Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results

CleanNet: Transfer Learning for Scalable Image Classifier Training with Label Noise

In this paper, we study the problem of learning image classification models with label noise. Existing approaches depending on human supervision are generally not scalable as manually identifying correct or incorrect labels is time-consuming, whereas approaches not relying on human supervision are scalable but less effective. To reduce the amount of human supervision for label noise cleaning, we introduce CleanNet, a joint neural embedding network, which only requires a fraction of the classes being manually verified to provide the knowledge of label noise that can be transferred to other classes. We further integrate CleanNet and conventional convolutional neural network classifier into one framework for image classification learning. We demonstrate the effectiveness of the proposed algorithm on both of the label noise detection task and the image classification on noisy data task on several large-scale datasets. Experimental results show that CleanNet can reduce label noise detection error rate on held-out classes where no human supervision available by 41.5% compared to current weakly supervised methods. It also achieves 47% of the performance gain of verifying all images with only 3.2% images verified on an image classification task. Source code and dataset will be available at kuanghuei.github.io/CleanNetProject.Comment: Accepted to CVPR 201

Estimating Fire Weather Indices via Semantic Reasoning over Wireless Sensor Network Data Streams

Wildfires are frequent, devastating events in Australia that regularly cause significant loss of life and widespread property damage. Fire weather indices are a widely-adopted method for measuring fire danger and they play a significant role in issuing bushfire warnings and in anticipating demand for bushfire management resources. Existing systems that calculate fire weather indices are limited due to low spatial and temporal resolution. Localized wireless sensor networks, on the other hand, gather continuous sensor data measuring variables such as air temperature, relative humidity, rainfall and wind speed at high resolutions. However, using wireless sensor networks to estimate fire weather indices is a challenge due to data quality issues, lack of standard data formats and lack of agreement on thresholds and methods for calculating fire weather indices. Within the scope of this paper, we propose a standardized approach to calculating Fire Weather Indices (a.k.a. fire danger ratings) and overcome a number of the challenges by applying Semantic Web Technologies to the processing of data streams from a wireless sensor network deployed in the Springbrook region of South East Queensland. This paper describes the underlying ontologies, the semantic reasoning and the Semantic Fire Weather Index (SFWI) system that we have developed to enable domain experts to specify and adapt rules for calculating Fire Weather Indices. We also describe the Web-based mapping interface that we have developed, that enables users to improve their understanding of how fire weather indices vary over time within a particular region.Finally, we discuss our evaluation results that indicate that the proposed system outperforms state-of-the-art techniques in terms of accuracy, precision and query performance.Comment: 20pages, 12 figure

Semantically Guided Depth Upsampling

We present a novel method for accurate and efficient up- sampling of sparse depth data, guided by high-resolution imagery. Our approach goes beyond the use of intensity cues only and additionally exploits object boundary cues through structured edge detection and semantic scene labeling for guidance. Both cues are combined within a geodesic distance measure that allows for boundary-preserving depth in- terpolation while utilizing local context. We model the observed scene structure by locally planar elements and formulate the upsampling task as a global energy minimization problem. Our method determines glob- ally consistent solutions and preserves fine details and sharp depth bound- aries. In our experiments on several public datasets at different levels of application, we demonstrate superior performance of our approach over the state-of-the-art, even for very sparse measurements.Comment: German Conference on Pattern Recognition 2016 (Oral

Towards information profiling: data lake content metadata management

There is currently a burst of Big Data (BD) processed and stored in huge raw data repositories, commonly called Data Lakes (DL). These BD require new techniques of data integration and schema alignment in order to make the data usable by its consumers and to discover the relationships linking their content. This can be provided by metadata services which discover and describe their content. However, there is currently a lack of a systematic approach for such kind of metadata discovery and management. Thus, we propose a framework for the profiling of informational content stored in the DL, which we call information profiling. The profiles are stored as metadata to support data analysis. We formally define a metadata management process which identifies the key activities required to effectively handle this.We demonstrate the alternative techniques and performance of our process using a prototype implementation handling a real-life case-study from the OpenML DL, which showcases the value and feasibility of our approach.Peer ReviewedPostprint (author's final draft