Characterization and Reduction of Noise in Manifold Representations of Hyperspectral Imagery

A new workflow to produce dimensionality reduced manifold coordinates based on the improvements of landmark Isometric Mapping (ISOMAP) algorithms using local spectral models is proposed. Manifold space from nonlinear dimensionality reduction better addresses the nonlinearity of the hyperspectral data and often has better per- formance comparing to the results of linear methods such as Minimum Noise Fraction (MNF). The dissertation mainly focuses on using adaptive local spectral models to fur- ther improve the performance of ISOMAP algorithms by addressing local noise issues and perform guided landmark selection and nearest neighborhood construction in local spectral subsets. This work could benefit the performance of common hyperspectral image analysis tasks, such as classification, target detection, etc., but also keep the computational burden low. This work is based on and improves the previous ENH- ISOMAP algorithm in various ways. The workflow is based on a unified local spectral subsetting framework. Embedding spaces in local spectral subsets as local noise models are first proposed and used to perform noise estimation, MNF regression and guided landmark selection in a local sense. Passive and active methods are proposed and ver- ified to select landmarks deliberately to ensure local geometric structure coverage and local noise avoidance. Then, a novel local spectral adaptive method is used to construct the k-nearest neighbor graph. Finally, a global MNF transformation in the manifold space is also introduced to further compress the signal dimensions. The workflow is implemented using C++ with multiple implementation optimizations, including using heterogeneous computing platforms that are available in personal computers. The re- sults are presented and evaluated by Jeffries-Matsushita separability metric, as well as the classification accuracy of supervised classifiers. The proposed workflow shows sig- nificant and stable improvements over the dimensionality reduction performance from traditional MNF and ENH-ISOMAP on various hyperspectral datasets. The computa- tional speed of the proposed implementation is also improved

WLAN-paikannuksen elinkaaren tukeminen

The advent of GPS positioning at the turn of the millennium provided consumers with worldwide access to outdoor location information. For the purposes of indoor positioning, however, the GPS signal rarely penetrates buildings well enough to maintain the same level of positioning granularity as outdoors. Arriving around the same time, wireless local area networks (WLAN) have gained widespread support both in terms of infrastructure deployments and client proliferation. A promising approach to bridge the location context then has been positioning based on WLAN signals. In addition to being readily available in most environments needing support for location information, the adoption of a WLAN positioning system is financially low-cost compared to dedicated infrastructure approaches, partly due to operating on an unlicensed frequency band. Furthermore, the accuracy provided by this approach is enough for a wide range of location-based services, such as navigation and location-aware advertisements. In spite of this attractive proposition and extensive research in both academia and industry, WLAN positioning has yet to become the de facto choice for indoor positioning. This is despite over 20 000 publications and the foundation of several companies. The main reasons for this include: (i) the cost of deployment, and re-deployment, which is often significant, if not prohibitive, in terms of work hours; (ii) the complex propagation of the wireless signal, which -- through interaction with the environment -- renders it inherently stochastic; (iii) the use of an unlicensed frequency band, which means the wireless medium faces fierce competition by other technologies, and even unintentional radiators, that can impair traffic in unforeseen ways and impact positioning accuracy. This thesis addresses these issues by developing novel solutions for reducing the effort of deployment, including optimizing the indoor location topology for the use of WLAN positioning, as well as automatically detecting sources of cross-technology interference. These contributions pave the way for WLAN positioning to become as ubiquitous as the underlying technology.GPS-paikannus avattiin julkiseen käyttöön vuosituhannen vaihteessa, jonka jälkeen sitä on voinut käyttää sijainnin paikantamiseen ulkotiloissa kaikkialla maailmassa. Sisätiloissa GPS-signaali kuitenkin harvoin läpäisee rakennuksia kyllin hyvin voidakseen tarjota vastaavaa paikannustarkkuutta. Langattomat lähiverkot (WLAN), mukaan lukien tukiasemat ja käyttölaitteet, yleistyivät nopeasti samoihin aikoihin. Näiden verkkojen signaalien käyttö on siksi alusta asti tarjonnut lupaavia mahdollisuuksia sisätilapaikannukseen. Useimmissa ympäristöissä on jo valmiit WLAN-verkot, joten paikannuksen käyttöönotto on edullista verrattuna järjestelmiin, jotka vaativat erillisen laitteiston. Tämä johtuu osittain lisenssivapaasta taajuusalueesta, joka mahdollistaa kohtuuhintaiset päätelaitteet. WLAN-paikannuksen tarjoama tarkkuus on lisäksi riittävä monille sijaintipohjaisille palveluille, kuten suunnistamiselle ja paikkatietoisille mainoksille. Näistä lupaavista alkuasetelmista ja laajasta tutkimuksesta huolimatta WLAN-paikannus ei ole kuitenkaan pystynyt lunastamaan paikkaansa pääasiallisena sisätilapaikannusmenetelmänä. Vaivannäöstä ei ole puutetta; vuosien saatossa on julkaistu yli 20 000 tieteellistä artikkelia sekä perustettu useita yrityksiä. Syitä tähän kehitykseen on useita. Ensinnäkin, paikannuksen pystyttäminen ja ylläpito vaativat aikaa ja vaivaa. Toiseksi, langattoman signaalin eteneminen ja vuorovaikutus ympäristön kanssa on hyvin monimutkaista, mikä tekee mallintamisesta vaikeaa. Kolmanneksi, eri teknologiat ja laitteet kilpailevat lisenssivapaan taajuusalueen käytöstä, mikä johtaa satunnaisiin paikannustarkkuuteen vaikuttaviin tietoliikennehäiriöihin. Väitöskirja esittelee uusia menetelmiä joilla voidaan merkittävästi pienentää paikannusjärjestelmän asennuskustannuksia, jakaa ympäristö automaattisesti osiin WLAN-paikannusta varten, sekä tunnistaa mahdolliset langattomat häiriölähteet. Nämä kehitysaskeleet edesauttavat WLAN-paikannuksen yleistymistä jokapäiväiseen käyttöön

Machine learning methods for the characterization and classification of complex data

This thesis work presents novel methods for the analysis and classification of medical images and, more generally, complex data. First, an unsupervised machine learning method is proposed to order anterior chamber OCT (Optical Coherence Tomography) images according to a patient's risk of developing angle-closure glaucoma. In a second study, two outlier finding techniques are proposed to improve the results of above mentioned machine learning algorithm, we also show that they are applicable to a wide variety of data, including fraud detection in credit card transactions. In a third study, the topology of the vascular network of the retina, considering it a complex tree-like network is analyzed and we show that structural differences reveal the presence of glaucoma and diabetic retinopathy. In a fourth study we use a model of a laser with optical injection that presents extreme events in its intensity time-series to evaluate machine learning methods to forecast such extreme events.El presente trabajo de tesis desarrolla nuevos métodos para el análisis y clasificación de imágenes médicas y datos complejos en general. Primero, proponemos un método de aprendizaje automático sin supervisión que ordena imágenes OCT (tomografía de coherencia óptica) de la cámara anterior del ojo en función del grado de riesgo del paciente de padecer glaucoma de ángulo cerrado. Luego, desarrollamos dos métodos de detección automática de anomalías que utilizamos para mejorar los resultados del algoritmo anterior, pero que su aplicabilidad va mucho más allá, siendo útil, incluso, para la detección automática de fraudes en transacciones de tarjetas de crédito. Mostramos también, cómo al analizar la topología de la red vascular de la retina considerándola una red compleja, podemos detectar la presencia de glaucoma y de retinopatía diabética a través de diferencias estructurales. Estudiamos también un modelo de un láser con inyección óptica que presenta eventos extremos en la serie temporal de intensidad para evaluar diferentes métodos de aprendizaje automático para predecir dichos eventos extremos.Aquesta tesi desenvolupa nous mètodes per a l’anàlisi i la classificació d’imatges mèdiques i dades complexes. Hem proposat, primer, un mètode d’aprenentatge automàtic sense supervisió que ordena imatges OCT (tomografia de coherència òptica) de la cambra anterior de l’ull en funció del grau de risc del pacient de patir glaucoma d’angle tancat. Després, hem desenvolupat dos mètodes de detecció automàtica d’anomalies que hem utilitzat per millorar els resultats de l’algoritme anterior, però que la seva aplicabilitat va molt més enllà, sent útil, fins i tot, per a la detecció automàtica de fraus en transaccions de targetes de crèdit. Mostrem també, com en analitzar la topologia de la xarxa vascular de la retina considerant-la una xarxa complexa, podem detectar la presència de glaucoma i de retinopatia diabètica a través de diferències estructurals. Finalment, hem estudiat un làser amb injecció òptica, el qual presenta esdeveniments extrems en la sèrie temporal d’intensitat. Hem avaluat diferents mètodes per tal de predir-los.Postprint (published version

Behaviour Profiling using Wearable Sensors for Pervasive Healthcare

In recent years, sensor technology has advanced in terms of hardware sophistication and miniaturisation. This has led to the incorporation of unobtrusive, low-power sensors into networks centred on human participants, called Body Sensor Networks. Amongst the most important applications of these networks is their use in healthcare and healthy living. The technology has the possibility of decreasing burden on the healthcare systems by providing care at home, enabling early detection of symptoms, monitoring recovery remotely, and avoiding serious chronic illnesses by promoting healthy living through objective feedback. In this thesis, machine learning and data mining techniques are developed to estimate medically relevant parameters from a participant‘s activity and behaviour parameters, derived from simple, body-worn sensors. The first abstraction from raw sensor data is the recognition and analysis of activity. Machine learning analysis is applied to a study of activity profiling to detect impaired limb and torso mobility. One of the advances in this thesis to activity recognition research is in the application of machine learning to the analysis of 'transitional activities': transient activity that occurs as people change their activity. A framework is proposed for the detection and analysis of transitional activities. To demonstrate the utility of transition analysis, we apply the algorithms to a study of participants undergoing and recovering from surgery. We demonstrate that it is possible to see meaningful changes in the transitional activity as the participants recover. Assuming long-term monitoring, we expect a large historical database of activity to quickly accumulate. We develop algorithms to mine temporal associations to activity patterns. This gives an outline of the user‘s routine. Methods for visual and quantitative analysis of routine using this summary data structure are proposed and validated. The activity and routine mining methodologies developed for specialised sensors are adapted to a smartphone application, enabling large-scale use. Validation of the algorithms is performed using datasets collected in laboratory settings, and free living scenarios. Finally, future research directions and potential improvements to the techniques developed in this thesis are outlined

Segmentation of pelvic structures from preoperative images for surgical planning and guidance

Prostate cancer is one of the most frequently diagnosed malignancies globally and the second leading cause of cancer-related mortality in males in the developed world. In recent decades, many techniques have been proposed for prostate cancer diagnosis and treatment. With the development of imaging technologies such as CT and MRI, image-guided procedures have become increasingly important as a means to improve clinical outcomes. Analysis of the preoperative images and construction of 3D models prior to treatment would help doctors to better localize and visualize the structures of interest, plan the procedure, diagnose disease and guide the surgery or therapy. This requires efficient and robust medical image analysis and segmentation technologies to be developed. The thesis mainly focuses on the development of segmentation techniques in pelvic MRI for image-guided robotic-assisted laparoscopic radical prostatectomy and external-beam radiation therapy. A fully automated multi-atlas framework is proposed for bony pelvis segmentation in MRI, using the guidance of MRI AE-SDM. With the guidance of the AE-SDM, a multi-atlas segmentation algorithm is used to delineate the bony pelvis in a new \ac{MRI} where there is no CT available. The proposed technique outperforms state-of-the-art algorithms for MRI bony pelvis segmentation. With the SDM of pelvis and its segmented surface, an accurate 3D pelvimetry system is designed and implemented to measure a comprehensive set of pelvic geometric parameters for the examination of the relationship between these parameters and the difficulty of robotic-assisted laparoscopic radical prostatectomy. This system can be used in both manual and automated manner with a user-friendly interface. A fully automated and robust multi-atlas based segmentation has also been developed to delineate the prostate in diagnostic MR scans, which have large variation in both intensity and shape of prostate. Two image analysis techniques are proposed, including patch-based label fusion with local appearance-specific atlases and multi-atlas propagation via a manifold graph on a database of both labeled and unlabeled images when limited labeled atlases are available. The proposed techniques can achieve more robust and accurate segmentation results than other multi-atlas based methods. The seminal vesicles are also an interesting structure for therapy planning, particularly for external-beam radiation therapy. As existing methods fail for the very onerous task of segmenting the seminal vesicles, a multi-atlas learning framework via random decision forests with graph cuts refinement has further been proposed to solve this difficult problem. Motivated by the performance of this technique, I further extend the multi-atlas learning to segment the prostate fully automatically using multispectral (T1 and T2-weighted) MR images via hybrid \ac{RF} classifiers and a multi-image graph cuts technique. The proposed method compares favorably to the previously proposed multi-atlas based prostate segmentation. The work in this thesis covers different techniques for pelvic image segmentation in MRI. These techniques have been continually developed and refined, and their application to different specific problems shows ever more promising results.Open Acces

Automatic Recognition and Generation of Affective Movements

Body movements are an important non-verbal communication medium through which affective states of the demonstrator can be discerned. For machines, the capability to recognize affective expressions of their users and generate appropriate actuated responses with recognizable affective content has the potential to improve their life-like attributes and to create an engaging, entertaining, and empathic human-machine interaction. This thesis develops approaches to systematically identify movement features most salient to affective expressions and to exploit these features to design computational models for automatic recognition and generation of affective movements. The proposed approaches enable 1) identifying which features of movement convey affective expressions, 2) the automatic recognition of affective expressions from movements, 3) understanding the impact of kinematic embodiment on the perception of affective movements, and 4) adapting pre-defined motion paths in order to "overlay" specific affective content. Statistical learning and stochastic modeling approaches are leveraged, extended, and adapted to derive a concise representation of the movements that isolates movement features salient to affective expressions and enables efficient and accurate affective movement recognition and generation. In particular, the thesis presents two new approaches to fixed-length affective movement representation based on 1) functional feature transformation, and 2) stochastic feature transformation (Fisher scores). The resulting representations are then exploited for recognition of affective expressions in movements and for salient movement feature identification. For functional representation, the thesis adapts dimensionality reduction techniques (namely, principal component analysis (PCA), Fisher discriminant analysis, Isomap) for functional datasets and applies the resulting reduction techniques to extract a minimal set of features along which affect-specific movements are best separable. Furthermore, the centroids of affect-specific clusters of movements in the resulting functional PCA subspace along with the inverse mapping of functional PCA are used to generate prototypical movements for each affective expression. The functional discriminative modeling is however limited to cases where affect-specific movements also have similar kinematic trajectories and does not address the interpersonal and stochastic variations inherent to bodily expression of affect. To account for these variations, the thesis presents a novel affective movement representation in terms of stochastically-transformed features referred to as Fisher scores. The Fisher scores are derived from affect-specific hidden Markov model encoding of the movements and exploited to discriminate between different affective expressions using a support vector machine (SVM) classification. Furthermore, the thesis presents a new approach for systematic identification of a minimal set of movement features most salient to discriminating between different affective expressions. The salient features are identified by mapping Fisher scores to a low-dimensional subspace where dependencies between the movements and their affective labels are maximized. This is done by maximizing Hilbert Schmidt independence criterion between the Fisher score representation of movements and their affective labels. The resulting subspace forms a suitable basis for affective movement recognition using nearest neighbour classification and retains the high recognition rates achieved by SVM classification in the Fisher score space. The dimensions of the subspace form a minimal set of salient features and are used to explore the movement kinematic and dynamic cues that connote affective expressions. Furthermore, the thesis proposes the use of movement notation systems from the dance community (specifically, the Laban system) for abstract coding and computational analysis of movement. A quantification approach for Laban Effort and Shape is proposed and used to develop a new computational model for affective movement generation. Using the Laban Effort and Shape components, the proposed generation approach searches a labeled dataset for movements that are kinematically similar to a desired motion path and convey a target emotion. A hidden Markov model of the identified movements is obtained and used with the desired motion path in the Viterbi state estimation. The estimated state sequence is then used to generate a novel movement that is a version of the desired motion path, modulated to convey the target emotion. Various affective human movement corpora are used to evaluate and demonstrate the efficacy of the developed approaches for the automatic recognition and generation of affective expressions in movements. Finally, the thesis assesses the human perception of affective movements and the impact of display embodiment and the observer's gender on the affective movement perception via user studies in which participants rate the expressivity of synthetically-generated and human-generated affective movements animated on anthropomorphic and non-anthropomorphic embodiments. The user studies show that the human perception of affective movements is mainly shaped by intended emotions, and that the display embodiment and the observer's gender can significantly impact the perception of affective movements

Dynamic Hyperspectral and Polarized Endoscopic Imaging

The health of rich, developed nations has seen drastic improvement in the last two centuries. For it to continue improving at a similar rate new or improved diagnostic and treatment technologies are required, especially for those diseases such as cancer which are forecast to constitute the majority of disease burden in the future. Optical techniques such as microscopy have long played their part in the diagnostic process. However there are several new biophotonic modalities that aim to exploit various interactions between light and tissue to provide enhanced diagnostic information. Many of these show promise in a laboratory setting but few have progressed to a clinical setting. We have designed and constructed a flexible, multi-modal, multi-spectral laparoscopic imaging system that could be used to demonstrate several different techniques in a clinical setting. The core of this system is a dynamic hyperspectral illumination system based around a supercontinuum laser and Digital Micromirror Device that can provide specified excitation light in the visible and near infra-red ranges. This is a powerful tool for spectroscopic techniques as it is not limited to interrogating a fixed range of wavelengths and can switch between excitation bands instantaneously. The excitation spectra can be customised to match particular fluorophores or absorption features, introducing new possibilities for spectral imaging. A standard 10 mm diameter rigid endoscope was incorporated into the system to reduce cost and demonstrate compatibility with existing equipment. The polarization properties of two commercial endoscopes were characterised and found to be unsuited to current polarization imaging techniques as birefringent materials used in their construction introduce complex, spatially dependent transformations of the polarization state. Preliminary exemplar data from phantoms and ex vivo tissue was collected and the feasibility and accuracy of different analysis techniques demonstrated including multiple class classification algorithms. Finally, a novel visualisation method was implemented in order to display the complex hyperspectral data sets in a meaningful and intuitive way to the user

Landmark Localization, Feature Matching and Biomarker Discovery from Magnetic Resonance Images

The work presented in this thesis proposes several methods that can be roughly divided into three different categories: I) landmark localization in medical images, II) feature matching for image registration, and III) biomarker discovery in neuroimaging. The first part deals with the identification of anatomical landmarks. The motivation stems from the fact that the manual identification and labeling of these landmarks is very time consuming and prone to observer errors, especially when large datasets must be analyzed. In this thesis we present three methods to tackle this challenge: A landmark descriptor based on local self-similarities (SS), a subspace building framework based on manifold learning and a sparse coding landmark descriptor based on data-specific learned dictionary basis. The second part of this thesis deals with finding matching features between a pair of images. These matches can be used to perform a registration between them. Registration is a powerful tool that allows mapping images in a common space in order to aid in their analysis. Accurate registration can be challenging to achieve using intensity based registration algorithms. Here, a framework is proposed for learning correspondences in pairs of images by matching SS features and random sample and consensus (RANSAC) is employed as a robust model estimator to learn a deformation model based on feature matches. Finally, the third part of the thesis deals with biomarker discovery using machine learning. In this section a framework for feature extraction from learned low-dimensional subspaces that represent inter-subject variability is proposed. The manifold subspace is built using data-driven regions of interest (ROI). These regions are learned via sparse regression, with stability selection. Also, probabilistic distribution models for different stages in the disease trajectory are estimated for different class populations in the low-dimensional manifold and used to construct a probabilistic scoring function.Open Acces

Nonlinear Dimensionality Reduction by Manifold Unfolding

Every second, an enormous volume of data is being gathered from various sources and stored in huge data banks. Most of the time, monitoring a data source requires several parallel measurements, which form a high-dimensional sample vector. Due to the curse of dimensionality, applying machine learning methods, that is, studying and analyzing high-dimensional data, could be difficult. The essential task of dimensionality reduction is to faithfully represent a given set of high-dimensional data samples with a few variables. The goal of this thesis is to develop and propose new techniques for handling high-dimensional data, in order to address contemporary demand in machine learning applications. Most prominent nonlinear dimensionality reduction methods do not explicitly provide a way to handle out-of-samples. The starting point of this thesis is a nonlinear technique, called Embedding by Affine Transformations (EAT), which reduces the dimensionality of out-of-sample data as well. In this method, a convex optimization is solved for estimating a transformation between the high-dimensional input space and the low-dimensional embedding space. To the best of our knowledge, EAT is the only distance-preserving method for nonlinear dimensionality reduction capable of handling out-of-samples. The second method that we propose is TesseraMap. This method is a scalable extension of EAT. Conceptually, TesseraMap partitions the underlying manifold of data into a set of tesserae and then unfolds it by constructing a tessellation in a low-dimensional subspace of the embedding space. Crucially, the desired tessellation is obtained through solving a small semidefinite program; therefore, this method can efficiently handle tens of thousands of data points in a short time. The final outcome of this thesis is a novel method in dimensionality reduction called Isometric Patch Alignment (IPA). Intuitively speaking, IPA first considers a number of overlapping flat patches, which cover the underlying manifold of the high-dimensional input data. Then, IPA rearranges the patches and stitches the neighbors together on their overlapping parts. We prove that stitching two neighboring patches aligns them together; thereby, IPA unfolds the underlying manifold of data. Although this method and TesseraMap have similar approaches, IPA is more scalable; it embeds one million data points in only a few minutes. More importantly, unlike EAT and TesseraMap, which unfold the underlying manifold by stretching it, IPA constructs the unfolded manifold through patch alignment. We show this novel approach is advantageous in many cases. In addition, compared to the other well-known dimensionality reduction methods, IPA has several important characteristics; for example, it is noise tolerant, it handles non-uniform samples, and it can embed non-convex manifolds properly. In addition to these three dimensionality reduction methods, we propose a method for subspace clustering called Low-dimensional Localized Clustering (LDLC). In subspace clustering, data is partitioned into clusters, such that the points of each cluster lie close to a low-dimensional subspace. The unique property of LDLC is that it produces localized clusters on the underlying manifold of data. By conducting several experiments, we show this property is an asset in many machine learning tasks. This method can also be used for local dimensionality reduction. Moreover, LDLC is a suitable tool for forming the tesserae in TesseraMap, and also for creating the patches in IPA.1 yea