Automatic alignment of surgical videos using kinematic data

Over the past one hundred years, the classic teaching methodology of "see one, do one, teach one" has governed the surgical education systems worldwide. With the advent of Operation Room 2.0, recording video, kinematic and many other types of data during the surgery became an easy task, thus allowing artificial intelligence systems to be deployed and used in surgical and medical practice. Recently, surgical videos has been shown to provide a structure for peer coaching enabling novice trainees to learn from experienced surgeons by replaying those videos. However, the high inter-operator variability in surgical gesture duration and execution renders learning from comparing novice to expert surgical videos a very difficult task. In this paper, we propose a novel technique to align multiple videos based on the alignment of their corresponding kinematic multivariate time series data. By leveraging the Dynamic Time Warping measure, our algorithm synchronizes a set of videos in order to show the same gesture being performed at different speed. We believe that the proposed approach is a valuable addition to the existing learning tools for surgery.Comment: Accepted at AIME 201

Highly comparative feature-based time-series classification

A highly comparative, feature-based approach to time series classification is introduced that uses an extensive database of algorithms to extract thousands of interpretable features from time series. These features are derived from across the scientific time-series analysis literature, and include summaries of time series in terms of their correlation structure, distribution, entropy, stationarity, scaling properties, and fits to a range of time-series models. After computing thousands of features for each time series in a training set, those that are most informative of the class structure are selected using greedy forward feature selection with a linear classifier. The resulting feature-based classifiers automatically learn the differences between classes using a reduced number of time-series properties, and circumvent the need to calculate distances between time series. Representing time series in this way results in orders of magnitude of dimensionality reduction, allowing the method to perform well on very large datasets containing long time series or time series of different lengths. For many of the datasets studied, classification performance exceeded that of conventional instance-based classifiers, including one nearest neighbor classifiers using Euclidean distances and dynamic time warping and, most importantly, the features selected provide an understanding of the properties of the dataset, insight that can guide further scientific investigation

Final Research Report for Sound Design and Audio Player

This deliverable describes the work on Task 4.3 Algorithms for sound design and feature developments for audio player. The audio player runs on the in-store player (ISP) and takes care of rendering the music playlists via beat-synchronous automatic DJ mixing, taking advantage of the rich musical content description extracted in T4.2 (beat markers, structural segmentation into intro and outro, musical and sound content classification). The deliverable covers prototypes and final results on: (1) automatic beat-synchronous mixing by beat alignment and time stretching – we developed an algorithm for beat alignment and scheduling of time-stretched tracks; (2) compensation of play duration changes introduced by time stretching – in order to make the playlist generator independent of beat mixing, we chose to readjust the tempo of played tracks such that their stretched duration is the same as their original duration; (3) prospective research on the extraction of data from DJ mixes – to alleviate the lack of extensive ground truth databases of DJ mixing practices, we propose steps towards extracting this data from existing mixes by alignment and unmixing of the tracks in a mix. We also show how these methods can be evaluated even without labelled test data, and propose an open dataset for further research; (4) a description of the software player module, a GUI-less application to run on the ISP that performs streaming of tracks from disk and beat-synchronous mixing. The estimation of cue points where tracks should cross-fade is now described in D4.7 Final Research Report on Auto-Tagging of Music.EC/H2020/688122/EU/Artist-to-Business-to-Business-to-Consumer Audio Branding System/ABC D

Feature-based time-series analysis

This work presents an introduction to feature-based time-series analysis. The time series as a data type is first described, along with an overview of the interdisciplinary time-series analysis literature. I then summarize the range of feature-based representations for time series that have been developed to aid interpretable insights into time-series structure. Particular emphasis is given to emerging research that facilitates wide comparison of feature-based representations that allow us to understand the properties of a time-series dataset that make it suited to a particular feature-based representation or analysis algorithm. The future of time-series analysis is likely to embrace approaches that exploit machine learning methods to partially automate human learning to aid understanding of the complex dynamical patterns in the time series we measure from the world.Comment: 28 pages, 9 figure

Discrete Elastic Inner Vector Spaces with Application in Time Series and Sequence Mining

This paper proposes a framework dedicated to the construction of what we call discrete elastic inner product allowing one to embed sets of non-uniformly sampled multivariate time series or sequences of varying lengths into inner product space structures. This framework is based on a recursive definition that covers the case of multiple embedded time elastic dimensions. We prove that such inner products exist in our general framework and show how a simple instance of this inner product class operates on some prospective applications, while generalizing the Euclidean inner product. Classification experimentations on time series and symbolic sequences datasets demonstrate the benefits that we can expect by embedding time series or sequences into elastic inner spaces rather than into classical Euclidean spaces. These experiments show good accuracy when compared to the euclidean distance or even dynamic programming algorithms while maintaining a linear algorithmic complexity at exploitation stage, although a quadratic indexing phase beforehand is required.Comment: arXiv admin note: substantial text overlap with arXiv:1101.431

Time Series Data Mining Algorithms for Identifying Short RNA in Arabidopsis thaliana

The class of molecules called short RNAs (sRNAs) are known to play a key role in gene regulation. Th are typically sequences of nucleotides between 21-25 nucleotides in length. They are known to play a key role in gene regulation. The identification, clustering and classification of sRNA has recently become the focus of much research activity. The basic problem involves detecting regions of interest on the chromosome where the pattern of candidate matches is somehow unusual. Currently, there are no published algorithms for detecting regions of interest, and the unpublished methods that we are aware of involve bespoke rule based systems designed for a specific organism. Work in this very new field has understandably focused on the outcomes rather than the methods used to obtain the results. In this paper we propose two generic approaches that place the specific biological problem in the wider context of time series data mining problems. Both methods are based on treating the occurrences on a chromosome, or “hit count” data, as a time series, then running a sliding window along a chromosome and measuring unusualness. This formulation means we can treat finding unusual areas of candidate RNA activity as a variety of time series anomaly detection problem. The first set of approaches is model based. We specify a null hypothesis distribution for not being a sRNA, then estimate the p-values along the chromosome. The second approach is instance based. We identify some typical shapes from known sRNA, then use dynamic time warping and fourier trans-form based distance to measure how closely the candidate series matches. We demonstrate that these methods can find known sRNA on Arabidopsis thaliana chromosomes and illustrate the benefits of the added information provided by these algorithms

Image similarity using dynamic time warping of fractal features

Hashing algorithms such as MD/SHA variants have been used for years by forensic investigators to look for known artefacts of interest such as malicious files. However, such hashing algorithms are not effective when their hashes change with the slightest alteration in the file. Fuzzy hashing overcame this limitation to a certain extent by providing a close enough measure for slight modifications. As such, image forensics is an essential part of any digital crime investigation, especially in cases involving child pornography. Unfortunately such hashing algorithms can be thwarted easily by operations as simple as saving the original file in a different image format. This paper introduces a novel technique for measuring image similarity using Dynamic Time Warping (DTW) of fractal features taken from the frequency domain. DTW has traditionally been used successfully for speech recognition. Our experiments have shown that it is also effective for measuring image similarity while tolerating minor modifications, which is currently not capable by state-of-the-art tools