1,044 research outputs found
Self-supervised learning for transferable representations
Machine learning has undeniably achieved remarkable advances thanks to large labelled datasets and supervised learning. However, this progress is constrained by the labour-intensive annotation process. It is not feasible to generate extensive labelled datasets for every problem we aim to address. Consequently, there has been a notable shift in recent times toward approaches that solely leverage raw data. Among these, self-supervised learning has emerged as a particularly powerful approach, offering scalability to massive datasets and showcasing considerable potential for effective knowledge transfer. This thesis investigates self-supervised representation learning with a strong focus on computer vision applications. We provide a comprehensive survey of self-supervised methods across various modalities, introducing a taxonomy that categorises them into four distinct families while also highlighting practical considerations for real-world implementation. Our focus thenceforth is on the computer vision modality, where we perform a comprehensive benchmark evaluation of state-of-the-art self supervised models against many diverse downstream transfer tasks. Our findings reveal that self-supervised models often outperform supervised learning across a spectrum of tasks, albeit with correlations weakening as tasks transition beyond classification, particularly for datasets with distribution shifts. Digging deeper, we investigate the influence of data augmentation on the transferability of contrastive learners, uncovering a trade-off between spatial and appearance-based invariances that generalise to real-world transformations. This begins to explain the differing empirical performances achieved by self-supervised learners on different downstream tasks, and it showcases the advantages of specialised representations produced with tailored augmentation. Finally, we introduce a novel self-supervised pre-training algorithm for object detection, aligning pre-training with downstream architecture and objectives, leading to reduced localisation errors and improved label efficiency. In conclusion, this thesis contributes a comprehensive understanding of self-supervised representation learning and its role in enabling effective transfer across computer vision tasks
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
Subgroup discovery for structured target concepts
The main object of study in this thesis is subgroup discovery, a theoretical framework for finding subgroups in data—i.e., named sub-populations— whose behaviour with respect to a specified target concept is exceptional when compared to the rest of the dataset. This is a powerful tool that conveys crucial information to a human audience, but despite past advances has been limited to simple target concepts. In this work we propose algorithms that bring this framework to novel application domains. We introduce the concept of representative subgroups, which we use not only to ensure the fairness of a sub-population with regard to a sensitive trait, such as race or gender, but also to go beyond known trends in the data. For entities with additional relational information that can be encoded as a graph, we introduce a novel measure of robust connectedness which improves on established alternative measures of density; we then provide a method that uses this measure to discover which named sub-populations are more well-connected. Our contributions within subgroup discovery crescent with the introduction of kernelised subgroup discovery: a novel framework that enables the discovery of subgroups on i.i.d. target concepts with virtually any kind of structure. Importantly, our framework additionally provides a concrete and efficient tool that works out-of-the-box without any modification, apart from specifying the Gramian of a positive definite kernel. To use within kernelised subgroup discovery, but also on any other kind of kernel method, we additionally introduce a novel random walk graph kernel. Our kernel allows the fine tuning of the alignment between the vertices of the two compared graphs, during the count of the random walks, while we also propose meaningful structure-aware vertex labels to utilise this new capability. With these contributions we thoroughly extend the applicability of subgroup discovery and ultimately re-define it as a kernel method.Der Hauptgegenstand dieser Arbeit ist die Subgruppenentdeckung (Subgroup Discovery), ein theoretischer Rahmen für das Auffinden von Subgruppen in Daten—d. h. benannte Teilpopulationen—deren Verhalten in Bezug auf ein bestimmtes Targetkonzept im Vergleich zum Rest des Datensatzes außergewöhnlich ist. Es handelt sich hierbei um ein leistungsfähiges Instrument, das einem menschlichen Publikum wichtige Informationen vermittelt. Allerdings ist es trotz bisherigen Fortschritte auf einfache Targetkonzepte beschränkt. In dieser Arbeit schlagen wir Algorithmen vor, die diesen Rahmen auf neuartige Anwendungsbereiche übertragen. Wir führen das Konzept der repräsentativen Untergruppen ein, mit dem wir nicht nur die Fairness einer Teilpopulation in Bezug auf ein sensibles Merkmal wie Rasse oder Geschlecht sicherstellen, sondern auch über bekannte Trends in den Daten hinausgehen können. Für Entitäten mit zusätzlicher relationalen Information, die als Graph kodiert werden kann, führen wir ein neuartiges Maß für robuste Verbundenheit ein, das die etablierten alternativen Dichtemaße verbessert; anschließend stellen wir eine Methode bereit, die dieses Maß verwendet, um herauszufinden, welche benannte Teilpopulationen besser verbunden sind. Unsere Beiträge in diesem Rahmen gipfeln in der Einführung der kernelisierten Subgruppenentdeckung: ein neuartiger Rahmen, der die Entdeckung von Subgruppen für u.i.v. Targetkonzepten mit praktisch jeder Art von Struktur ermöglicht. Wichtigerweise, unser Rahmen bereitstellt zusätzlich ein konkretes und effizientes Werkzeug, das ohne jegliche Modifikation funktioniert, abgesehen von der Angabe des Gramian eines positiv definitiven Kernels. Für den Einsatz innerhalb der kernelisierten Subgruppentdeckung, aber auch für jede andere Art von Kernel-Methode, führen wir zusätzlich einen neuartigen Random-Walk-Graph-Kernel ein. Unser Kernel ermöglicht die Feinabstimmung der Ausrichtung zwischen den Eckpunkten der beiden unter-Vergleich-gestelltenen Graphen während der Zählung der Random Walks, während wir auch sinnvolle strukturbewusste Vertex-Labels vorschlagen, um diese neue Fähigkeit zu nutzen. Mit diesen Beiträgen erweitern wir die Anwendbarkeit der Subgruppentdeckung gründlich und definieren wir sie im Endeffekt als Kernel-Methode neu
Computational Approaches to Drug Profiling and Drug-Protein Interactions
Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a
long period of stagnation in drug approvals. Due to the extreme costs associated with
introducing a drug to the market, locating and understanding the reasons for clinical failure
is key to future productivity. As part of this PhD, three main contributions were made in
this respect. First, the web platform, LigNFam enables users to interactively explore
similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly,
two deep-learning-based binding site comparison tools were developed, competing with
the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the
open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold
relationships and has already been used in multiple projects, including integration into a
virtual screening pipeline to increase the tractability of ultra-large screening experiments.
Together, and with existing tools, the contributions made will aid in the understanding of
drug-protein relationships, particularly in the fields of off-target prediction and drug
repurposing, helping to design better drugs faster
Implementing and evaluating graph algorithms for long vector architectures
High-Performance Computing can be accelerated using long-vector architectures. However, creating efficient coding implementations for these architectures can be challenging. This Master's thesis focuses on implementing four well-known and widely-used graph processing algorithms using the RISC-V Vector Extension, leveraging an experimental system in an FPGA. I present a graph storage format that benefits from long vectors and describe how these four algorithms can be rewritten to utilize it. This thesis also introduces an instrumentation tool for FPGA that I developed to link the output of electrical engineering software with performance analysis tools for HPC. This tool allows users to visualize information coming from the logic analyzer internal to the FPGA with powerful visualization tools, permitting fine-grain analysis of the FPGA signals correlated with the code running on it. This tool has been integrated into the experimental performance analysis tools of BSC. In this thesis I leverage this tool to analyze and improve my implementations of graph algorithms for long-vector architectures, collecting the process and thoughts behind each optimization. Finally, I compare the performance of my vector implementations with other machines, such as the NEC SX-Aurora, a commercial RISC-V board, and an Intel chip
Measuring the impact of COVID-19 on hospital care pathways
Care pathways in hospitals around the world reported significant disruption during the recent COVID-19 pandemic but measuring the actual impact is more problematic. Process mining can be useful for hospital management to measure the conformance of real-life care to what might be considered normal operations. In this study, we aim to demonstrate that process mining can be used to investigate process changes associated with complex disruptive events. We studied perturbations to accident and emergency (A &E) and maternity pathways in a UK public hospital during the COVID-19 pandemic. Co-incidentally the hospital had implemented a Command Centre approach for patient-flow management affording an opportunity to study both the planned improvement and the disruption due to the pandemic. Our study proposes and demonstrates a method for measuring and investigating the impact of such planned and unplanned disruptions affecting hospital care pathways. We found that during the pandemic, both A &E and maternity pathways had measurable reductions in the mean length of stay and a measurable drop in the percentage of pathways conforming to normative models. There were no distinctive patterns of monthly mean values of length of stay nor conformance throughout the phases of the installation of the hospital’s new Command Centre approach. Due to a deficit in the available A &E data, the findings for A &E pathways could not be interpreted
Geometric Learning on Graph Structured Data
Graphs provide a ubiquitous and universal data structure that can be applied in many domains such as social networks, biology, chemistry, physics, and computer science. In this thesis we focus on two fundamental paradigms in graph learning: representation learning and similarity learning over graph-structured data. Graph representation learning aims to learn embeddings for nodes by integrating topological and feature information of a graph. Graph similarity learning brings into play with similarity functions that allow to compute similarity between pairs of graphs in a vector space. We address several challenging issues in these two paradigms, designing powerful, yet efficient and theoretical guaranteed machine learning models that can leverage rich topological structural properties of real-world graphs.
This thesis is structured into two parts. In the first part of the thesis, we will present how to develop powerful Graph Neural Networks (GNNs) for graph representation learning from three different perspectives: (1) spatial GNNs, (2) spectral GNNs, and (3) diffusion GNNs. We will discuss the model architecture, representational power, and convergence properties of these GNN models. Specifically, we first study how to develop expressive, yet efficient and simple message-passing aggregation schemes that can go beyond the Weisfeiler-Leman test (1-WL). We propose a generalized message-passing framework by incorporating graph structural properties into an aggregation scheme. Then, we introduce a new local isomorphism hierarchy on neighborhood subgraphs. We further develop a novel neural model, namely GraphSNN, and theoretically prove that this model is more expressive than the 1-WL test. After that, we study how to build an effective and efficient graph convolution model with spectral graph filters. In this study, we propose a spectral GNN model, called DFNets, which incorporates a novel spectral graph filter, namely feedback-looped filters. As a result, this model can provide better localization on neighborhood while achieving fast convergence and linear memory requirements. Finally, we study how to capture the rich topological information of a graph using graph diffusion. We propose a novel GNN architecture with dynamic PageRank, based on a learnable transition matrix. We explore two variants of this GNN architecture: forward-euler solution and invariable feature solution, and theoretically prove that our forward-euler GNN architecture is guaranteed with the convergence to a stationary distribution.
In the second part of this thesis, we will introduce a new optimal transport distance metric on graphs in a regularized learning framework for graph kernels. This optimal transport distance metric can preserve both local and global structures between graphs during the transport, in addition to preserving features and their local variations. Furthermore, we propose two strongly convex regularization terms to theoretically guarantee the convergence and numerical stability in finding an optimal assignment between graphs. One regularization term is used to regularize a Wasserstein distance between graphs in the same ground space. This helps to preserve the local clustering structure on graphs by relaxing the optimal transport problem to be a cluster-to-cluster assignment between locally connected vertices. The other regularization term is used to regularize a Gromov-Wasserstein distance between graphs across different ground spaces based on degree-entropy KL divergence. This helps to improve the matching robustness of an optimal alignment to preserve the global connectivity structure of graphs. We have evaluated our optimal transport-based graph kernel using different benchmark tasks. The experimental results show that our models considerably outperform all the state-of-the-art methods in all benchmark tasks
BDS GNSS for Earth Observation
For millennia, human communities have wondered about the possibility of observing
phenomena in their surroundings, and in particular those affecting the Earth on which they live.
More generally, it can be conceptually defined as Earth observation (EO) and is the collection of
information about the biological, chemical and physical systems of planet Earth. It can be undertaken
through sensors in direct contact with the ground or airborne platforms (such as weather balloons and
stations) or remote-sensing technologies. However, the definition of EO has only become significant
in the last 50 years, since it has been possible to send artificial satellites out of Earth’s orbit.
Referring strictly to civil applications, satellites of this type were initially designed to provide
satellite images; later, their purpose expanded to include the study of information on land
characteristics, growing vegetation, crops, and environmental pollution. The data collected are used
for several purposes, including the identification of natural resources and the production of accurate
cartography. Satellite observations can cover the land, the atmosphere, and the oceans.
Remote-sensing satellites may be equipped with passive instrumentation such as infrared or
cameras for imaging the visible or active instrumentation such as radar. Generally, such satellites are
non-geostationary satellites, i.e., they move at a certain speed along orbits inclined with respect to the
Earth’s equatorial plane, often in polar orbit, at low or medium altitude, Low Earth Orbit (LEO) and
Medium Earth Orbit (MEO), thus covering the entire Earth’s surface in a certain scan time (properly
called ’temporal resolution’), i.e., in a certain number of orbits around the Earth.
The first remote-sensing satellites were the American NASA/USGS Landsat Program;
subsequently, the European: ENVISAT (ENVironmental SATellite), ERS (European Remote-Sensing
satellite), RapidEye, the French SPOT (Satellite Pour l’Observation de laTerre), and the Canadian
RADARSAT satellites were launched. The IKONOS, QuickBird, and GeoEye-1 satellites were
dedicated to cartography. The WorldView-1 and WorldView-2 satellites and the COSMO-SkyMed
system are more recent. The latest generation are the low payloads called Small Satellites, e.g., the
Chinese BuFeng-1 and Fengyun-3 series.
Also, Global Navigation Satellite Systems (GNSSs) have captured the attention of researchers
worldwide for a multitude of Earth monitoring and exploration applications. On the other hand,
over the past 40 years, GNSSs have become an essential part of many human activities. As is widely
noted, there are currently four fully operational GNSSs; two of these were developed for military
purposes (American NAVstar GPS and Russian GLONASS), whilst two others were developed for
civil purposes such as the Chinese BeiDou satellite navigation system (BDS) and the European
Galileo. In addition, many other regional GNSSs, such as the South Korean Regional Positioning
System (KPS), the Japanese quasi-zenital satellite system (QZSS), and the Indian Regional Navigation
Satellite System (IRNSS/NavIC), will become available in the next few years, which will have
enormous potential for scientific applications and geomatics professionals.
In addition to their traditional role of providing global positioning, navigation, and timing (PNT)
information, GNSS navigation signals are now being used in new and innovative ways. Across the
globe, new fields of scientific study are opening up to examine how signals can provide information
about the characteristics of the atmosphere and even the surfaces from which they are reflected before
being collected by a receiver.
EO researchers monitor global environmental systems using in situ and remote monitoring tools.
Their findings provide tools to support decision makers in various areas of interest, from security
to the natural environment. GNSS signals are considered an important new source of information
because they are a free, real-time, and globally available resource for the EO community
A Survey on Interpretable Cross-modal Reasoning
In recent years, cross-modal reasoning (CMR), the process of understanding
and reasoning across different modalities, has emerged as a pivotal area with
applications spanning from multimedia analysis to healthcare diagnostics. As
the deployment of AI systems becomes more ubiquitous, the demand for
transparency and comprehensibility in these systems' decision-making processes
has intensified. This survey delves into the realm of interpretable cross-modal
reasoning (I-CMR), where the objective is not only to achieve high predictive
performance but also to provide human-understandable explanations for the
results. This survey presents a comprehensive overview of the typical methods
with a three-level taxonomy for I-CMR. Furthermore, this survey reviews the
existing CMR datasets with annotations for explanations. Finally, this survey
summarizes the challenges for I-CMR and discusses potential future directions.
In conclusion, this survey aims to catalyze the progress of this emerging
research area by providing researchers with a panoramic and comprehensive
perspective, illuminating the state of the art and discerning the
opportunities
Improving Expressivity of Graph Neural Networks using Localization
In this paper, we propose localized versions of Weisfeiler-Leman (WL)
algorithms in an effort to both increase the expressivity, as well as decrease
the computational overhead. We focus on the specific problem of subgraph
counting and give localized versions of WL for any . We analyze the
power of Local WL and prove that it is more expressive than WL and at
most as expressive as WL. We give a characterization of patterns whose
count as a subgraph and induced subgraph are invariant if two graphs are Local
WL equivalent. We also introduce two variants of WL: Layer WL and
recursive WL. These methods are more time and space efficient than applying
WL on the whole graph. We also propose a fragmentation technique that
guarantees the exact count of all induced subgraphs of size at most 4 using
just WL. The same idea can be extended further for larger patterns using
. We also compare the expressive power of Local WL with other GNN
hierarchies and show that given a bound on the time-complexity, our methods are
more expressive than the ones mentioned in Papp and Wattenhofer[2022a]
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