Alternative splicing analysis benchmark with DICAST

Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data. Previous benchmarks focused on isoform quantification and mapping. They neglected event detection tools, which arguably provide the most detailed insights into the alternative splicing process. DICAST offers a modular and extensible framework for the analysis of alternative splicing integrating 11 splice-aware mapping and eight event detection tools. We benchmark all tools extensively on simulated as well as whole blood RNA-seq data. STAR and HISAT2 demonstrated the best balance between performance and run time. The performance of event detection tools varies widely with no tool outperforming all others. DICAST allows researchers to employ a consensus approach to consider the most successful tools jointly for robust event detection. Furthermore, we propose the first reporting standard to unify existing formats and to guide future tool development.

Toward Real-time Microseismic Event Detection using the YOLOv3 Algorithm

Real-time microseismic monitoring is essential for understanding fractures associated with underground fluid injection in unconventional reservoirs. However, microseismic events recorded on monitoring arrays are usually contaminated with strong noise. With a low signal-to-noise ratio (S/R), the detection of microseismic events is challenging using conventional detection methods such as the short-term average/long-term average (STA/LTA) technique. Common machine learning methods, e.g., feature extraction plus support vector machine (SVM) and convolutional neural networks (CNNs), can achieve higher accuracy with strong noise, but they are usually time-consuming and memory-intensive to run. We propose the use of YOLOv3, a state-of-art real-time object detection system in microseismic event detection. YOLOv3 is a one-stage deep CNN detector that predicts class confidence and bounding boxes for images at high speed and with great precision. With pre-trained weights from the ImageNet 1000-class competition dataset, physics-based training of the YOLOv3 algorithm is performed on a group of forward modeled synthetic microseismic data with varying S/R. We also add randomized forward-modeled surface seismic events and Gaussian white noise to generate ``semi-realistic'' training and testing datasets. YOLOv3 is able to detect weaker microseismic event signals with low signal-to-noise ratios (e.g., S/N=0.1) and achieves a mean average precision of 88.71\% in near real time. Further work is required to test YOLOv3 in field production settings.

Method for Estimating Temporal Gait Parameters Concerning Bilateral Lower Limbs of Healthy Subjects Using a Single In-Shoe Motion Sensor through a Gait Event Detection Approach

To expand the potential use of in-shoe motion sensors (IMSs) in daily healthcare or activity monitoring applications for healthy subjects, we propose a real-time temporal estimation method for gait parameters concerning bilateral lower limbs (GPBLLs) that uses a single IMS and is based on a gait event detection approach. To validate the established methods, data from 26 participants recorded by an IMS and a reference 3D motion analysis system were compared. The agreement between the proposed method and the reference system was evaluated by the intraclass correlation coefficient (ICC). The results showed that, by averaging over five continuous effective strides, all time parameters achieved precisions of no more than 30 ms and agreement at the “excellent” level, and the symmetry indexes of the stride time and stance phase time achieved precisions of 1.0% and 3.0%, respectively, and agreement at the “good” level. These results suggest our method is effective and shows promise for wide use in many daily healthcare or activity monitoring applications for healthy subjects.

SMAFED: Real-Time Event Detection in Social Media Streams

Interactions via social media platforms have made it possible for anyone, irrespective of physical location, to gain access to quick information on events taking place all over the globe. However, the semantic processing of social media data is complicated due to challenges such as language complexity, unstructured data, and ambiguity. In this paper, we proposed the Social Media Analysis Framework for Event Detection (SMAFED). SMAFED aims to facilitate improved semantic analysis of noisy terms in social media streams, improved representation/embedding of social media stream content, and improved summarisation of event clusters in social media streams. For this, we employed key concepts such as integrated knowledge base, resolving ambiguity, semantic representation of social media streams, and Semantic Histogram-based Incremental Clustering based on semantic relatedness. Two evaluation experiments were conducted to validate the approach. First, we evaluated the impact of the data enrichment layer of SMAFED. We found that SMAFED outperformed other pre-processing frameworks with a lower loss function of 0.15 on the first dataset and 0.05 on the second dataset. Secondly, we determined the accuracy of SMAFED at detecting events from social media streams. The result of this second experiment showed that SMAFED outperformed existing event detection approaches with better Precision (0.922), Recall (0.793), and F-Measure (0.853) metric scores. The findings of the study present SMAFED as a more efficient approach to event detection in social media.