A toolbox for animal call recognition

Monitoring the natural environment is increasingly important as habit degradation and climate change reduce theworld’s biodiversity.We have developed software tools and applications to assist ecologists with the collection and analysis of acoustic data at large spatial and temporal scales.One of our key objectives is automated animal call recognition, and our approach has three novel attributes. First, we work with raw environmental audio, contaminated by noise and artefacts and containing calls that vary greatly in volume depending on the animal’s proximity to the microphone. Second, initial experimentation suggested that no single recognizer could dealwith the enormous variety of calls. Therefore, we developed a toolbox of generic recognizers to extract invariant features for each call type. Third, many species are cryptic and offer little data with which to train a recognizer. Many popular machine learning methods require large volumes of training and validation data and considerable time and expertise to prepare. Consequently we adopt bootstrap techniques that can be initiated with little data and refined subsequently. In this paper, we describe our recognition tools and present results for real ecological problems.

A comparison of methods for classifying clinical samples based on proteomics data : a case study for statistical and machine learning approaches

The discovery of protein variation is an important strategy in disease diagnosis within the biological sciences. The current benchmark for elucidating information from multiple biological variables is the so called “omics” disciplines of the biological sciences. Such variability is uncovered by implementation of multivariable data mining techniques which come under two primary categories, machine learning strategies and statistical based approaches. Typically proteomic studies can produce hundreds or thousands of variables, p, per observation, n, depending on the analytical platform or method employed to generate the data. Many classification methods are limited by an n≪p constraint, and as such, require pre-treatment to reduce the dimensionality prior to classification. Recently machine learning techniques have gained popularity in the field for their ability to successfully classify unknown samples. One limitation of such methods is the lack of a functional model allowing meaningful interpretation of results in terms of the features used for classification. This is a problem that might be solved using a statistical model-based approach where not only is the importance of the individual protein explicit, they are combined into a readily interpretable classification rule without relying on a black box approach. Here we incorporate statistical dimension reduction techniques Partial Least Squares (PLS) and Principal Components Analysis (PCA) followed by both statistical and machine learning classification methods, and compared them to a popular machine learning technique, Support Vector Machines (SVM). Both PLS and SVM demonstrate strong utility for proteomic classification problems.

Granule mining and its application for network traffic characterization

Decision table and decision rules play an important role in rough set based data analysis, which compress databases into granules and describe the associations between granules. Granule mining was also proposed to interpret decision rules in terms of association rules and multi-tier structure. In this paper, we further extend granule mining to describe the relationships between granules not only by traditional support and confidence, but by diversity and condition diversity as well. Diversity measures how diverse of a granule associated with the other ganules, it provides a kind of novel knowledge in databases. Some experiments are conducted to test the proposed new concepts for describing the characteristics of a real network traffic data collection. The results show that the proposed concepts are promising.

Seed-based biclustering of gene expression data

Background Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. Methods In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns: (a) a gene set, and (b) the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater than the minimum threshold number of genes in a bicluster. If so, a bicluster is outputted and the corresponding row is removed from the table. Repeating this process, all biclusters in the table are systematically identified until the table becomes empty. Conclusions This paper presents a novel biclustering algorithm for the identification of additive biclusters. Since it involves exhaustively testing combinations of genes and conditions, the additive biclusters can be found more readily.

Kernel analysis on Grassmann manifolds for action recognition

Modelling video sequences by subspaces has recently shown promise for recognising human actions. Subspaces are able to accommodate the effects of various image variations and can capture the dynamic properties of actions. Subspaces form a non-Euclidean and curved Riemannian manifold known as a Grassmann manifold. Inference on manifold spaces usually is achieved by embedding the manifolds in higher dimensional Euclidean spaces. In this paper, we instead propose to embed the Grassmann manifolds into reproducing kernel Hilbert spaces and then tackle the problem of discriminant analysis on such manifolds. To achieve efficient machinery, we propose graph-based local discriminant analysis that utilises within-class and between-class similarity graphs to characterise intra-class compactness and inter-class separability, respectively. Experiments on KTH, UCF Sports, and Ballet datasets show that the proposed approach obtains marked improvements in discrimination accuracy in comparison to several state-of-the-art methods, such as the kernel version of affine hull image-set distance, tensor canonical correlation analysis, spatial-temporal words and hierarchy of discriminative space-time neighbourhood features.

On robust face recognition via sparse encoding : the good, the bad, and the ugly

In the field of face recognition, Sparse Representation (SR) has received considerable attention during the past few years. Most of the relevant literature focuses on holistic descriptors in closed-set identification applications. The underlying assumption in SR-based methods is that each class in the gallery has sufficient samples and the query lies on the subspace spanned by the gallery of the same class. Unfortunately, such assumption is easily violated in the more challenging face verification scenario, where an algorithm is required to determine if two faces (where one or both have not been seen before) belong to the same person. In this paper, we first discuss why previous attempts with SR might not be applicable to verification problems. We then propose an alternative approach to face verification via SR. Specifically, we propose to use explicit SR encoding on local image patches rather than the entire face. The obtained sparse signals are pooled via averaging to form multiple region descriptors, which are then concatenated to form an overall face descriptor. Due to the deliberate loss spatial relations within each region (caused by averaging), the resulting descriptor is robust to misalignment & various image deformations. Within the proposed framework, we evaluate several SR encoding techniques: l1-minimisation, Sparse Autoencoder Neural Network (SANN), and an implicit probabilistic technique based on Gaussian Mixture Models. Thorough experiments on AR, FERET, exYaleB, BANCA and ChokePoint datasets show that the proposed local SR approach obtains considerably better and more robust performance than several previous state-of-the-art holistic SR methods, in both verification and closed-set identification problems. The experiments also show that l1-minimisation based encoding has a considerably higher computational than the other techniques, but leads to higher recognition rates.

Examination of distracted driving and yellow light running : analysis of simulator data

Driving on an approach to a signalized intersection while distracted is particularly dangerous, as potential vehicular conflicts and resulting angle collisions tend to be severe. Given the prevalence and importance of this particular scenario, the decisions and actions of distracted drivers during the onset of yellow lights are the focus of this study. Driving simulator data were obtained from a sample of 58 drivers under baseline and handheld mobile phone conditions at the University of Iowa - National Advanced Driving Simulator. Explanatory variables included age, gender, cell phone use, distance to stop-line, and speed. Although there is extensive research on drivers’ responses to yellow traffic signals, the examination has been conducted from a traditional regression-based approach, which does not necessary provide the underlying relations and patterns among the sampled data. In this paper, we exploit the benefits of both classical statistical inference and data mining techniques to identify the a priori relationships among main effects, non-linearities, and interaction effects. Results suggest that novice (16-17 years) and young drivers’ (18-25 years) have heightened yellow light running risk while distracted by a cell phone conversation. Driver experience captured by age has a multiplicative effect with distraction, making the combined effect of being inexperienced and distracted particularly risky. Overall, distracted drivers across most tested groups tend to reduce the propensity of yellow light running as the distance to stop line increases, exhibiting risk compensation on a critical driving situation.

Querying a building information model for construction-specific spatial information

The design and construction community has shown increasing interest in adopting building information models (BIMs). The richness of information provided by BIMs has the potential to streamline the design and construction processes by enabling enhanced communication, coordination, automation and analysis. However, there are many challenges in extracting construction-specific information out of BIMs. In most cases, construction practitioners have to manually identify the required information, which is inefficient and prone to error, particularly for complex, large-scale projects. This paper describes the process and methods we have formalized to partially automate the extraction and querying of construction-specific information from a BIM. We describe methods for analyzing a BIM to query for spatial information that is relevant for construction practitioners, and that is typically represented implicitly in a BIM. Our approach integrates ifcXML data and other spatial data to develop a richer model for construction users. We employ custom 2D topological XQuery predicates to answer a variety of spatial queries. The validation results demonstrate that this approach provides a richer representation of construction-specific information compared to existing BIM tools.

Using patterns co-occurrence matrix for cleaning closed sequential patterns for text mining

With the overwhelming increase in the amount of texts on the web, it is almost impossible for people to keep abreast of up-to-date information. Text mining is a process by which interesting information is derived from text through the discovery of patterns and trends. Text mining algorithms are used to guarantee the quality of extracted knowledge. However, the extracted patterns using text or data mining algorithms or methods leads to noisy patterns and inconsistency. Thus, different challenges arise, such as the question of how to understand these patterns, whether the model that has been used is suitable, and if all the patterns that have been extracted are relevant. Furthermore, the research raises the question of how to give a correct weight to the extracted knowledge. To address these issues, this paper presents a text post-processing method, which uses a pattern co-occurrence matrix to find the relation between extracted patterns in order to reduce noisy patterns. The main objective of this paper is not only reducing the number of closed sequential patterns, but also improving the performance of pattern mining as well. The experimental results on Reuters Corpus Volume 1 data collection and TREC filtering topics show that the proposed method is promising.

Semantic labelling for document feature patterns using ontological subjects

Finding and labelling semantic features patterns of documents in a large, spatial corpus is a challenging problem. Text documents have characteristics that make semantic labelling difficult; the rapidly increasing volume of online documents makes a bottleneck in finding meaningful textual patterns. Aiming to deal with these issues, we propose an unsupervised documnent labelling approach based on semantic content and feature patterns. A world ontology with extensive topic coverage is exploited to supply controlled, structured subjects for labelling. An algorithm is also introduced to reduce dimensionality based on the study of ontological structure. The proposed approach was promisingly evaluated by compared with typical machine learning methods including SVMs, Rocchio, and kNN.

Usability of small crisis data sets in the absence of big data

Big data is big news in almost every sector including crisis communication. However, not everyone has access to big data and even if we have access to big data, we often do not have necessary tools to analyze and cross reference such a large data set. Therefore this paper looks at patterns in small data sets that we have ability to collect with our current tools to understand if we can find actionable information from what we already have. We have analyzed 164390 tweets collected during 2011 earthquake to find out what type of location specific information people mention in their tweet and when do they talk about that. Based on our analysis we find that even a small data set that has far less data than a big data set can be useful to find priority disaster specific areas quickly.

A hybrid association rule mining approach for characterizing network traffic behaviour

Understanding network traffic behaviour is crucial for managing and securing computer networks. One important technique is to mine frequent patterns or association rules from analysed traffic data. On the one hand, association rule mining usually generates a huge number of patterns and rules, many of them meaningless or user-unwanted; on the other hand, association rule mining can miss some necessary knowledge if it does not consider the hierarchy relationships in the network traffic data. Aiming to address such issues, this paper proposes a hybrid association rule mining method for characterizing network traffic behaviour. Rather than frequent patterns, the proposed method generates non-similar closed frequent patterns from network traffic data, which can significantly reduce the number of patterns. This method also proposes to derive new attributes from the original data to discover novel knowledge according to hierarchy relationships in network traffic data and user interests. Experiments performed on real network traffic data show that the proposed method is promising and can be used in real applications. Copyright2013 John Wiley & Sons, Ltd.

A novel representation of bioacoustic events for content-based search in field audio data

Bioacoustic data can provide an important base for environmental monitoring. To explore a large amount of field recordings collected, an automated similarity search algorithm is presented in this paper. A region of an audio defined by frequency and time bounds is provided by a user; the content of the region is used to construct a query. In the retrieving process, our algorithm will automatically scan through recordings to search for similar regions. In detail, we present a feature extraction approach based on the visual content of vocalisations – in this case ridges, and develop a generic regional representation of vocalisations for indexing. Our feature extraction method works best for bird vocalisations showing ridge characteristics. The regional representation method allows the content of an arbitrary region of a continuous recording to be described in a compressed format.

A people-to-people matching system using graph mining techniques

A people-to-people matching system (or a match-making system) refers to a system in which users join with the objective of meeting other users with the common need. Some real-world examples of these systems are employer-employee (in job search networks), mentor-student (in university social networks), consume-to-consumer (in marketplaces) and male-female (in an online dating network). The network underlying in these systems consists of two groups of users, and the relationships between users need to be captured for developing an efficient match-making system. Most of the existing studies utilize information either about each of the users in isolation or their interaction separately, and develop recommender systems using the one form of information only. It is imperative to understand the linkages among the users in the network and use them in developing a match-making system. This study utilizes several social network analysis methods such as graph theory, small world phenomenon, centrality analysis, density analysis to gain insight into the entities and their relationships present in this network. This paper also proposes a new type of graph called “attributed bipartite graph”. By using these analyses and the proposed type of graph, an efficient hybrid recommender system is developed which generates recommendation for new users as well as shows improvement in accuracy over the baseline methods.