High-Content Analysis of Breast Cancer Using Single-Cell Deep Transfer Learning

High-content analysis has revolutionized cancer drug discovery by identifying substances that alter the phenotype of a cell, which prevents tumor growth and metastasis. The high-resolution biofluorescence images from assays allow precise quantitative measures enabling the distinction of small molecules of a host cell from a tumor. In this work, we are particularly interested in the application of deep neural networks (DNNs), a cutting-edge machine learning method, to the classification of compounds in chemical mechanisms of action (MOAs). Compound classification has been performed using image-based profiling methods sometimes combined with feature reduction methods such as principal component analysis or factor analysis. In this article, we map the input features of each cell to a particular MOA class without using any treatment-level profiles or feature reduction methods. To the best of our knowledge, this is the first application of DNN in this domain, leveraging single-cell information. Furthermore, we use deep transfer learning (DTL) to alleviate the intensive and computational demanding effort of searching the huge parameter's space of a DNN. Results show that using this approach, we obtain a 30% speedup and a 2% accuracy improvement.

Evaluation Metrics and Transfer Learning for Sales Prediction

Sales prediction plays a huge role in modern business strategies. One of it's many use cases revolves around estimating the effects of promotions. While promotions generally have a positive effect on sales of the promoted product, they can also have a negative effect on those of other products. This phenomenon is calles sales cannibalisation. Sales cannibalisation can pose a big problem to sales forcasting algorithms. A lot of times, these algorithms focus on sales over time of a single product in a single store (a couple). This research focusses on using knowledge of a product across multiple different stores. To achieve this, we applied transfer learning on a neural model developed by Kantar Consulting to demo an approach to estimating the effect of cannibalisation. Our results show a performance increase of between 10 and 14 percent. This is a very good and desired result, and Kantar will use the approach when integrating this test method into their actual systems.

Application of active and transfer learning to wound image segmentation

Wound management is a fundamental task in standard clinical practice. Automated solutions already exist for humans, but there is a lack of applications on wound management for pets. The importance of a precise and efficient wound assessment is helpful to improve diagnosis and to increase the effectiveness of treatment plans for the chronic wounds. The goal of the research was to propose an automated pipeline capable of segmenting natural light-reflected wound images of animals. Two datasets composed by light-reflected images were used in this work: Deepskin dataset, 1564 human wound images obtained during routine dermatological exams, with 145 manual annotated images; Petwound dataset, a set of 290 wound photos of dogs and cats with 0 annotated images. Two implementations of U-Net Convolutioal Neural Network model were proposed for the automated segmentation. Active Semi-Supervised Learning techniques were applied for human-wound images to perform segmentation from 10% of annotated images. Then the same models were trained, via Transfer Learning, adopting an Active Semi- upervised Learning to unlabelled animal-wound images. The combination of the two training strategies proved their effectiveness in generating large amounts of annotated samples (94% of Deepskin, 80% of PetWound) with the minimal human intervention. The correctness of automated segmentation were evaluated by clinical experts at each round of training thus we can assert that the results obtained in this thesis stands as a reliable solution to perform a correct wound image segmentation. The use of Transfer Learning and Active Semi-Supervied Learning allows to minimize labelling effort from clinicians, even requiring no starting manual annotation at all. Moreover the performances of the model with limited number of parameters suggest the implementation of smartphone-based application to this topic, helping the future standardization of light-reflected images as acknowledge medical images.

Deep learning based style transfer for low altitude aerial imagery

Unmanned Aerial Vehicle (UAVs) equipped with cameras have been fast deployed to a wide range of applications, such as smart cities, agriculture or search and rescue applications. Even though UAV datasets exist, the amount of open and quality UAV datasets is limited. So far, we want to overcome this lack of high quality annotation data by developing a simulation framework for a parametric generation of synthetic data. The framework accepts input via a serializable format. The input specifies which environment preset is used, the objects to be placed in the environment along with their position and orientation as well as additional information such as object color and size. The result is an environment that is able to produce UAV typical data: RGB image from the UAVs camera, altitude, roll, pitch and yawn of the UAV. Beyond the image generation process, we improve the resulting image data photorealism by using Synthetic-To-Real transfer learning methods. Transfer learning focuses on storing knowledge gained while solving one problem and applying it to a different - although related - problem. This approach has been widely researched in other affine fields and results demonstrate it to be an interesing area to investigate. Since simulated images are easy to create and synthetic-to-real translation has shown good quality results, we are able to generate pseudo-realistic images. Furthermore, object labels are inherently given, so we are capable of extending the already existing UAV datasets with realistic quality images and high resolution meta-data. During the development of this thesis we have been able to produce a result of 68.4% on UAVid. This can be considered a new state-of-art result on this dataset.

Analyzing the learning of the taking personal and social responsibility model within a new physical education undergraduate degree program in El Salvador

EI Salvador presents an unfortunate history that includes a military regime and a civil war that together created a legacy of violence in which the country still struggle nowadays. Salud Escolar Integral (SEI) was created in 2005 as a program to combat youth violence throughout the re-formulation of physical education (PE) classes in public schools, promoting life skills learning that supports the resolution of conflicts with nonviolent ways. In 2007, SEI supported the creation of a physical e~ucation teacher education (PETE) degree at the Universidad Pedag6gica de EI Salvador (UPES), having the goal to assist pre-service teachers with a better understanding of humanistic principles. The present research analyzed if after attending all three years ofUPES PETE program, students presented high self-perception levels of competence and confidence related to attitude, skills and knowledge to teach PE within humanistic principles. Taking Personal and Social Responsibility (TPSR) was the theoretical framework used to analyze the development of humanistic principles. The study had a mixed-method longitudinal design that included questionnaires, reflection templates and interviews. In conclusion, although it is suggested that UPES should provide better support for the development of the teaching principles of empowering students and transfer learning, most of the humanistic principles were highly promoted by the program. At last, it is suggested that future research should track teachers' progress while teaching in schools, in order to analyze if the theory of promoting humanistic principles have also become a daily practice.

Action learning: how learning transfers from entrepreneurs to small firms

The paper presents research with small and medium enterprise (SME) owners who have participated in a leadership development programme. The primary focus of the paper is on learning transfer and factors affecting it, arguing that entrepreneurs must engage in ‘action’ in order to ‘learn’ and that under certain conditions they may transfer learning to their firm. The paper draws on data from 19 focus groups undertaken from 2010 to 2012, involving 51 participants in the LEAD Wales programme. It considers the literatures exploring learning transfer and develops a conceptual framework, outlining four areas of focus for entrepreneurial learning. Utilising thematic analysis, it describes and evaluates what (actual facts and information) and how (techniques, styles of learning) participants transfer and what actions they take to improve the business and develop their people. The paper illustrates the complex mechanisms involved in this process and concludes that action learning is a method of facilitating entrepreneurial learning which is able to help address some of the problems of engagement, relevance and value that have been highlighted previously. The paper concludes that the efficacy of an entrepreneurial learning intervention in SMEs may depend on the effectiveness of learning transfer.

Editorial:knowledge flows, learning and development in an international context

In the editorial of this special issue we argue that knowledge flows, learning and development are becoming increasingly important in all organisations operating in an international context. The possession of capabilities relating to acquisition, configuration and transfer of relevant knowledge effectively within and across different organisational units, teams, and countries is integrally related to superior organisational performance. In mastering such capabilities, internationalised organisations need to grapple with the inherent challenges relating to contextual variation and different work modes between subsidiaries, partners or team members. The papers in this special issue cast light on crucial aspects of knowledge flows, learning and development in internationalised organisations. Their contribution varies from the provision of frameworks to systematise investigation of these issues, to empirical evidence about effective mechanisms, as well as enabling and constraining forces, in facilitating knowledge transfer, learning and human capital development. © 2012 Inderscience Enterprises Ltd.

Bayesian Learning with Dependency Structures via Latent Factors, Mixtures, and Copulas

Bayesian methods offer a flexible and convenient probabilistic learning framework to extract interpretable knowledge from complex and structured data. Such methods can characterize dependencies among multiple levels of hidden variables and share statistical strength across heterogeneous sources. In the first part of this dissertation, we develop two dependent variational inference methods for full posterior approximation in non-conjugate Bayesian models through hierarchical mixture- and copula-based variational proposals, respectively. The proposed methods move beyond the widely used factorized approximation to the posterior and provide generic applicability to a broad class of probabilistic models with minimal model-specific derivations. In the second part of this dissertation, we design probabilistic graphical models to accommodate multimodal data, describe dynamical behaviors and account for task heterogeneity. In particular, the sparse latent factor model is able to reveal common low-dimensional structures from high-dimensional data. We demonstrate the effectiveness of the proposed statistical learning methods on both synthetic and real-world data.

Development and characterization of deep learning techniques for neuroimaging data

Deep learning methods are extremely promising machine learning tools to analyze neuroimaging data. However, their potential use in clinical settings is limited because of the existing challenges of applying these methods to neuroimaging data. In this study, first a data leakage type caused by slice-level data split that is introduced during training and validation of a 2D CNN is surveyed and a quantitative assessment of the model’s performance overestimation is presented. Second, an interpretable, leakage-fee deep learning software written in a python language with a wide range of options has been developed to conduct both classification and regression analysis. The software was applied to the study of mild cognitive impairment (MCI) in patients with small vessel disease (SVD) using multi-parametric MRI data where the cognitive performance of 58 patients measured by five neuropsychological tests is predicted using a multi-input CNN model taking brain image and demographic data. Each of the cognitive test scores was predicted using different MRI-derived features. As MCI due to SVD has been hypothesized to be the effect of white matter damage, DTI-derived features MD and FA produced the best prediction outcome of the TMT-A score which is consistent with the existing literature. In a second study, an interpretable deep learning system aimed at 1) classifying Alzheimer disease and healthy subjects 2) examining the neural correlates of the disease that causes a cognitive decline in AD patients using CNN visualization tools and 3) highlighting the potential of interpretability techniques to capture a biased deep learning model is developed. Structural magnetic resonance imaging (MRI) data of 200 subjects was used by the proposed CNN model which was trained using a transfer learning-based approach producing a balanced accuracy of 71.6%. Brain regions in the frontal and parietal lobe showing the cerebral cortex atrophy were highlighted by the visualization tools.

Computer vision in aseptic pharmaceutical manufacturing: a deep learning-based approach to vial inspection and pack formation during a lyophilizer loading cycle

Vision systems are powerful tools playing an increasingly important role in modern industry, to detect errors and maintain product standards. With the enlarged availability of affordable industrial cameras, computer vision algorithms have been increasingly applied in industrial manufacturing processes monitoring. Until a few years ago, industrial computer vision applications relied only on ad-hoc algorithms designed for the specific object and acquisition setup being monitored, with a strong focus on co-designing the acquisition and processing pipeline. Deep learning has overcome these limits providing greater flexibility and faster re-configuration. In this work, the process to be inspected consists in vials’ pack formation entering a freeze-dryer, which is a common scenario in pharmaceutical active ingredient packaging lines. To ensure that the machine produces proper packs, a vision system is installed at the entrance of the freeze-dryer to detect eventual anomalies with execution times compatible with the production specifications. Other constraints come from sterility and safety standards required in pharmaceutical manufacturing. This work presents an overview about the production line, with particular focus on the vision system designed, and about all trials conducted to obtain the final performance. Transfer learning, alleviating the requirement for a large number of training data, combined with data augmentation methods, consisting in the generation of synthetic images, were used to effectively increase the performances while reducing the cost of data acquisition and annotation. The proposed vision algorithm is composed by two main subtasks, designed respectively to vials counting and discrepancy detection. The first one was trained on more than 23k vials (about 300 images) and tested on 5k more (about 75 images), whereas 60 training images and 52 testing images were used for the second one.

Apprentissage d'espaces sémantiques

Dans cette dissertation, nous présentons plusieurs techniques d’apprentissage d’espaces sémantiques pour plusieurs domaines, par exemple des mots et des images, mais aussi à l’intersection de différents domaines. Un espace de représentation est appelé sémantique si des entités jugées similaires par un être humain, ont leur similarité préservée dans cet espace. La première publication présente un enchaînement de méthodes d’apprentissage incluant plusieurs techniques d’apprentissage non supervisé qui nous a permis de remporter la compétition “Unsupervised and Transfer Learning Challenge” en 2011. Le deuxième article présente une manière d’extraire de l’information à partir d’un contexte structuré (177 détecteurs d’objets à différentes positions et échelles). On montrera que l’utilisation de la structure des données combinée à un apprentissage non supervisé permet de réduire la dimensionnalité de 97% tout en améliorant les performances de reconnaissance de scènes de +5% à +11% selon l’ensemble de données. Dans le troisième travail, on s’intéresse à la structure apprise par les réseaux de neurones profonds utilisés dans les deux précédentes publications. Plusieurs hypothèses sont présentées et testées expérimentalement montrant que l’espace appris a de meilleures propriétés de mixage (facilitant l’exploration de différentes classes durant le processus d’échantillonnage). Pour la quatrième publication, on s’intéresse à résoudre un problème d’analyse syntaxique et sémantique avec des réseaux de neurones récurrents appris sur des fenêtres de contexte de mots. Dans notre cinquième travail, nous proposons une façon d’effectuer de la recherche d’image ”augmentée” en apprenant un espace sémantique joint où une recherche d’image contenant un objet retournerait aussi des images des parties de l’objet, par exemple une recherche retournant des images de ”voiture” retournerait aussi des images de ”pare-brises”, ”coffres”, ”roues” en plus des images initiales.

Ability assessment and job structure measures in occupational mobility

Recent and potential changes in technology have resulted in the anticipation of increases in the frequency of job changes. This has led manpower policy makers to investigate the feasibility of incorporating the employment skills of job groups in the general prediction of future job learning and performance with a view to the establishment of "job families" within which transfer might be considered reciprocally high. A structured job analysis instrument (the Position Analysis Questionnaire) is evaluated in terms of two distinct sets of scores; job dimensions and synthetically established attribute/trait profiles. Studies demonstrate that estimates of a job's structure/dimensions and requisite human attributes can be reliably established. Three alternative techniques of statistically assembling profiles of the requisite human attributes for jobs are found to have differential levels of reliability and differential degrees of validity in their estimation of the "actual" ability requirements of jobs. The utility of these two sets of job descriptors to serve as representations of the cognitive structure similarity of job groups is investigated in a study which simulates a job transfer situation. The central role of the index of similarity used to assess the relationship between "target" and "present" job is demonstrated. The relative extents to which job structure similarity and job attribute similariity are associated with positive transfer are investigated. The studies demonstrate that the dimensions of jobs, and more fruitfully their requisite human attributes can serve as bases to predict job transfer learning and performance. The nature of the index of similarity used to optimally formulate predictions of transfer is such that networks of jobs might be establishable to which current job incumbents could be expected to transfer positively. The derivation of "job families" with anticipated reciprocal transfer consequences is considered to be less appropriate.

The dynamics of global sourcing : perspectives and practices:6th global sourcing workshop 2012, Courchevel, France, March 12-15, 2012, revised selected papers

This edited book is intended for use by students, academics and practitioners who take interest in the outsourcing and offshoring of information technology and business services and processes. The book offers a review of the key topics in outsourcing and offshoring, populated with practical frameworks that serve as a tool kit for practitioners, academics and students. The range of topics covered in this book is wide and diverse, and represents both client and supplier perspectives on sourcing of global services. Various aspects related to the decision making process (e.g., asset transfer), learning mechanisms and organizational practices for managing outsourcing relationships are discussed in great depth. Contemporary sourcing models, including cloud services, are examined. Client dependency on the outsourcing provider, and social aspects, such as identity, are discussed in detail. Furthermore, resistance in outsourcing and failures are investigated to derive lessons as to how to avoid them and improve efficiency in outsourcing. Topics discussed in this book combine theoretical and practical insights regarding challenges that both clients and vendors face. Case studies from client and vendor organizations are used extensively throughout the book. Last but not least, the book examines current and future trends in outsourcing and offshoring, placing particular attention on the centrality of innovation in sourcing arrangements, and how innovation can be realized in outsourcing. The book is based on a vast empirical base brought together through years of extensive research by leading researchers in information systems, strategic management and operations.

Preface

This edited book is intended for use by students, academics and practitioners who take interest in the outsourcing and offshoring of information technology and business services and processes. The book offers a review of the key topics in outsourcing and offshoring, populated with practical frameworks that serve as a tool kit for practitioners, academics and students. The range of topics covered in this book is wide and diverse, and represents both client and supplier perspectives on sourcing of global services. Various aspects related to the decision making process (e.g., asset transfer), learning mechanisms and organizational practices for managing outsourcing relationships are discussed in great depth. Contemporary sourcing models, including cloud services, are examined. Client dependency on the outsourcing provider, and social aspects, such as identity, are discussed in detail. Furthermore, resistance in outsourcing and failures are investigated to derive lessons as to how to avoid them and improve efficiency in outsourcing. Topics discussed in this book combine theoretical and practical insights regarding challenges that both clients and vendors face. Case studies from client and vendor organizations are used extensively throughout the book. Last but not least, the book examines current and future trends in outsourcing and offshoring, placing particular attention on the centrality of innovation in sourcing arrangements, and how innovation can be realized in outsourcing. The book is based on a vast empirical base brought together through years of extensive research by leading researchers in information systems, strategic management and operations.

Stretching the life of Twitter classifiers with time-stamped semantic graphs

Social media has become an effective channel for communicating both trends and public opinion on current events. However the automatic topic classification of social media content pose various challenges. Topic classification is a common technique used for automatically capturing themes that emerge from social media streams. However, such techniques are sensitive to the evolution of topics when new event-dependent vocabularies start to emerge (e.g., Crimea becoming relevant to War Conflict during the Ukraine crisis in 2014). Therefore, traditional supervised classification methods which rely on labelled data could rapidly become outdated. In this paper we propose a novel transfer learning approach to address the classification task of new data when the only available labelled data belong to a previous epoch. This approach relies on the incorporation of knowledge from DBpedia graphs. Our findings show promising results in understanding how features age, and how semantic features can support the evolution of topic classifiers.