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Why take a doctoral degree at the UPC

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Because of Excellence

The UPC is listed in the main international rankings as one of the top technological and research universities in southern Europe and is among the world's 40 best young universities.

Its main asset: people

Satisfaction with the work of the thesis supervisor is highlighted by 7 out of 10 UPC doctoral students. Support and availability get the best ratings.

Internationalisation

More than half of the students of the UPC’s Doctoral School are international and a third obtain the International Doctorate mention.

 

Graduate employment of a high quality

Almost all UPC doctoral degree holders are successful in finding employment, mostly in jobs related to their degree.

The best industrial doctorate

The UPC offers the most industrial doctoral programmes in Catalonia (a third) with a hundred companies involved.

The industrial setting

The UPC’s location in an especially creative and innovative industrial and technological ecosystem is an added value for UPC doctoral students.

Theses for defense agenda

Reading date: 19/03/2024
  • HAGHI, ABBAS: FPGA and ASIC accelerators for genome data analysis
    Author: HAGHI, ABBAS
    Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
    Programme: DOCTORAL DEGREE IN COMPUTER ARCHITECTURE
    Department: (DAC)
    Mode: Normal
    Deposit date: 08/02/2024
    Reading date: 19/03/2024
    Reading time: 10:00
    Reading place: Edifici C6, UPC_Campus Nord. Sala C6-E106 (Facultat d'Informàtica de Barcelona)
    Thesis director: MORETÓ PLANAS, MIQUEL | ÁLVAREZ MARTÍ, LLUC
    Committee:
         PRESIDENT: PETERSEN MOURA TRANCOSO, PEDRO
         SECRETARI: JIMENEZ GONZALEZ, DANIEL
         VOCAL: GOMEZ LUNA, JUAN
    Thesis abstract: The continuous progress of Moore¿s Law in improving single-threaded performance (executiontime) through clock frequency and process node improvements has slowed down due to physicallimitations in silicon device physics. This has resulted in a shift towards using multicoreprocessors to achieve performance gains. However, the use of multiprocessing is limitedby Amdahl¿s Law, in which the sequential parts of the applications restrict the speedups inparallel systems. Consequently, the technology industry is now emphasizing specialization anddeveloping domain-specific accelerators to enhance performance compared to general-purposecomputers.Genomics is a field that deals with the study of genes and their functions. Thanks to currentand ongoing advancements, each stage of development in sequencing technologies is able toproduce enormous amounts of data at an increasingly faster and cheaper way compared to itsprevious stage. However, the assembly and analysis of this data take extensive time on general-purpose processors, and the processor performance is growing at a much slower pace thanthe DNA sequencing speed. Hence, domain-specific accelerators are becoming increasinglyessential in the genomics field, especially for DNA assembly. Specialized hardware computingdevices designed for this specific domain can achieve significant performance improvementscompared to general-purpose computers. Thus, with domain-specific accelerators, the speed ofDNA assembly can keep up with the pace of DNA sequencing, allowing for quicker analysisand discoveries in the genomics field.The main goal of this thesis is to accelerate two critical applications of DNA assembly,k-mer counting and pairwise read alignment, using FPGAs and ASICs. The first contribution ofthis thesis targets accelerating the k-mer counting application using FPGAs and its adaptationin a genomics application called SMUFIN, a Somatic MUtation FINder. The second andthird contributions focus on exploiting FPGAs for accelerating the Wavefront Alignment(WFA), a novel pairwise read alignment algorithm for aligning DNA sequences generated bydifferent sequencing technologies. The accelerator in the second contribution is customized forshort DNA sequences of up to 300 bases, which are generated by next generation sequencingtechnologies, while the accelerator in the third contribution is customized for long DNAsequences of up to 50K bases, which are generated by third generation sequencing technologies.The fourth contribution proposes an ASIC accelerator of the WFA algorithm and its integrationin a RISC-V SoC. In all contributions, we analyze different parts of the application and portthe most time-consuming parts to the accelerator. We also modify and re-design the remainingCPU parts to better adapt them to the accelerator code and finally propose efficient co-designedaccelerated designs.In our first contribution, the integration of our k-mer counting accelerator improves theSMUFIN k-mer counting performance by 2.14× while consuming 2.93× less energy and1.57× less memory compared to the baseline multi-threaded software implementation. Theperformance of the WFA accelerators in the second and third contributions is evaluated usingone and two FPGAs. Compared to the baseline multi-threaded software implementation of theWFA running on a IBM POWER9 high-performance processor, our WFA accelerator for shortreads reaches performance improvements of up to 8.8× and 13.5× with one and two FPGAs,respectively. The WFA accelerator for long reads reaches performance improvementsof up to 5.6× and 9.9× with one and two FPGAs, respectively. In our fourthcontribution, our ASIC WFA accelerator integrated in the RISC-V SoC reaches performanceimprovements of up to 1076× compared to the single-threaded software implementation of theWFA on Sargantana, the RISC-V CPU of the chip.
  • ROTKEVICH, MIKHAIL: Revealing the hidden language of DNA
    Author: ROTKEVICH, MIKHAIL
    Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
    Programme: DOCTORAL DEGREE IN ARTIFICIAL INTELLIGENCE
    Department: Department of Computer Science (CS)
    Mode: Normal
    Deposit date: 08/02/2024
    Reading date: 19/03/2024
    Reading time: 10:00
    Reading place: FIB Sala d'actes Manuel Martí Recober B6-planta 0, Campus Barcelona Nord UPC. URL videoconferencia pública: meet.google.com/feh-vhcb-iij
    Thesis director: PRZULJ, NATASA
    Committee:
         PRESIDENT: SKUPIN, ALEXANDER
         SECRETARI: VELLIDO ALCACENA, ALFREDO
         VOCAL: GUIGO SERRA, RODERIC
    Thesis abstract: Genomics has revolutionized in recent years due to the rapid advancements in high-throughput sequencing technologies, leading to an explosion of genomic data. This has opened up new opportunities for utilizing natural language processing (NLP) techniques to analyze and extract knowledge from genomic data. However, applying NLP techniques in genomics presents unique challenges due to the differences in genetic data's underlying structure and complexity.State-of-art biological embedding algorithms, such as DNA2VEC, split biological sequences into overlapping sub-sequences of length k, called k-mers, and learn a k-mer-based embedding space. By representing k-mers as continuous vectors, a strong correlation has been observed between the cosine similarity of these embeddings and the global sequence alignment score. This correlation suggests that the k-mer embeddings effectively capture sequence similarities. In other words, if two genes or proteins are embedded closely in the embedding space, they will likely exhibit high sequence similarity.We proposed new embedding methods to go beyond the sequence similarity: untangle 1 (UNT1) and untangle 2 (UNT2). By changing the calculation of the co-occurrences of k-mers in the contextual window, we significantly reduced the correlation to sequence similarity. While capturing fewer semantically similar GO terms, we showed that the novel methods UNT1 and UNT2 provide a broader representation of functional relationships than DNA2VEC.In addition to sequence data, the availability of diverse omics data has witnessed a remarkable surge, with the recognition of its potential to provide complementary insights. In our research, we depart from the conventional use of Singular Value Decomposition (SVD) to represent sequences in a low-dimensional space. Instead, we employ Non-negative Matrix Tri-Factorization (NMTF) to build a directly interpretable biological sequence embedding method. While Singular Value Decomposition (SVD) has successfully produced high-quality embeddings, our choice of NMTF aligns with the goals of explainable AI (XAI) and the need to understand the biological implications of the generated embeddings. NMTF serves as a potent instrument for data fusion, enabling the integration of information from various sources to achieve a deeper knowledge of complex biological systems. By utilizing NMTF, we aim to provide a more comprehensive understanding of the relationships between biological entities, such as k-mer, coding or non-coding regions, and their functional characteristics.We developed a versatile approach for annotating k-mers with genes, which allowed us to investigate the inheritance of annotations across different k-mer lengths. Specifically, we mapped k-mers to genes and vice-versa based on their over-representation in the sequences of the genes. Our study showed that the k-mer clusters are significantly enriched in GO annotations, indicating that the embeddings of k-mers capture functional genome organization.We showed that the same embedding models based on k-mers of DNA not only capture a functional structure of genes, but also effectively distinguish non-coding regions of DNA. We analyzed the non-coding regions of the yeast genome and compared the performance of the models DNA2VEC, UNT1, and UNT2. Our findings suggest that the optimal length of k-mers to classify ncRNAs is shorter than 7. This observation is fundamental since the feasibility of mostly all k-mer-based methods is highly dependent on the volume of the vocabulary increasing exponentially with the k-mer's length.Furthermore, our findings indicate that models utilizing k-mers of length 6 and larger outperform models based on shorter subsequences when predicting chromatin interactions. By emphasizing the importance of longer k-mers, our study provides valuable insights into the potential of utilizing extended sequence motifs to advance our understanding of the structural organization of the genome.
Reading date: 20/03/2024
  • BRUGUÉS MORA, JOAQUIN: Floer Homology for b-symplectic manifolds
    Author: BRUGUÉS MORA, JOAQUIN
    Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
    Programme: DOCTORAL DEGREE IN APPLIED MATHEMATICS
    Department: Department of Mathematics (MAT)
    Mode: Change of supervisor
    Deposit date: 19/02/2024
    Reading date: 20/03/2024
    Reading time: 12:00
    Reading place: Sala d'Actes de la Faculat de Matemàtiques i Estadística, Edifici U, Campus Sud.
    Thesis director: MIRANDA GALCERÁN, EVA | HOHLOCH, SONJA VERENA
    Committee:
         PRESIDENT: FRAUENFELD, URS
         SECRETARI: DELSHAMS I VALDES, AMADEU
         VOCAL: PASQUOTTO, FEDERICA
         VOCAL: MUNDET RIERA, IGNASI
         VOCAL: MESTDAG, TOM
    Thesis abstract: In this thesis we investigate various aspects of the dynamics of Hamiltonian vector fields in singular symplectic manifolds. We concentrate on two questions: first, we investigate a generalization of the Arnold conjecture in the setting of singular symplectic geometry. Second, we explore constructions for integrable systems in this context. In Chapter 2 we provide the background material required for this thesis. We start by delving into the theory of symplectic geometry. Then we present the Arnold conjecture, which asserts that there is a lower bound on the number of 1-periodic orbits for a non-degenerate Hamiltonian system, and that this lower bound can be formulated strictly in topological terms. We also present a tool used in the investigation of this conjecture: Floer theory. We explain some notions of Poisson geometry before we explore a notion fundamental to this thesis: that of a b-m-symplectic manifold. These are manifolds with a structure that is symplectic almost everywhere but ¿blows up¿ at a hypersurface, which we call the singular hypersurface. We lay out some techniques used in the study of b-m-symplectic manifolds, with an emphasis on a procedure called "desingularization". Finally, we give a summary of the theory of integrable systems and the study of their singular points. In Chapter 3 we investigate the dynamical behaviour of certain vector fields in b-m-symplectic geometry, coming from b-m-Hamiltonians. We focus on the study of their dynamics in a neighbourhood of the singular hypersurface, and find a family of b-m-Hamiltonians where a version of the Arnold conjecture can be formulated. Then, we explore new aspects of the desingularization procedure in relation to the b-m-Hamiltonian dynamics, and provide some techniques that allow us to relate these dynamics to those of classical symplectic geometry. We conclude with two results yielding partial versions of the Arnold conjecture for b-m-Hamiltonian vector fields. In Chapter 4 we show the existence of a Floer homology for b-m-symplectic manifolds. This we manage through an investigation of the Floer equation for the family of b-m-Hamiltonians presented in Chapter 3. In Chapter 5 we introduce the notion of the classes of b-integrable and b-semitoric systems. We study the features of b-semitoric systems using some interesting examples and the investigation of their singular points.
  • PUGLISI, GIUSEPPE MASSIMO: From Barcelona to Vancouver: the use of the green areas along space/time
    Author: PUGLISI, GIUSEPPE MASSIMO
    Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
    Programme: DOCTORAL DEGREE IN ARCHITECTURAL, CIVIL AND URBAN HERITAGE AND REFURBISHMENT OF EXISTING BUILDINGS
    Department: (RA)
    Mode: Normal
    Deposit date: 01/02/2024
    Reading date: 20/03/2024
    Reading time: 12:00
    Reading place: Presencial (Sala de Graus ETSAB. Planta Baixa) + videoconferència: meet.google.com/tsm-tdvm-dfs
    Thesis director: PUJADAS GISPERT, ESTER | DE MENDONÇA ESPINHEIRA GOMES, RENATA
    Committee:
         PRESIDENT: CARRA\', NATALINA
         SECRETARI: LLOP TORNE, CARLOS JUAN
         VOCAL: PUGLIESE, MICHELANGELO
    Thesis abstract: The subject of the thesis focuses on landscape, including how it relates to gardens, architecture, the environment, and how different areas are used over space and time. Natural spaces have a high potential to be developed in the new smart cities, and the fusion of the physical environment and digital information is undergoing a fundamental transition. In this, the composition of the landscape can open the way to the renewal of culture, a characteristic searched in the Victorian era and slightly forgotten after the First World War. The characteristics to be considered in green areas planning to maximize the rising of culture can include the use of the same along the various hours of day and night. In this research, the hypothesis is that parks are positively correlated with the establishment of social activities, and provide the opportunity for promoting the release of stress in a behavioral setting. The implication of this study may assist urban and landscape designers, planners, and architects in creating a sociable green environment. After reviewing existing literature in this field and identifying a scientific gap, a set of theoretical frameworks was conducted to facilitate the grasp of notions developed in this study. Afterward, by describing of implemented methods, the process of applying different procedures was explained, including questionnaires and interviews with key figures in the field. Subsequently, the obtained findings were presented and discussion and conclusions were presented, joined with a simulation project presented within the annexes, to visually express the high potentiality discovered with the research. All this, therefore, can be the basis for further research oriented towards a new type of ecological design. The goal is to guide knowledge and innovation in green design through the use of new technologies, going beyond the process of traditional design production. In envisioning the future of urban parks, the study proposes a transformative direction, advocating for parks to evolve beyond recreational spaces into vital hubs for education, culture, sustainability, and technological innovation. The research, conducted in newly built parks in Barcelona compared to Vancouver's model, offers insights into potential new uses for these spaces. Acknowledging its geographical and historical limitations, the study emphasizes its relevance to contemporary parks, highlighting the need for specific studies to explore how modern technologies can be integrated into historic parks: without compromising their heritage value.
Reading date: 05/04/2024
  • JIMÉNEZ REYES, SERGIO: Development of a unified fatigue constitutive model: from high to low cycle regime.
    Author: JIMÉNEZ REYES, SERGIO
    Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
    Programme: DOCTORAL DEGREE IN STRUCTURAL ANALYSIS
    Department: (DECA)
    Mode: Normal
    Deposit date: 01/03/2024
    Reading date: 05/04/2024
    Reading time: 12:00
    Reading place: Sala Zienkiewicz del Centre Internacional de Mètodes Numèrics a l'Enginyeria (CIMNE) Edifici C1, planta 2, Campus Nord - UPC C.Gran Capità s/n. 08034 BCN- Enllaç https://meet.google.com/zon-mupk-jui
    Thesis director: OÑATE IBAÑEZ DE NAVARRA, EUGENIO | BARBU, LUCIA GRATIELA
    Committee:
         PRESIDENT: MARTINEZ GARCIA, JAVIER
         SECRETARI: PEREZ MARTINEZ, MARCO ANTONIO
         VOCAL NO PRESENCIAL: LUCCIONI, BIBIANA MARIA
    Thesis abstract: n a context in which research lines such as optimised design, smart design, use of new materials, weight reduction, etc. are becoming more and more common in the engineering field, techniques that allow for an accurate analysis of the real behaviour of materials, parts and structures are becoming essential. This involves understanding the actual overall response exhibited by a material subjected to a heterogeneous set of external forces, which is only possible by abandoning the reductionist view typically adopted in the design phases in which external forces are amplified, resistance properties are diminished and deterioration phenomena are studied one by one. A clear example of this is the treatment given to the study of fatigue phenomenon, which, in general, is limited to an extrapolation of results obtained in a controlled laboratory environment in order to predict failure, disregarding the process and focusing only on the consequences, thus preventing an integrated study of fatigue with any other inelastic process.Unlike conventional approaches based on simplified analytical calculations or specific numerical models for certain regimes, a unified treatment of fatigue is proposed in this thesis based on plastic-damage constitutive laws. Using the Finite Element method, a framework is built to capture the response of a material exposed to quasi-static loading states in both monotonic and fatigue regimes, resulting in the accumulation of plastic strains and/or stiffness degradation.To reach this point, a study of the individual mechanisms of deterioration encompassed within the unified approach proposed in the thesis is carried out. On the one hand, the characterisation of the constitutive response associated with plastic-damage processes is undertaken. This analysis is carried out by adopting three approaches that involve different levels of coupling in the description of damage and plasticity, resulting in three laws that are further exploited for their potential to be adapted for the study of fatigue processes, yielding to fluctuating plastic-damage models. On the other hand, the characterisation of the behaviour under fatigue loading conditions is addressed by studying the effects that cyclic loads inducing dominant tensile stresses have in a material, including scenarios where the stress level may exceed the yield limit. Having identified the inelastic processes associated with fatigue, the objective methodology is then constructed to coherently study and quantify the successive deterioration mechanisms to which a material may be subjected.This sets the guidelines for further work in the simulation of complex processes involving multiple mechanical deterioration phenomena. Thus, this thesis serves as the first step aimed at: defining the foundations, outlining the applications and initiating the exploration of the potential of the proposed approach.

The Doctoral School today

  • 45PhD programs
  • 2131doctoral students 21/22
  • 1591thesis supervisors 21/22
  • 305read theses 2021
  • 982021 thesis with I.M. and/or I.D.
  • 233 I.D. projects (29% from G.C. total)

I.M: International Mention, I.D.: Industrial Doctorate, G.C.: Generalitat de Catalunya