Topographic mappings and feed-forward neural networks

This thesis is a study of the generation of topographic mappings - dimension reducing transformations of data that preserve some element of geometric structure - with feed-forward neural networks. As an alternative to established methods, a transformational variant of Sammon's method is proposed, where the projection is effected by a radial basis function neural network. This approach is related to the statistical field of multidimensional scaling, and from that the concept of a 'subjective metric' is defined, which permits the exploitation of additional prior knowledge concerning the data in the mapping process. This then enables the generation of more appropriate feature spaces for the purposes of enhanced visualisation or subsequent classification. A comparison with established methods for feature extraction is given for data taken from the 1992 Research Assessment Exercise for higher educational institutions in the United Kingdom. This is a difficult high-dimensional dataset, and illustrates well the benefit of the new topographic technique. A generalisation of the proposed model is considered for implementation of the classical multidimensional scaling (¸mds}) routine. This is related to Oja's principal subspace neural network, whose learning rule is shown to descend the error surface of the proposed ¸mds model. Some of the technical issues concerning the design and training of topographic neural networks are investigated. It is shown that neural network models can be less sensitive to entrapment in the sub-optimal global minima that badly affect the standard Sammon algorithm, and tend to exhibit good generalisation as a result of implicit weight decay in the training process. It is further argued that for ideal structure retention, the network transformation should be perfectly smooth for all inter-data directions in input space. Finally, there is a critique of optimisation techniques for topographic mappings, and a new training algorithm is proposed. A convergence proof is given, and the method is shown to produce lower-error mappings more rapidly than previous algorithms.

Metastable de-excitation spectroscopy and density functional theory study of the selective oxidation of crotyl alcohol over Pd(111)

The extremely surface sensitive technique of metastable de-excitation spectroscopy (MDS) has been utilized to probe the bonding and reactivity of crotyl alcohol over Pd(111) and provide insight into the selective oxidation pathway to crotonaldehyde. Auger de-excitation (AD) of metastable He (23S) atoms reveals distinct features associated with the molecular orbitals of the adsorbed alcohol, corresponding to emission from the hydrocarbon skeleton, the O n nonbonding, and C═C π states. The O n and C═C π states of the alcohol are reversed when compared to those of the aldehyde. Density functional theory (DFT) calculations of the alcohol show that an adsorption mode with both C═C and O bonds aligned somewhat parallel to the surface is energetically favored at a substrate temperature below 200 K. Density of states calculations for such configurations are in excellent agreement with experimental MDS measurements. MDS revealed oxidative dehydrogenation of crotyl alcohol to crotonaldehyde between 200 and 250 K, resulting in small peak shifts to higher binding energy. Intramolecular changes lead to the opposite assignment of the first two MOs in the alcohol versus the aldehyde, in accordance with DFT and UPS studies of the free molecules. Subsequent crotonaldehyde decarbonylation and associated propylidyne formation above 260 K could also be identified by MDS and complementary theoretical calculations as the origin of deactivation and selectivity loss. Combining MDS and DFT in this way represents a novel approach to elucidating surface catalyzed reaction pathways associated with a “real-world” practical chemical transformation, namely the selective oxidation of alcohols to aldehydes.

On the Automorphism Groups of some AG-Codes Based on Ca;b Curves

*Partially supported by NATO.

Improved data visualisation through multiple dissimilarity modelling

Popular dimension reduction and visualisation algorithms rely on the assumption that input dissimilarities are typically Euclidean, for instance Metric Multidimensional Scaling, t-distributed Stochastic Neighbour Embedding and the Gaussian Process Latent Variable Model. It is well known that this assumption does not hold for most datasets and often high-dimensional data sits upon a manifold of unknown global geometry. We present a method for improving the manifold charting process, coupled with Elastic MDS, such that we no longer assume that the manifold is Euclidean, or of any particular structure. We draw on the benefits of different dissimilarity measures allowing for the relative responsibilities, under a linear combination, to drive the visualisation process.

A csomagoláson található információtartalom újragondolása sokdimenziós skálázással az élelmiszeripar példáján (Rethinking of information content on food packaging using multidimensional scaling)

A csomagolás részét képezi a jelölés – vagy más néven címke, label –, aminek elsődleges funkciója a termék tulajdonságairól való tájékoztatás, amellett, hogy a vállalat és a fogyasztó egyik legfontosabb találkozási pontja. Kiemelt szerepe van a marketing és a vállalati menedzsment eszköztárában, hiszen a fogyasztói döntéshozatal meghatározó forrása. A szerző írásában a jelölések definícióját, fajtáit és csoportosítását tárja az olvasó elé, majd ismerteti jelentőségét, fontosságát és szerepét az élelmiszer-ipari termékek segítségével. Ezután egy 630 fős megkérdezés eredményeképp a sokdimenziós skálázás (MDS) módszerével a jelölések új értelmezését mutatja be: a jelöléseket három dimenzió mentén lehet elhelyezni (előzetes tudás, érdek, megbízhatóság), valamint ezenkívül a jelölések öt homogén csoportot alkotnak (klasszikus, diétás, funkcionális, tudatos, előállítási). A téma jelentőségét az egészség és a környezet iránti növekvő érdeklődés, valamint a változó jogszabályi környezet is alátámasztja. / === / Signs, labels, claims are to inform consumers of product attributes, and are part of the packaging. Labeling is one of the most important marketing and management tool, while purchase decision is made at the point of purchase. The aim of this paper is to present the basic definitions and elements of information content on food packaging. The author developed a new approach to examine labeling using multidimensional scaling as a result of a pilot study. Labels are to distinguish through three dimensions: precognition, interest and reliability. Beyond that labels can be sorted to five homogeneous clusters based on classic, dietary, functional, conscious and production attributes. The relevancy of labeling is supported by growing interest of health and environmental issues and changing law environment.

Svájci rendszerű sakk csapatversenyek rangsorolása (Ranking in Swiss system chess team tournaments)

A cikk a páros összehasonlításokon alapuló pontozási eljárásokat alkalmazza svájci rendszerű sakk csapatversenyek eredményének meghatározására. Bemutatjuk a nem körmérkőzéses esetben felmerülő kérdéseket, az egyéni és csapatversenyek jellemzőit, valamint a hivatalos lexikografikus rendezések hibáit. Axiomatikus alapokon rangsorolási problémaként modellezzük a bajnokságokat, definícióinkat összekapcsoljuk a pontszám, az általánosított sorösszeg és a legkisebb négyzetek módszerének tulajdonságaival. A javasolt eljárást két sakkcsapat Európa-bajnokság részletes elemzésével illusztráljuk. A végső rangsorok összehasonlítását távolságfüggvények segítségével végezzük el, majd a sokdimenziós skálázás révén ábrázoljuk azokat. A hivatalos sorrendtől való eltérés okait a legkisebb négyzetek módszerének dekompozíciójával tárjuk fel. A sorrendeket három szempont, az előrejelző képesség, a mintailleszkedés és a robusztusság alapján értékeljük, és a legkisebb négyzetek módszerének alkalmas eredménymátrixszal történő használata mellett érvelünk. ____ The paper uses paired comparison-based scoring procedures in order to determine the result of Swiss system chess team tournaments. We present the main challenges of ranking in these tournaments, the features of individual and team competitions as well as the failures of official lexicographical orders. The tournament is represented as a ranking problem, our model is discussed with respect to the properties of the score, generalised row sum and least squares methods. The proposed method is illustrated with a detailed analysis of the two recent chess team European championships. Final rankings are compared through their distances and visualized by multidimensional scaling (MDS). Differences to official ranking are revealed due to the decomposition of least squares method. Rankings are evaluated by prediction accuracy, retrodictive performance, and stability. The paper argues for the use of least squares method with an appropriate generalised results matrix favouring match points.

Ranking in Swiss system chess team tournaments

The paper uses paired comparison-based scoring procedures for ranking the participants of a Swiss system chess team tournament. We present the main challenges of ranking in Swiss system, the features of individual and team competitions as well as the failures of official lexicographical orders. The tournament is represented as a ranking problem, our model is discussed with respect to the properties of the score, generalized row sum and least squares methods. The proposed procedure is illustrated with a detailed analysis of the two recent chess team European championships. Final rankings are compared by their distances and visualized with multidimensional scaling (MDS). Differences to official ranking are revealed by the decomposition of least squares method. Rankings are evaluated by prediction accuracy, retrodictive performance, and stability. The paper argues for the use of least squares method with a results matrix favoring match points.

Understanding Ten-Eleven Translocation-2 in Hematological and Nervous Systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.

Foraminíferos como ferramenta de estudo na geologia ambiental do estuário do Rio Potengi e da plataforma interna, RN, Brasil

The Potengi River estuary has been affected by various anthropogenic factors over the years, as periodic dredging, industrial and domestic waste, traffic and other factors, causing various environmental disasters, including the notorious ecological accident in July 2007, which covered the municipalities of São Gonçalo do Amarante, Macaíba and Natal. Foraminifera serve as viable study tools in these environments; they are able to identify ecologically stressed environments, pointing out hydrographic changes and depositional environments in estuaries. The necessity to check the differences in environmental gradients in places anthropically impacted in Potengi River and adjacent inner shelf through species of foraminifera, and, the responses of these organisms to physical, chemical and geological factors is to provide baseline in the diagnosis of environments. The results show the dominance of opportunistic Ammonia tepida, Bolivina striatula, Quinqueloculina patagonica and Q. miletti especially in regions close to shrimp farms and Baldo Channel sewage in fine grain environments; and Q. lamarckiana indicates penetration of the saline waters in Potengi River. The occurrence of low-salinity tolerant foraminiferal species typical of mangrove environments as Trochammina inflata and T. squamata in Potengi River Channel suggest they probably could have been transported from mangrove area near the Potengi river mouth to the inner shelf regions. These findings suggest Potengi River is able to export mixohaline and mangrove organisms to inner shelf. Two distinct environments were observed, the outermost area is more influenced by marine influence and the innermost area is less influenced. Calcareous and agglutinated species dominate Potengi River, while mouth and inner shelf areas are dominated by calcareous, agglutinated and porcelaneous species, which are typical of highly saline and hydrodynamic environments and the contributive factors that controls foraminiferal distribution were balance of marine and freshwater currents, grain size, availability of CaCO3 and organic matter.

Foraminíferos como ferramenta de estudo na geologia ambiental do estuário do Rio Potengi e da plataforma interna, RN, Brasil

The Potengi River estuary has been affected by various anthropogenic factors over the years, as periodic dredging, industrial and domestic waste, traffic and other factors, causing various environmental disasters, including the notorious ecological accident in July 2007, which covered the municipalities of São Gonçalo do Amarante, Macaíba and Natal. Foraminifera serve as viable study tools in these environments; they are able to identify ecologically stressed environments, pointing out hydrographic changes and depositional environments in estuaries. The necessity to check the differences in environmental gradients in places anthropically impacted in Potengi River and adjacent inner shelf through species of foraminifera, and, the responses of these organisms to physical, chemical and geological factors is to provide baseline in the diagnosis of environments. The results show the dominance of opportunistic Ammonia tepida, Bolivina striatula, Quinqueloculina patagonica and Q. miletti especially in regions close to shrimp farms and Baldo Channel sewage in fine grain environments; and Q. lamarckiana indicates penetration of the saline waters in Potengi River. The occurrence of low-salinity tolerant foraminiferal species typical of mangrove environments as Trochammina inflata and T. squamata in Potengi River Channel suggest they probably could have been transported from mangrove area near the Potengi river mouth to the inner shelf regions. These findings suggest Potengi River is able to export mixohaline and mangrove organisms to inner shelf. Two distinct environments were observed, the outermost area is more influenced by marine influence and the innermost area is less influenced. Calcareous and agglutinated species dominate Potengi River, while mouth and inner shelf areas are dominated by calcareous, agglutinated and porcelaneous species, which are typical of highly saline and hydrodynamic environments and the contributive factors that controls foraminiferal distribution were balance of marine and freshwater currents, grain size, availability of CaCO3 and organic matter.

Targeting androgen receptor activation function-1 with EPI to overcome resistance mechanisms in castration-resistant prostate cancer

Financial support: This research was supported by grants to MDS from the NCI (2R01CA105304), the Canadian Institutes of Health Research (MOP79308) and the US Army Medical Research and Materiel Command Prostate Cancer Research Program (E81XWH-11-1-0551). Research by IJM’s group was supported by the Chief Scientist’s Office of the Scottish Government (ETM-258 and -382). We are grateful to Country Meadows Senior Men’s Golf Charity Classic for financial support of this research.

Predictors of functional dependency in Parkinson’s disease

Financial disclosures/conflicts of interest: Dr Macleod was funded by a Clinical Academic Fellowship from the Chief Scientist Office of the Scottish Government and received grant funding from Parkinson’s UK, the Wellcome Trust, University of Aberdeen, and NHS Grampian endowments relating to this research. Dr Counsell received grant funding from Parkinson’s UK, National Institute for Health Research, the Scottish Chief Scientist Office, the BMA Doris Hillier award, RS Macdonald Trust, the BUPA Foundation, NHS Grampian endowments and SPRING relating to this research. We declare we have no conflicts of interest. Financial support: This study was funded by Parkinson’s UK, the Scottish Chief Scientist Office, NHS Grampian endowments, the BMA Doris Hillier award, RS Macdonald Trust, the BUPA Foundation, and SPRING.  

Positionality and Comparisons: Critical Views on Qualitative Research across Asia

Ce cahier est basé sur la réflexion autobiographique de deux chercheuses ayant effectué des recherches qualitatives et ethnographiques, de 2008 à 2014, en Asie centrale et du Sud-­‐Est. Les expériences sur le terrain constituent des moyens de comparaisons dans le présent document. En mettant l’accent sur le positionnement sur le terrain, l’étude montre que, d’abord, il est essentiel de détenir une poste intermédiaire et de parler une langue locale afin de garantir un accès et de mener des activités de recherche sur le terrain. Deuxièmement, différentes régions prédéterminent des contextes culturels et politiques ponctuels qui, à leur tour, façonneraient la recherche en sciences sociales. Troisièmement, le fait d’être une femme présente à la fois des avantages et des inconvénients. Enfin, en termes de méthodologie, les stages et les entrevues se sont avérés des méthodes fiables pour la collecte des données empiriques sur les régions ci-­‐dessus mentionnées, sans pour autant permettre de bâtir la confiance.

Detection and Classification of Whale Acoustic Signals

This dissertation focuses on two vital challenges in relation to whale acoustic signals: detection and classification.

In detection, we evaluated the influence of the uncertain ocean environment on the spectrogram-based detector, and derived the likelihood ratio of the proposed Short Time Fourier Transform detector. Experimental results showed that the proposed detector outperforms detectors based on the spectrogram. The proposed detector is more sensitive to environmental changes because it includes phase information.

In classification, our focus is on finding a robust and sparse representation of whale vocalizations. Because whale vocalizations can be modeled as polynomial phase signals, we can represent the whale calls by their polynomial phase coefficients. In this dissertation, we used the Weyl transform to capture chirp rate information, and used a two dimensional feature set to represent whale vocalizations globally. Experimental results showed that our Weyl feature set outperforms chirplet coefficients and MFCC (Mel Frequency Cepstral Coefficients) when applied to our collected data.

Since whale vocalizations can be represented by polynomial phase coefficients, it is plausible that the signals lie on a manifold parameterized by these coefficients. We also studied the intrinsic structure of high dimensional whale data by exploiting its geometry. Experimental results showed that nonlinear mappings such as Laplacian Eigenmap and ISOMAP outperform linear mappings such as PCA and MDS, suggesting that the whale acoustic data is nonlinear.

We also explored deep learning algorithms on whale acoustic data. We built each layer as convolutions with either a PCA filter bank (PCANet) or a DCT filter bank (DCTNet). With the DCT filter bank, each layer has different a time-frequency scale representation, and from this, one can extract different physical information. Experimental results showed that our PCANet and DCTNet achieve high classification rate on the whale vocalization data set. The word error rate of the DCTNet feature is similar to the MFSC in speech recognition tasks, suggesting that the convolutional network is able to reveal acoustic content of speech signals.

Positionality and Comparisons: Critical Views on Qualitative Research across Asia

Ce cahier est basé sur la réflexion autobiographique de deux chercheuses ayant effectué des recherches qualitatives et ethnographiques, de 2008 à 2014, en Asie centrale et du Sud-­‐Est. Les expériences sur le terrain constituent des moyens de comparaisons dans le présent document. En mettant l’accent sur le positionnement sur le terrain, l’étude montre que, d’abord, il est essentiel de détenir une poste intermédiaire et de parler une langue locale afin de garantir un accès et de mener des activités de recherche sur le terrain. Deuxièmement, différentes régions prédéterminent des contextes culturels et politiques ponctuels qui, à leur tour, façonneraient la recherche en sciences sociales. Troisièmement, le fait d’être une femme présente à la fois des avantages et des inconvénients. Enfin, en termes de méthodologie, les stages et les entrevues se sont avérés des méthodes fiables pour la collecte des données empiriques sur les régions ci-­‐dessus mentionnées, sans pour autant permettre de bâtir la confiance.