Extracting Synonymous Gene and Protein Terms From Biological Literature

Genes and proteins are often associated with multiple names. More names are added as new functional or structural information is discovered. Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance

Multi-Sensor Event Detection using Shape Histograms

Vehicular sensor data consists of multiple time-series arising from a number of sensors. Using such multi-sensor data we would like to detect occurrences of specific events that vehicles encounter, e.g., corresponding to particular maneuvers that a vehicle makes or conditions that it encounters. Events are characterized by similar waveform patterns re-appearing within one or more sensors. Further such patterns can be of variable duration. In this work, we propose a method for detecting such events in time-series data using a novel feature descriptor motivated by similar ideas in image processing. We define the shape histogram: a constant dimension descriptor that nevertheless captures patterns of variable duration. We demonstrate the efficacy of using shape histograms as features to detect events in an SVM-based, multi-sensor, supervised learning scenario, i.e., multiple time-series are used to detect an event. We present results on real-life vehicular sensor data and show that our technique performs better than available pattern detection implementations on our data, and that it can also be used to combine features from multiple sensors resulting in better accuracy than using any single sensor. Since previous work on pattern detection in time-series has been in the single series context, we also present results using our technique on multiple standard time-series datasets and show that it is the most versatile in terms of how it ranks compared to other published results

Learning sound representations using trainable COPE feature extractors

Sound analysis research has mainly been focused on speech and music processing. The deployed methodologies are not suitable for analysis of sounds with varying background noise, in many cases with very low signal-to-noise ratio (SNR). In this paper, we present a method for the detection of patterns of interest in audio signals. We propose novel trainable feature extractors, which we call COPE (Combination of Peaks of Energy). The structure of a COPE feature extractor is determined using a single prototype sound pattern in an automatic configuration process, which is a type of representation learning. We construct a set of COPE feature extractors, configured on a number of training patterns. Then we take their responses to build feature vectors that we use in combination with a classifier to detect and classify patterns of interest in audio signals. We carried out experiments on four public data sets: MIVIA audio events, MIVIA road events, ESC-10 and TU Dortmund data sets. The results that we achieved (recognition rate equal to 91.71% on the MIVIA audio events, 94% on the MIVIA road events, 81.25% on the ESC-10 and 94.27% on the TU Dortmund) demonstrate the effectiveness of the proposed method and are higher than the ones obtained by other existing approaches. The COPE feature extractors have high robustness to variations of SNR. Real-time performance is achieved even when the value of a large number of features is computed.Comment: Accepted for publication in Pattern Recognitio

Solving the challenges of concept drift in data stream classification.

The rise of network connected devices and applications leads to a significant increase in the volume of data that are continuously generated overtime time, called data streams. In real world applications, storing the entirety of a data stream for analyzing later is often not practical, due to the data stream’s potentially infinite volume. Data stream mining techniques and frameworks are therefore created to analyze streaming data as they arrive. However, compared to traditional data mining techniques, challenges unique to data stream mining also emerge, due to the high arrival rate of data streams and their dynamic nature. In this dissertation, an array of techniques and frameworks are presented to improve the solutions on some of the challenges. First, this dissertation acknowledges that a “no free lunch” theorem exists for data stream mining, where no silver bullet solution can solve all problems of data stream mining. The dissertation focuses on detection of changes of data distribution in data stream mining. These changes are called concept drift. Concept drift can be categorized into many types. A detection algorithm often works only on some types of drift, but not all of them. Because of this, the dissertation finds specific techniques to solve specific challenges, instead of looking for a general solution. Then, this dissertation considers improving solutions for the challenges of high arrival rate of data streams. Data stream mining frameworks often need to process vast among of data samples in limited time. Some data mining activities, notably data sample labeling for classification, are too costly or too slow in such large scale. This dissertation presents two techniques that reduce the amount of labeling needed for data stream classification. The first technique presents a grid-based label selection process that apply to highly imbalanced data streams. Such data streams have one class of data samples vastly outnumber another class. Many majority class samples need to be labeled before a minority class sample can be found due to the imbalance. The presented technique divides the data samples into groups, called grids, and actively search for minority class samples that are close by within a grid. Experiment results show the technique can reduce the total number of data samples needed to be labeled. The second technique presents a smart preprocessing technique that reduce the number of times a new learning model needs to be trained due to concept drift. Less model training means less data labels required, and thus costs less. Experiment results show that in some cases the reduced performance of learning models is the result of improper preprocessing of the data, not due to concept drift. By adapting preprocessing to the changes in data streams, models can retain high performance without retraining. Acknowledging the high cost of labeling, the dissertation then considers the scenario where labels are unavailable when needed. The framework Sliding Reservoir Approach for Delayed Labeling (SRADL) is presented to explore solutions to such problem. SRADL tries to solve the delayed labeling problem where concept drift occurs, and no labels are immediately available. SRADL uses semi-supervised learning by employing a sliding windowed approach to store historical data, which is combined with newly unlabeled data to train new models. Experiments show that SRADL perform well in some cases of delayed labeling. Next, the dissertation considers improving solutions for the challenge of dynamism within data streams, most notably concept drift. The complex nature of concept drift means that most existing detection algorithms can only detect limited types of concept drift. To detect more types of concept drift, an ensemble approach that employs various algorithms, called Heuristic Ensemble Framework for Concept Drift Detection (HEFDD), is presented. The occurrence of each type of concept drift is voted on by the detection results of each algorithm in the ensemble. Types of concept drift with votes past majority are then declared detected. Experiment results show that HEFDD is able to improve detection accuracy significantly while reducing false positives. With the ability to detect various types of concept drift provided by HEFDD, the dissertation tries to improve the delayed labeling framework SRADL. A new combined framework, SRADL-HEFDD is presented, which produces synthetic labels to handle the unavailability of labels by human expert. SRADL-HEFDD employs different synthetic labeling techniques based on different types of drift detected by HEFDD. Experimental results show that comparing to the default SRADL, the combined framework improves prediction performance when small amount of labeled samples is available. Finally, as machine learning applications are increasingly used in critical domains such as medical diagnostics, accountability, explainability and interpretability of machine learning algorithms needs to be considered. Explainable machine learning aims to use a white box approach for data analytics, which enables learning models to be explained and interpreted by human users. However, few studies have been done on explaining what has changed in a dynamic data stream environment. This dissertation thus presents Data Stream Explainability (DSE) framework. DSE visualizes changes in data distribution and model classification boundaries between chunks of streaming data. The visualizations can then be used by a data mining researcher to generate explanations of what has changed within the data stream. To show that DSE can help average users understand data stream mining better, a survey was conducted with an expert group and a non-expert group of users. Results show DSE can reduce the gap of understanding what changed in data stream mining between the two groups