Variational and learning models for image and time series inverse problems

Inverse problems are at the core of many challenging applications. Variational and learning models provide estimated solutions of inverse problems as the outcome of specific reconstruction maps. In the variational approach, the result of the reconstruction map is the solution of a regularized minimization problem encoding information on the acquisition process and prior knowledge on the solution. In the learning approach, the reconstruction map is a parametric function whose parameters are identified by solving a minimization problem depending on a large set of data. In this thesis, we go beyond this apparent dichotomy between variational and learning models and we show they can be harmoniously merged in unified hybrid frameworks preserving their main advantages. We develop several highly efficient methods based on both these model-driven and data-driven strategies, for which we provide a detailed convergence analysis. The arising algorithms are applied to solve inverse problems involving images and time series. For each task, we show the proposed schemes improve the performances of many other existing methods in terms of both computational burden and quality of the solution. In the first part, we focus on gradient-based regularized variational models which are shown to be effective for segmentation purposes and thermal and medical image enhancement. We consider gradient sparsity-promoting regularized models for which we develop different strategies to estimate the regularization strength. Furthermore, we introduce a novel gradient-based Plug-and-Play convergent scheme considering a deep learning based denoiser trained on the gradient domain. In the second part, we address the tasks of natural image deblurring, image and video super resolution microscopy and positioning time series prediction, through deep learning based methods. We boost the performances of supervised, such as trained convolutional and recurrent networks, and unsupervised deep learning strategies, such as Deep Image Prior, by penalizing the losses with handcrafted regularization terms.

Deep learning and embeddings for problems of computational biology

The development of Next Generation Sequencing promotes Biology in the Big Data era. The ever-increasing gap between proteins with known sequences and those with a complete functional annotation requires computational methods for automatic structure and functional annotation. My research has been focusing on proteins and led so far to the development of three novel tools, DeepREx, E-SNPs&GO and ISPRED-SEQ, based on Machine and Deep Learning approaches. DeepREx computes the solvent exposure of residues in a protein chain. This problem is relevant for the definition of structural constraints regarding the possible folding of the protein. DeepREx exploits Long Short-Term Memory layers to capture residue-level interactions between positions distant in the sequence, achieving state-of-the-art performances. With DeepRex, I conducted a large-scale analysis investigating the relationship between solvent exposure of a residue and its probability to be pathogenic upon mutation. E-SNPs&GO predicts the pathogenicity of a Single Residue Variation. Variations occurring on a protein sequence can have different effects, possibly leading to the onset of diseases. E-SNPs&GO exploits protein embeddings generated by two novel Protein Language Models (PLMs), as well as a new way of representing functional information coming from the Gene Ontology. The method achieves state-of-the-art performances and is extremely time-efficient when compared to traditional approaches. ISPRED-SEQ predicts the presence of Protein-Protein Interaction sites in a protein sequence. Knowing how a protein interacts with other molecules is crucial for accurate functional characterization. ISPRED-SEQ exploits a convolutional layer to parse local context after embedding the protein sequence with two novel PLMs, greatly surpassing the current state-of-the-art. All methods are published in international journals and are available as user-friendly web servers. They have been developed keeping in mind standard guidelines for FAIRness (FAIR: Findable, Accessible, Interoperable, Reusable) and are integrated into the public collection of tools provided by ELIXIR, the European infrastructure for Bioinformatics.

Ecological Literacy And Beyond: Problem-based Learning For Future Professionals.

Ecological science contributes to solving a broad range of environmental problems. However, lack of ecological literacy in practice often limits application of this knowledge. In this paper, we highlight a critical but often overlooked demand on ecological literacy: to enable professionals of various careers to apply scientific knowledge when faced with environmental problems. Current university courses on ecology often fail to persuade students that ecological science provides important tools for environmental problem solving. We propose problem-based learning to improve the understanding of ecological science and its usefulness for real-world environmental issues that professionals in careers as diverse as engineering, public health, architecture, social sciences, or management will address. Courses should set clear learning objectives for cognitive skills they expect students to acquire. Thus, professionals in different fields will be enabled to improve environmental decision-making processes and to participate effectively in multidisciplinary work groups charged with tackling environmental issues.

Pedagogia do esporte : pressupostos para uma teoria da avaliação da aprendizagem = Sport pedagogy: presuppositions for a learning assessment theory

Universidade Estadual de Campinas . Faculdade de Educação Física

Triple objective team mentoring: achieving learning objectives with chemical engineering students

A sophisticated style of mentoring has been found to be essential to support engineering student teams undertaking technically demanding, real-world problems as part of a Project-Centred Curriculum (PCC) at The University of Queensland. The term ‘triple-objective’ mentoring was coined to define mentoring that addresses not only the student’s technical goal achievement but also their time and team management. This is achieved through a number of formal mentor meetings that are informed by a confidential instrument which requires students to individually reflect on team processes prior to the meeting, and a checklist of technical requirements against which the interim student team progress and achievements are assessed. Triple-objective mentoring requires significant time input and coordination by the academic but has been shown to ensure effective student team work and learning undiminished by team dysfunction. Student feedback shows they value the process and agree that the tools developed to support the process are effective in developing and assessing team work and skills with average scores mostly above 3 on a four point scale.

Development of educational policy and early intervention for learning difficulties in Australia: In the case of Queensland

This paper aims to describe the historical outline and current development of the educational policy for students with learning difficulties in Australia, focusing especially on the state of Queensland. In order to develop educational policy of learning difficulities at the state level, the concept of learning difficulities had been discussed until the middle of the 1970's. Receiving the submissions which argued strongly against a diagnostically-oriented definition of learning disabilities, the Select Comittee concluded that there was much conceptual confusion regarding the definition and cause of learining difficulties that might take many years to resolve. Despite that it was recongnised that action was needed to assist children by looking at their "total learning environmerit", and recommended the development of an educational policy for students with learning difficulties. During 1980's, support teachers for students with learning difficulties were employed in many schools. Scince the early 1980's support teachers have been making their efforts in regular classrooms rather than in the resource rooms. Their roles have been to help students with learning difficulties using effective and specific skills, and to consult with the regular classroom teacher in solving the problems related to learning difficulties in regular classes. Currently, the support system for students with learning difficulties has been employed to organize a more systematic and broader approach in Queensland based on the accountability of schools. In the context of enphasizing literacy and numeracy, a systematic whole school approach and particular programs, such as the Year 2 Diagnostic Net and Reading Recovery, have been introduced into the educational system for early identification and early intervention.

The Building Partnerships Program: An Approach to Community-based Learning for Medical Students in Australia

The Building Partnerships Program at the University of Queensland, Australia seeks to address the dual challenge of preparing doctors who are responsive to the community while providing a meaningful context for social sciences learning. Through partnerships with a diverse range of community agencies, the program offers students opportunities to gain non-clinical perspectives on health and illness through structured learning activities including: family visits; community agency visits and attachments; and interview training. Students learn first-hand about psychosocial influences on health and how people manage health problems on a day-to-day basis. They also gain insights into the work of community agencies and how they as future doctors might work in partnership with them to enhance patient care. We outline the main components of the program, identify challenges and successes from student and community agency perspectives, and consider areas that invite further development.

e-learning in the classroom?

As teachers, we are challenged everyday to solve pedagogical problems and we have to fight for our students’ attention in a media rich world. I will talk about how we use ICT in Initial Teacher Training and give you some insight on what we are doing. The most important benefit of using ICT in education is that it makes us reflect on our practice. There is no doubt that our classrooms need to be updated, but we need to be critical about every peace of hardware, software or service that we bring into them. It is not only because our budgets are short, but also because e‐learning is primarily about learning, not technology. Therefore, we need to have the knowledge and skills required to act in different situations, and choose the best tool for the job. Not all subjects are suitable for e‐learning, nor do all students have the skills to organize themselves their own study times. Also not all teachers want to spend time programming or learning about instructional design and metadata. The promised land of easy use of authoring tools (e.g. eXe and Reload) that will lead to all teachers become Learning Objects authors and share these LO in Repositories, all this failed, like previously HyperCard, Toolbook and others. We need to know a little bit of many different technologies so we can mobilize this knowledge when a situation requires it: integrate e‐learning technologies in the classroom, not a flipped classroom, just simple tools. Lecture capture, mobile phones and smartphones, pocket size camcorders, VoIP, VLE, live video broadcast, screen sharing, free services for collaborative work, save, share and sync your files. Do not feel stressed to use everything, every time. Just because we have a whiteboard does not mean we have to make it the centre of the classroom. Start from where you are, with your preferred subject and the tools you master. Them go slowly and try some new tool in a non‐formal situation and with just one or two students. And you don’t need to be alone: subscribe a mailing list and share your thoughts with other teachers in a dedicated forum, even better if both are part of a community of practice, and share resources. We did that for music teachers and it was a success, in two years arriving at 1.000 members. Just do it.

Learning in higher education: strategies to overcome challenges faced by adult students - lessons drawn from two studies in portugal

Int’l J. of Information and Communication Technology Education, 3(2), 1-14, April-June 2007

Improving the learning experience and learning environment of adults in Higher Education – Project LIHE: the Portuguese case

Project LIHE: the Portuguese Case. ESREA Fourth Access Network Conference – “Equity, Access and Participation: Research, Policy and Practice”. Edinburgh (Scotland), 11 – 13 December, 2003.

Problem-Based Learning e suas implicações: breve revisão teórica

A ESTSP-IPP implementou em 2008-2009 um novo modelo pedagógico, o PBL, em três licenciaturas. Este modelo tem sido considerado capaz de promover a aquisição de conhecimentos mas também o desenvolvimento de competências transversais valorizadas no mercado de trabalho; orienta-se em torno de problemas significativos da realidade profissional, trabalhados segundo a metodologia dos sete passos, destacando-se a aprendizagem através de pesquisa individual e trabalho de grupo; e visa ainda desenvolver processos cognitivos e metacognitivos como levantar hipóteses, comparar, analisar, interpretar e avaliar. Neste artigo, caracterizamos brevemente o modelo e respectivas implicações, justificando o interesse em investigar as repercussões da sua implementação.

Multi-apprentice learning for meta-heuristics parameter tuning in a multi agent scheduling system

The scheduling problem is considered in complexity theory as a NP-hard combinatorial optimization problem. Meta-heuristics proved to be very useful in the resolution of this class of problems. However, these techniques require parameter tuning which is a very hard task to perform. A Case-based Reasoning module is proposed in order to solve the parameter tuning problem in a Multi-Agent Scheduling System. A computational study is performed in order to evaluate the proposed CBR module performance.

The flipped-broadcast learning system, application on Azores

On this work we suggest a teaching solution that can be implemented in Azores, an archipelago of nine islands of Portugal, based in already known system of e-learning, with a twist based on the flipped method. Structured in a cooperative way, the organization of the system allows to isolated groups of people to have access to a certain level of teaching, if they cannot have the possibility to have physical presence in school due to problems emerging from territory discontinuity. Our suggestion can be elaborate in a model that can be adapted to any level of education, and can be adapted also in cases that a cut of budget exists. We suggest the name of fb-learning: Flipped Broadcast Learning.

Planning and implementing a new assessment strategy using an e-learning platform

One of the most difficult issues of e-Learning is the students’ assessment. Being this an outstanding task regarding theoretical topics, it becomes even more challenging when the topics under evaluation are practical. ISCAP’s Information Systems Department is composed of about twenty teachers who have been for several years using an e-learning environment (at the moment Moodle 2.3) combined with traditional assessment. They are now planning and implementing a new e-learning assessment strategy. This effort was undertaken in order to evaluate a practical topic (the use of spreadsheets to solve management problems) common to shared courses of several undergraduate degree programs. The same team group is already experienced in the assessment of theoretical information systems topics using the b-learning platform. Therefore, this project works as an extension to previous experiences being the team aware of the additional difficulties due to the practical nature of the topics. This paper describes this project and presents two cycles of the action research methodology, used to conduct the research. The first cycle goal was to produce a database of questions. When it was implemented in order to be used with a pilot group of students, several problems were identified. Subsequently, the second cycle consisted in solving the identified problems preparing the database and all the players to a broader scope implementation. For each cycle, all the phases, its drawbacks and achievements are described. This paper suits all those who are or are planning to be in the process of shifting their assessment strategy from a traditional to one supported by an e-learning platform.

Educational in a global environment: non-formal examples of learning practices at the international office

23rd SPACE AGM and Conference from 9 to 12 May 2012 Conference theme: The Role of Professional Higher Education: Responsibility and Reflection Venue: Mikkeli University of Applied Sciences, Mikkeli, Finland