On the analysis of musical performance by computer

Existing automatic methods of analysing musical performance can generally be described as music-oriented DSP analysis. However, this merely identifies attributes, or artefacts which can be found within the performance. This information, though invaluable, is not an analysis of the performance process. The process of performance first involves an analysis of the score (whether from a printed sheet or from memory), and through this analysis, the performer decides how to perform the piece. Thus, an analysis of the performance process requires an analysis of the performance attributes and artefacts in the context of the musical score. With this type analysis it is possible to ask profound questions such as “why or when does a performer use this technique”. The work presented in this thesis provides the tools which are required to investigate these performance issues. A new computer representation, Performance Markup Language (PML) is presented which combines the domains of the musical score, performance information and analytical structures. This representation provides the framework with which information within these domains can be cross-referenced internally, and the markup of information in external files. Most importantly, the rep resentation defines the relationship between performance events and the corresponding objects within the score, thus facilitating analysis of performance information in the context of the score and analyses of the score. To evaluate the correspondences between performance notes and notes within the score, the performance must be analysed using a score-performance matching algorithm. A new score-performance matching algorithm is presented in this document which is based on Dynamic Programming. In score-performance matching there are situations where dynamic programming alone is not sufficient to accurately identify correspondences. The algorithm presented here makes use of analyses of both the score and the performance to overcome the inherent shortcomings of the DP method and to improve the accuracy and robustness of DP matching in the presence of performance errors and expressive timing. Together with the musical score and performance markup, the correspondences identified by the matching algorithm provide the minimum information required to investigate musical performance, and forms the foundation of a PML representation. The Microtonalism project investigated the issues surrounding the performance of microtonal music on conventional (i.e. non microtonal specific) instruments, namely voice. This included the automatic analysis of vocal performances to extract information regarding pitch accuracy. This was possible using tools developed using the performance representation and the matching algorithm

An Investigation and Application of Biology and Bioinformatics for Activity Recognition

Activity recognition in a smart home context is inherently difficult due to the variable nature of human activities and tracking artifacts introduced by video-based tracking systems. This thesis addresses the activity recognition problem via introducing a biologically-inspired chemotactic approach and bioinformatics-inspired sequence alignment techniques to recognise spatial activities. The approaches are demonstrated in real world conditions to improve robustness and recognise activities in the presence of innate activity variability and tracking noise

Time Series classification through transformation and ensembles

The problem of time series classification (TSC), where we consider any real-valued ordered data a time series, offers a specific challenge. Unlike traditional classification problems, the ordering of attributes is often crucial for identifying discriminatory features between classes. TSC problems arise across a diverse range of domains, and this variety has meant that no single approach outperforms all others. The general consensus is that the benchmark for TSC is nearest neighbour (NN) classifiers using Euclidean distance or Dynamic Time Warping (DTW). Though conceptually simple, many have reported that NN classifiers are very diffi�cult to beat and new work is often compared to NN classifiers. The majority of approaches have focused on classification in the time domain, typically proposing alternative elastic similarity measures for NN classification. Other work has investigated more specialised approaches, such as building support vector machines on variable intervals and creating tree-based ensembles with summary measures. We wish to answer a specific research question: given a new TSC problem without any prior, specialised knowledge, what is the best way to approach the problem? Our thesis is that the best methodology is to first transform data into alternative representations where discriminatory features are more easily detected, and then build ensemble classifiers on each representation. In support of our thesis, we propose an elastic ensemble classifier that we believe is the first ever to significantly outperform DTW on the widely used UCR datasets. Next, we propose the shapelet-transform, a new data transformation that allows complex classifiers to be coupled with shapelets, which outperforms the original algorithm and is competitive with DTW. Finally, we combine these two works with with heterogeneous ensembles built on autocorrelation and spectral-transformed data to propose a collective of transformation-based ensembles (COTE). The results of COTE are, we believe, the best ever published on the UCR datasets

Hypotension Risk Prediction via Sequential Contrast Patterns of ICU Blood Pressure

© 2013 IEEE. Acute hypotension is a significant risk factor for in-hospital mortality at intensive care units. Prolonged hypotension can cause tissue hypoperfusion, leading to cellular dysfunction and severe injuries to multiple organs. Prompt medical interventions are thus extremely important for dealing with acute hypotensive episodes (AHE). Population level prognostic scoring systems for risk stratification of patients are suboptimal in such scenarios. However, the design of an efficient risk prediction system can significantly help in the identification of critical care patients, who are at risk of developing an AHE within a future time span. Toward this objective, a pattern mining algorithm is employed to extract informative sequential contrast patterns from hemodynamic data, for the prediction of hypotensive episodes. The hypotensive and normotensive patient groups are extracted from the MIMIC-II critical care research database, following an appropriate clinical inclusion criteria. The proposed method consists of a data preprocessing step to convert the blood pressure time series into symbolic sequences, using a symbolic aggregate approximation algorithm. Then, distinguishing subsequences are identified using the sequential contrast mining algorithm. These subsequences are used to predict the occurrence of an AHE in a future time window separated by a user-defined gap interval. Results indicate that the method performs well in terms of the prediction performance as well as in the generation of sequential patterns of clinical significance. Hence, the novelty of sequential patterns is in their usefulness as potential physiological biomarkers for building optimal patient risk stratification systems and for further clinical investigation of interesting patterns in critical care patients

A general state-based temporal pattern recognition

Time-series and state-sequences are ubiquitous patterns in temporal logic and are widely used to present temporal data in data mining. Generally speaking, there are three known choices for the time primitive: points, intervals, points and intervals. In this thesis, a formal characterization of time-series and state-sequences is presented for both complete and incomplete situations, where a state-sequence is defined as a list of sequential data validated on the corresponding time-series. In addition, subsequence matching is addressed to associate the state-sequences, where both non-temporal aspects as well as rich temporal aspects including temporal order, temporal duration and temporal gap should be taken into account. Firstly, based on the typed point based time-elements and time-series, a formal characterization of time-series and state-sequences is introduced for both complete and incomplete situations, where a state-sequence is defined as a list of sequential data validated on the corresponding time-series. A time-series is formalized as a tetrad (T, R, Tdur, Tgap), which denotes: the temporal order of time- elements; the temporal relationship between time-elements; the temporal duration of each time-element and the temporal gap between each adjacent pair of time-elements respectively. Secondly, benefiting from the formal characterization of time-series and state-sequences, a general similarity measurement (GSM) that takes into account both non-temporal and rich temporal information, including temporal order as well as temporal duration and temporal gap, is introduced for subsequence matching. This measurement is general enough to subsume most of the popular existing measurements as special cases. In particular, a new conception of temporal common subsequence is proposed. Furthermore, a new LCS-based algorithm named Optimal Temporal Common Subsequence (OTCS), which takes into account rich temporal information, is designed. The experimental results on 6 benchmark datasets demonstrate the effectiveness and robustness of GSM and its new case OTCS. Compared with binary-value distance measurements, GSM can distinguish between the distance caused by different states in the same operation; compared with the real-penalty distance measurements, it can filter out the noise that may push the similarity into abnormal levels. Finally, two case studies are investigated for temporal pattern recognition: basketball zone-defence detection and video copy detection. In the case of basketball zone-defence detection, the computational technique and algorithm for detecting zone-defence patterns from basketball videos is introduced, where the Laplacian Matrix-based algorithm is extended to take into account the effects from zoom and single defender‘s translation in zone-defence graph matching and a set of character-angle based features was proposed to describe the zone-defence graph. The experimental results show that the approach explored is useful in helping the coach of the defensive side check whether the players are keeping to the correct zone-defence strategy, as well as detecting the strategy of the opponent side. It can describe the structure relationship between defender-lines for basketball zone-defence, and has a robust performance in both simulation and real-life applications, especially when disturbances exist. In the case of video copy detection, a framework for subsequence matching is introduced. A hybrid similarity framework addressing both non-temporal and temporal relationships between state-sequences, represented by bipartite graphs, is proposed. The experimental results using real-life video databases demonstrated that the proposed similarity framework is robust to states alignment with different numbers and different values, and various reordering including inversion and crossover

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

Review and classification of trajectory summarisation algorithms: From compression to segmentation

With the continuous development and cost reduction of positioning and tracking technologies, a large amount of trajectories are being exploited in multiple domains for knowledge extraction. A trajectory is formed by a large number of measurements, where many of them are unnecessary to describe the actual trajectory of the vehicle, or even harmful due to sensor noise. This not only consumes large amounts of memory, but also makes the extracting knowledge process more difficult. Trajectory summarisation techniques can solve this problem, generating a smaller and more manageable representation and even semantic segments. In this comprehensive review, we explain and classify techniques for the summarisation of trajectories according to their search strategy and point evaluation criteria, describing connections with the line simplification problem. We also explain several special concepts in trajectory summarisation problem. Finally, we outline the recent trends and best practices to continue the research in next summarisation algorithms.The author(s) disclosed receipt of the following financial support for the research, authorship and/or publication of this article: This work was funded by public research projects of Spanish Ministry of Economy and Competitivity (MINECO), reference TEC2017-88048-C2-2-