimodal RNA-seq data to predict survival for other cancer types using a larger sample size and additional machine learning methods.

Insight is a Semantic Web technology-based platform to support large-scale secondary analysis of healthcare data for neurology clinical research. Insight features the novel use of: (1) provenance metadata, which describes the history or origin of patient data, in clinical research analysis, and (2) support for patient cohort queries across multiple institutions conducting research in epilepsy, which is the one of the most common neurological disorders affecting 50 million persons worldwide. Insight is being developed as a healthcare informatics infrastructure to support a national network of eight epilepsy research centers across the U.S. funded by the U.S. Centers for Disease Control and Prevention (CDC). This paper describes the use of the World Wide Web Consortium (W3C) PROV recommendation for provenance metadata that allows researchers to create patient cohorts based on the provenance of the research studies. In addition, the paper describes the use of descriptive logic-based OWL2 epilepsy ontology for cohort queries with "expansion of query expression" using ontology reasoning. Finally, the evaluation results for the data integration and query performance are described using data from three research studies with 180 epilepsy patients. The experiment results demonstrate that Insight is a scalable approach to use Semantic provenance metadata for context-based data analysis in healthcare informatics.

The objective of this paper is to provide a hybrid algorithm for non-negative matrix factorization based on a symmetric version of Kullback-Leibler divergence, known as intrinsic information. The convergence of the proposed algorithm is shown for several members of the exponential family such as the Gaussian, Poisson, gamma and inverse Gaussian models. The speed of this algorithm is examined and its usefulness is illustrated through some applied problems.

Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices.

Hyperperfusion detected on arterial spin labeling (ASL) images acquired after acute stroke onset has been shown to correlate with development of subsequent intracerebral hemorrhage. We present in this study a quantitative hyperperfusion detection model that can provide an objective decision support for the interpretation of ASL cerebral blood flow (CBF) maps and rapidly delineate hyperperfusion regions. The detection problem is solved using Deep Learning such that the model relates ASL image patches to the corresponding label (normal or hyperperfused). Our method takes into account the regional intensity values of contralateral hemisphere during the labeling of a pixel. Each input vector is associated to a label corresponding to the presence of hyperperfusion that was manually established by a clinical researcher in Neurology. When compared to the manually established hyperperfusion, the predicted maps reached an accuracy of 97.45 ± 2.49% after crossvalidation. Pattern recognition based on deep learning can provide an accurate and objective measure of hyperperfusion on ASL CBF images and could therefore improve the detection of hemorrhagic transformation in acute stroke patients.

Test based on electrocardiograms (ECG) that record the heart electrical activity can help in early detection of patients with hypertrophic cardiomyopathy (HCM) where the heart muscle is partially thickened and blood flow is (potentially fatally) obstructed. This paper presents a cardiovascular-patient classifier we developed to identify HCM patients using standard 10-seconds, 12-lead ECG signals. Patients are classified as having HCM if the majority of the heartbeats are recognized as HCM. Thus, the classifier's underlying task is to recognize individual heartbeats segmented from 12-lead ECG signals as HCM beats, where heartbeats from non-HCM cardiovascular patients are used as controls. We extracted 504 morphological and temporal features - both commonly used and newly-developed ones - from ECG signals for heartbeat classification. To assess classification performance, we trained and tested a random forest classifier and a support vector machine classifier using 5-fold cross validation. The patient-classification precision and F-measure of both classifiers are close to 0.85. Recall (sensitivity) and specificity are approximately 0.90. We also conducted feature selection experiments by gradually removing the least informative features; the results show that a relatively small subset of 304 highly informative features can achieve performance measures comparable to that achieved by using the complete set of features.

In this paper, we present a novel framework for microscopic image analysis of nuclei, data management, and high performance computation to support translational research involving nuclear morphometry features, molecular data, and clinical outcomes. Our image analysis pipeline consists of nuclei segmentation and feature computation facilitated by high performance computing with coordinated execution in multi-core CPUs and Graphical Processor Units (GPUs). All data derived from image analysis are managed in a spatial relational database supporting highly efficient scientific queries. We applied our image analysis workflow to 159 glioblastomas (GBM) from The Cancer Genome Atlas dataset. With integrative studies, we found statistics of four specific nuclear features were significantly associated with patient survival. Additionally, we correlated nuclear features with molecular data and found interesting results that support pathologic domain knowledge. We found that Proneural subtype GBMs had the smallest mean of nuclear Eccentricity and the largest mean of nuclear Extent, and MinorAxisLength. We also found gene expressions of stem cell marker MYC and cell proliferation maker MKI67 were correlated with nuclear features. To complement and inform pathologists of relevant diagnostic features, we queried the most representative nuclear instances from each patient population based on genetic and transcriptional classes. Our results demonstrate that specific nuclear features carry prognostic significance and associations with transcriptional and genetic classes, highlighting the potential of high throughput pathology image analysis as a complementary approach to human-based review and translational research.

Finding out the associations between an input gene set, such as genes associated with a certain phenotype, and annotated gene sets, such as known pathways, are a very important problem in modern molecular biology. The existing approaches mainly focus on the overlap between the two, and may miss important but subtle relationships between genes. In this paper, we propose a method, NetPEA, by combining the known pathways and high-throughput networks. Our method not only considers the shared genes, but also takes the gene interactions into account. It utilizes a protein-protein interaction network and a random walk procedure to identify hidden relationships between gene sets, and uses a randomization strategy to evaluate the significance for pathways to achieve such similarity scores. Compared with the over-representation based method, our method can identify more relationships. Compared with a state of the art network-based method, EnrichNet, our method not only provides a ranked list of pathways, but also provides the statistical significant information. Importantly, through independent tests, we show that our method likely has a higher sensitivity in revealing the true casual pathways, while at the same time achieve a higher specificity. Literature review of selected results indicates that some of the novel pathways reported by our method are biologically relevant and important.

Identifying drug-drug interactions is an important and challenging problem in computational biology and healthcare research. There are accurate, structured but limited domain knowledge and noisy, unstructured but abundant textual information available for building predictive models. The difficulty lies in mining the true patterns embedded in text data and developing efficient and effective ways to combine heterogenous types of information. We demonstrate a novel approach of leveraging augmented text-mining features to build a logistic regression model with improved prediction performance (in terms of discrimination and calibration). Our model based on synthesized features significantly outperforms the model trained with only structured features (AUC: 96% vs. 91%, Sensitivity: 90% vs. 82% and Specificity: 88% vs. 81%). Along with the quantitative results, we also show learned "latent topics", an intermediary result of our text mining module, and discuss their implications.