Machine Learning methods for hepatocellular malignancies segmentation and MVI prediction

The aim of this thesis project is to automatically localize HCC tumors in the human liver and subsequently predict if the tumor will undergo microvascular infiltration (MVI), the initial stage of metastasis development. The input data for the work have been partially supplied by Sant'Orsola Hospital and partially downloaded from online medical databases. Two Unet models have been implemented for the automatic segmentation of the livers and the HCC malignancies within it. The segmentation models have been evaluated with the Intersection-over-Union and the Dice Coefficient metrics. The outcomes obtained for the liver automatic segmentation are quite good (IOU = 0.82; DC = 0.35); the outcomes obtained for the tumor automatic segmentation (IOU = 0.35; DC = 0.46) are, instead, affected by some limitations: it can be state that the algorithm is almost always able to detect the location of the tumor, but it tends to underestimate its dimensions. The purpose is to achieve the CT images of the HCC tumors, necessary for features extraction. The 14 Haralick features calculated from the 3D-GLCM, the 120 Radiomic features and the patients' clinical information are collected to build a dataset of 153 features. Now, the goal is to build a model able to discriminate, based on the features given, the tumors that will undergo MVI and those that will not. This task can be seen as a classification problem: each tumor needs to be classified either as “MVI positive” or “MVI negative”. Techniques for features selection are implemented to identify the most descriptive features for the problem at hand and then, a set of classification models are trained and compared. Among all, the models with the best performances (around 80-84% ± 8-15%) result to be the XGBoost Classifier, the SDG Classifier and the Logist Regression models (without penalization and with Lasso, Ridge or Elastic Net penalization).

Development of unsupervised learning methods with applications to life sciences data

Machine Learning makes computers capable of performing tasks typically requiring human intelligence. A domain where it is having a considerable impact is the life sciences, allowing to devise new biological analysis protocols, develop patients’ treatments efficiently and faster, and reduce healthcare costs. This Thesis work presents new Machine Learning methods and pipelines for the life sciences focusing on the unsupervised field. At a methodological level, two methods are presented. The first is an “Ab Initio Local Principal Path” and it is a revised and improved version of a pre-existing algorithm in the manifold learning realm. The second contribution is an improvement over the Import Vector Domain Description (one-class learning) through the Kullback-Leibler divergence. It hybridizes kernel methods to Deep Learning obtaining a scalable solution, an improved probabilistic model, and state-of-the-art performances. Both methods are tested through several experiments, with a central focus on their relevance in life sciences. Results show that they improve the performances achieved by their previous versions. At the applicative level, two pipelines are presented. The first one is for the analysis of RNA-Seq datasets, both transcriptomic and single-cell data, and is aimed at identifying genes that may be involved in biological processes (e.g., the transition of tissues from normal to cancer). In this project, an R package is released on CRAN to make the pipeline accessible to the bioinformatic Community through high-level APIs. The second pipeline is in the drug discovery domain and is useful for identifying druggable pockets, namely regions of a protein with a high probability of accepting a small molecule (a drug). Both these pipelines achieve remarkable results. Lastly, a detour application is developed to identify the strengths/limitations of the “Principal Path” algorithm by analyzing Convolutional Neural Networks induced vector spaces. This application is conducted in the music and visual arts domains.

Development of machine learning methods for multi-modal biomarkers detection and integration

In medicine, innovation depends on a better knowledge of the human body mechanism, which represents a complex system of multi-scale constituents. Unraveling the complexity underneath diseases proves to be challenging. A deep understanding of the inner workings comes with dealing with many heterogeneous information. Exploring the molecular status and the organization of genes, proteins, metabolites provides insights on what is driving a disease, from aggressiveness to curability. Molecular constituents, however, are only the building blocks of the human body and cannot currently tell the whole story of diseases. This is why nowadays attention is growing towards the contemporary exploitation of multi-scale information. Holistic methods are then drawing interest to address the problem of integrating heterogeneous data. The heterogeneity may derive from the diversity across data types and from the diversity within diseases. Here, four studies conducted data integration using customly designed workflows that implement novel methods and views to tackle the heterogeneous characterization of diseases. The first study devoted to determine shared gene regulatory signatures for onco-hematology and it showed partial co-regulation across blood-related diseases. The second study focused on Acute Myeloid Leukemia and refined the unsupervised integration of genomic alterations, which turned out to better resemble clinical practice. In the third study, network integration for artherosclerosis demonstrated, as a proof of concept, the impact of network intelligibility when it comes to model heterogeneous data, which showed to accelerate the identification of new potential pharmaceutical targets. Lastly, the fourth study introduced a new method to integrate multiple data types in a unique latent heterogeneous-representation that facilitated the selection of important data types to predict the tumour stage of invasive ductal carcinoma. The results of these four studies laid the groundwork to ease the detection of new biomarkers ultimately beneficial to medical practice and to the ever-growing field of Personalized Medicine.

Satisfaction of clinical nurses with the formation of a university tutorial program

Degree in nursing from the Universitat Jaume I (UJI) maintains the continuity of learning with an integrated learning methodology (theory, simulated practice and clinical practice). The objective of this methodology is to achieve consistency between the knowledge, abilities and skills acquired in the classroom, laboratory and clinic to ensure skills related. Reference Nurse is a key figure in this process, you receive accredited training on Educational Methods, assessment of competence, and Evidence-Based Practice that plays the role of evaluating in conjunction with the subjects. It does not perceive economic remuneration. The main objective of this study is to determine the level of satisfaction of clinical nurses on the Nurses Training Program Reference in UJI (Castellon- Spain). A cross sectional study was performed and conducted on 150 nurses. 112 questionnaires were completed, collected and analysed at the end of training. The survey consists of 12 items measured with the Likert scale with 5 levels of response and two open questions regarding the positive and negative aspects of the course and to add in this formation. The training is always performed by the same faculty and it's used four sessions of 2012. We perform a quantitative analysis of the variables under study using measures of central tendency. The completion rate of the survey is 95.53% (n=107). Anonymity rate of 54,14% The overall satisfaction level of training was 3.65 (SD = 0.89) on 5 points. 54.2% (n = 58) of the reference nurses made a contribution in the open questions described in the overall results. The overall satisfaction level can be considered acceptable. It is considered necessary to elaborate a specific survey to detect areas of improvement of nurse training program reference and future recruitment strategies. The main objective of the present work is the selection and integration of different methodologies among those applicable within the framework of the European Higher Education Area to combine teaching methods with high implication from both lecturers and students.

Assessment of Preclinical Learning on Oral Surgery Using Three Instructional Strategies

The purpose of this investigation was to evaluate three learning methods for teaching basic oral surgical skills Thirty predoctoral dental students without any surgical knowledge or previous surgical experience were divided Into three groups (n=10 each) according to instructional strategy Group 1, active learning Group 2, text reading only, and Group 3, text reading and video demonstration After instruction, the apprentices were allowed to practice incision dissection and suture maneuvers in a bench learning model During the students' performance, a structured practice evaluation test to account for correct or incorrect maneuvers was applied by trained observers Evaluation tests were repeated after thirty and sixty days Data from resulting scores between groups and periods were considered for statistical analysis (ANOVA and Tukey Kramer) with a significant level of a=0 05 Results showed that the active learning group presented the significantly best learning outcomes related to immediate assimilation of surgical procedures compared to other groups All groups results were similar after sixty days of the first practice Assessment tests were fundamental to evaluate teaching strategies and allowed theoretical and proficiency learning feedbacks Repetition and interactive practice promoted retention of knowledge on basic oral surgical skills

An interactive learning approach to accounting classes

This working paper explores the use of interactive learning tools, such as business simulations, to facilitate the active learning process in accounting classes. Although business simulations were firstly introduced in the United States in the 1950s, the vast majority of accounting professors still use traditional teaching methods, based in end-of-chapter exercises and written cases. Moreover, the current students’ generation brings new challenges to the classroom related with their video, game, internet and mobile culture. Thus, a survey and an experimentation were conducted to understand, on one hand, if accounting professors are willing to adjust their teaching methods with the adoption of interactive learning tools and, on the other hand, if the adoption of interactive learning tools in accounting classes yield better academic results and levels of satisfaction among students. Students using more interactive learning approaches scored significantly higher means than others that did not. Accounting professors are clearly willing to try, at least once, the use of an accounting simulator in classes.

Advanced Kernel Methods For Remote Sensing Image Classification

Résumé Suite aux recentes avancées technologiques, les archives d'images digitales ont connu une croissance qualitative et quantitative sans précédent. Malgré les énormes possibilités qu'elles offrent, ces avancées posent de nouvelles questions quant au traitement des masses de données saisies. Cette question est à la base de cette Thèse: les problèmes de traitement d'information digitale à très haute résolution spatiale et/ou spectrale y sont considérés en recourant à des approches d'apprentissage statistique, les méthodes à noyau. Cette Thèse étudie des problèmes de classification d'images, c'est à dire de catégorisation de pixels en un nombre réduit de classes refletant les propriétés spectrales et contextuelles des objets qu'elles représentent. L'accent est mis sur l'efficience des algorithmes, ainsi que sur leur simplicité, de manière à augmenter leur potentiel d'implementation pour les utilisateurs. De plus, le défi de cette Thèse est de rester proche des problèmes concrets des utilisateurs d'images satellite sans pour autant perdre de vue l'intéret des méthodes proposées pour le milieu du machine learning dont elles sont issues. En ce sens, ce travail joue la carte de la transdisciplinarité en maintenant un lien fort entre les deux sciences dans tous les développements proposés. Quatre modèles sont proposés: le premier répond au problème de la haute dimensionalité et de la redondance des données par un modèle optimisant les performances en classification en s'adaptant aux particularités de l'image. Ceci est rendu possible par un système de ranking des variables (les bandes) qui est optimisé en même temps que le modèle de base: ce faisant, seules les variables importantes pour résoudre le problème sont utilisées par le classifieur. Le manque d'information étiquétée et l'incertitude quant à sa pertinence pour le problème sont à la source des deux modèles suivants, basés respectivement sur l'apprentissage actif et les méthodes semi-supervisées: le premier permet d'améliorer la qualité d'un ensemble d'entraînement par interaction directe entre l'utilisateur et la machine, alors que le deuxième utilise les pixels non étiquetés pour améliorer la description des données disponibles et la robustesse du modèle. Enfin, le dernier modèle proposé considère la question plus théorique de la structure entre les outputs: l'intègration de cette source d'information, jusqu'à présent jamais considérée en télédétection, ouvre des nouveaux défis de recherche. Advanced kernel methods for remote sensing image classification Devis Tuia Institut de Géomatique et d'Analyse du Risque September 2009 Abstract The technical developments in recent years have brought the quantity and quality of digital information to an unprecedented level, as enormous archives of satellite images are available to the users. However, even if these advances open more and more possibilities in the use of digital imagery, they also rise several problems of storage and treatment. The latter is considered in this Thesis: the processing of very high spatial and spectral resolution images is treated with approaches based on data-driven algorithms relying on kernel methods. In particular, the problem of image classification, i.e. the categorization of the image's pixels into a reduced number of classes reflecting spectral and contextual properties, is studied through the different models presented. The accent is put on algorithmic efficiency and the simplicity of the approaches proposed, to avoid too complex models that would not be used by users. The major challenge of the Thesis is to remain close to concrete remote sensing problems, without losing the methodological interest from the machine learning viewpoint: in this sense, this work aims at building a bridge between the machine learning and remote sensing communities and all the models proposed have been developed keeping in mind the need for such a synergy. Four models are proposed: first, an adaptive model learning the relevant image features has been proposed to solve the problem of high dimensionality and collinearity of the image features. This model provides automatically an accurate classifier and a ranking of the relevance of the single features. The scarcity and unreliability of labeled. information were the common root of the second and third models proposed: when confronted to such problems, the user can either construct the labeled set iteratively by direct interaction with the machine or use the unlabeled data to increase robustness and quality of the description of data. Both solutions have been explored resulting into two methodological contributions, based respectively on active learning and semisupervised learning. Finally, the more theoretical issue of structured outputs has been considered in the last model, which, by integrating outputs similarity into a model, opens new challenges and opportunities for remote sensing image processing.

Learning Preferences with Kernel-Based Methods

Learning of preference relations has recently received significant attention in machine learning community. It is closely related to the classification and regression analysis and can be reduced to these tasks. However, preference learning involves prediction of ordering of the data points rather than prediction of a single numerical value as in case of regression or a class label as in case of classification. Therefore, studying preference relations within a separate framework facilitates not only better theoretical understanding of the problem, but also motivates development of the efficient algorithms for the task. Preference learning has many applications in domains such as information retrieval, bioinformatics, natural language processing, etc. For example, algorithms that learn to rank are frequently used in search engines for ordering documents retrieved by the query. Preference learning methods have been also applied to collaborative filtering problems for predicting individual customer choices from the vast amount of user generated feedback. In this thesis we propose several algorithms for learning preference relations. These algorithms stem from well founded and robust class of regularized least-squares methods and have many attractive computational properties. In order to improve the performance of our methods, we introduce several non-linear kernel functions. Thus, contribution of this thesis is twofold: kernel functions for structured data that are used to take advantage of various non-vectorial data representations and the preference learning algorithms that are suitable for different tasks, namely efficient learning of preference relations, learning with large amount of training data, and semi-supervised preference learning. Proposed kernel-based algorithms and kernels are applied to the parse ranking task in natural language processing, document ranking in information retrieval, and remote homology detection in bioinformatics domain. Training of kernel-based ranking algorithms can be infeasible when the size of the training set is large. This problem is addressed by proposing a preference learning algorithm whose computation complexity scales linearly with the number of training data points. We also introduce sparse approximation of the algorithm that can be efficiently trained with large amount of data. For situations when small amount of labeled data but a large amount of unlabeled data is available, we propose a co-regularized preference learning algorithm. To conclude, the methods presented in this thesis address not only the problem of the efficient training of the algorithms but also fast regularization parameter selection, multiple output prediction, and cross-validation. Furthermore, proposed algorithms lead to notably better performance in many preference learning tasks considered.

Conditions for EFL learning and professional development : Finland-Swedish learner and teacher perspectives

Engelskans dominerande roll som internationellt språk och andra globaliseringstrender påverkar också Svenskfinland. Dessa trender påverkar i sin tur förutsättningarna för lärande och undervisning i engelska som främmande språk, det vill säga undervisningsmålen, de förväntade elev- och lärarroller, materialens ändamålsenlighet, lärares och elevers initiala erfarenheter av engelska och engelskspråkiga länder. Denna studie undersöker förutsättningarna för lärande och professionell utveckling i det svenskspråkiga nybörjarklassrummet i engelska som främmande språk. Utgångsläget för 351 nybörjare i engelska som främmande språk och 19 av deras lärare beskrivs och analyseras. Resultaten tyder på att engelska håller på att bli ett andraspråk snarare än ett traditionellt främmande språk för många unga elever. Dessa elever har också goda förutsättningar att lära sig engelska utanför skolan. Sådan var dock inte situationen för alla elever, vilket tyder på att det finns en anmärkningsvärd heterogenitet och även regional variation i det finlandssvenska klassrummet i engelska som främmande språk. Lärarresultaten tyder på att vissa lärare har klarat av att på ett konstruktivt sätt att tackla de förutsättningar de möter. Andra lärare uttrycker frustration över sin arbetssituation, läroplanen, undervisningsmaterialen och andra aktörer som kommer är av betydelse för skolmiljön. Studien påvisar att förutsättningarna för lärande och undervisning i engelska som främmande språk varierar i Svenskfinland. För att stöda elevers och lärares utveckling föreslås att dialogen mellan aktörer på olika nivå i samhället bör förbättras och systematiseras.

Combined active and semi-supervised learning using particle walking temporal dynamicscombined active and semi-supervised learning using particle walking temporal dynamics

Both Semi-Supervised Leaning and Active Learning are techniques used when unlabeled data is abundant, but the process of labeling them is expensive and/or time consuming. In this paper, those two machine learning techniques are combined into a single nature-inspired method. It features particles walking on a network built from the data set, using a unique random-greedy rule to select neighbors to visit. The particles, which have both competitive and cooperative behavior, are created on the network as the result of label queries. They may be created as the algorithm executes and only nodes affected by the new particles have to be updated. Therefore, it saves execution time compared to traditional active learning frameworks, in which the learning algorithm has to be executed several times. The data items to be queried are select based on information extracted from the nodes and particles temporal dynamics. Two different rules for queries are explored in this paper, one of them is based on querying by uncertainty approaches and the other is based on data and labeled nodes distribution. Each of them may perform better than the other according to some data sets peculiarities. Experimental results on some real-world data sets are provided, and the proposed method outperforms the semi-supervised learning method, from which it is derived, in all of them.

Balancing Exploration and Exploitation: A New Algorithm for Active Machine Learning

Active machine learning algorithms are used when large numbers of unlabeled examples are available and getting labels for them is costly (e.g. requiring consulting a human expert). Many conventional active learning algorithms focus on refining the decision boundary, at the expense of exploring new regions that the current hypothesis misclassifies. We propose a new active learning algorithm that balances such exploration with refining of the decision boundary by dynamically adjusting the probability to explore at each step. Our experimental results demonstrate improved performance on data sets that require extensive exploration while remaining competitive on data sets that do not. Our algorithm also shows significant tolerance of noise.

Computer game-based and traditional learning method: a comparison regarding students’ knowledge retention

Abstract Background Educational computer games are examples of computer-assisted learning objects, representing an educational strategy of growing interest. Given the changes in the digital world over the last decades, students of the current generation expect technology to be used in advancing their learning requiring a need to change traditional passive learning methodologies to an active multisensory experimental learning methodology. The objective of this study was to compare a computer game-based learning method with a traditional learning method, regarding learning gains and knowledge retention, as means of teaching head and neck Anatomy and Physiology to Speech-Language and Hearing pathology undergraduate students. Methods Students were randomized to participate to one of the learning methods and the data analyst was blinded to which method of learning the students had received. Students’ prior knowledge (i.e. before undergoing the learning method), short-term knowledge retention and long-term knowledge retention (i.e. six months after undergoing the learning method) were assessed with a multiple choice questionnaire. Students’ performance was compared considering the three moments of assessment for both for the mean total score and for separated mean scores for Anatomy questions and for Physiology questions. Results Students that received the game-based method performed better in the pos-test assessment only when considering the Anatomy questions section. Students that received the traditional lecture performed better in both post-test and long-term post-test when considering the Anatomy and Physiology questions. Conclusions The game-based learning method is comparable to the traditional learning method in general and in short-term gains, while the traditional lecture still seems to be more effective to improve students’ short and long-term knowledge retention.

Good practice guide in learning and teaching

Once again this publication is produced to celebrate and promote good teaching and learning support and to offer encouragement to those imaginative and innovative staff who continue to wish to challenge students to learn to maximum effect. It is hoped that others will pick up some good ideas from the articles contained in this volume. We have again changed our approach for this 2006/07 edition (our fourth) of the Aston Business School Good Practice Guide. As before, some contributions were selected from those identifying interesting best practice on their Annual Module reflection forms in 2005/2006. Other contributors received HELM (Research Centre in Higher Education Learning and Management) small research grants in 2005/2006. Part of the conditions were for them to write an article for this publication. We have also been less tight on the length of the articles this year. Some contributions are, therefore, on the way to being journal articles. HELM will be working with these authors to help develop these for publication. The themes covered in this year?s articles are all central to the issues faced by those providing HE teaching and learning opportunities in the 21st Century. Specifically this is providing support and feedback to students in large classes, embracing new uses of technology to encourage active learning and addressing cultural issues in a diverse student population. Michael Grojean and Yves Guillaume used Blackboard™ to give a more interactive learning experience and improve feedback to students. It would be easy for other staff to adopt this approach. Patrick Tissington and Qin Zhou (HELM small research grant holders) were keen to improve the efficiency of student support, as does Roger McDermott. Celine Chew shares her action learning project, completed as part of the Aston University PG Certificate in Teaching and Learning. Her use of Blackboard™ puts emphasis on the learner having to do something to help them meet the learning outcomes. This is what learning should be like, but many of our students seem used to a more passive learning experience, so much needs to be done on changing expectations and cultures about learning. Regina Herzfeldt also looks at cultures. She was awarded a HELM small research grant and carried out some significant new research on cultural diversity in ABS and what it means for developing teaching methods. Her results fit in with what many of us are experiencing in practice. Gina leaves us with some challenges for the future. Her paper certainly needs to be published. This volume finishes with Stuart Cooper and Matt Davies reflecting on how to keep students busy in lectures and Pavel Albores working with students on podcasting. Pavel?s work, which was the result of another HELM small research grant, will also be prepared for publication as a journal article. The students learnt more from this work that any formal lecture and Pavel will be using the approach again this year. Some staff have been awarded HELM small research grants in 2006/07 and these will be published in the next Good Practice Guide. In the second volume we mentioned the launch of the School?s Research Centre in Higher Education Learning and Management (HELM). Since then HELM has stimulated a lot of activity across the School (and University) particularly linking research and teaching. A list of the HELM seminars for 2006/2007 is listed as Appendix 1 of this publication. Further details can be obtained from Catherine Foster (c.s.foster@aston.ac.uk), who coordinates the HELM seminars. For 2006 and 2005 HELM listed, 20 refereed journal articles, 7 book chapters, 1 published conference papers, 20 conference presentations, two official reports, nine working papers and £71,535 of grant money produced in this research area across the School. I hope that this shows that reflection on learning is alive and well in ABS. We have also been working on a list of target journals to guide ABS staff who wish to publish in this area. These are included as Appendix 2 of this publication. May I thank the contributors for taking time out of their busy schedules to write the articles and to Julie Green, the Quality Manager, for putting the varying diverse approaches into a coherent and publishable form and for agreeing to fund the printing of this volume.

Patterns for Active E-Learning in CMS Environments

The proliferation of course management systems (CMS) in the last decade stimulated educators in establishing novel active e-learning practices. Only a few of these practices, however, have been systematically described and published as pedagogic patterns. The lack of formal patterns is an obstacle to the systematic reuse of beneficial active e-learning experiences. This paper aims to partially fill the void by offering a collection of active e-learning patterns that are derived from our continuous course design experience in standard CMS environments, such as Moodle and Black-board. Our technical focus is on active e-learning patterns that can boost student interest in computing-related fields and increase student enrolment in computing-related courses. Members of the international e-learning community can benefit from active e-learning patterns by applying them in the design of new CMS-based courses – in computing and other technical fields.

New Advancements of Scalable Statistical Methods for Learning Latent Structures in Big Data

Constant technology advances have caused data explosion in recent years. Accord- ingly modern statistical and machine learning methods must be adapted to deal with complex and heterogeneous data types. This phenomenon is particularly true for an- alyzing biological data. For example DNA sequence data can be viewed as categorical variables with each nucleotide taking four different categories. The gene expression data, depending on the quantitative technology, could be continuous numbers or counts. With the advancement of high-throughput technology, the abundance of such data becomes unprecedentedly rich. Therefore efficient statistical approaches are crucial in this big data era.

Previous statistical methods for big data often aim to find low dimensional struc- tures in the observed data. For example in a factor analysis model a latent Gaussian distributed multivariate vector is assumed. With this assumption a factor model produces a low rank estimation of the covariance of the observed variables. Another example is the latent Dirichlet allocation model for documents. The mixture pro- portions of topics, represented by a Dirichlet distributed variable, is assumed. This dissertation proposes several novel extensions to the previous statistical methods that are developed to address challenges in big data. Those novel methods are applied in multiple real world applications including construction of condition specific gene co-expression networks, estimating shared topics among newsgroups, analysis of pro- moter sequences, analysis of political-economics risk data and estimating population structure from genotype data.