8,737 research outputs found
DeepOnto: A Python Package for Ontology Engineering with Deep Learning
Applying deep learning techniques, particularly language models (LMs), in
ontology engineering has raised widespread attention. However, deep learning
frameworks like PyTorch and Tensorflow are predominantly developed for Python
programming, while widely-used ontology APIs, such as the OWL API and Jena, are
primarily Java-based. To facilitate seamless integration of these frameworks
and APIs, we present Deeponto, a Python package designed for ontology
engineering. The package encompasses a core ontology processing module founded
on the widely-recognised and reliable OWL API, encapsulating its fundamental
features in a more "Pythonic" manner and extending its capabilities to include
other essential components including reasoning, verbalisation, normalisation,
projection, and more. Building on this module, Deeponto offers a suite of
tools, resources, and algorithms that support various ontology engineering
tasks, such as ontology alignment and completion, by harnessing deep learning
methodologies, primarily pre-trained LMs. In this paper, we also demonstrate
the practical utility of Deeponto through two use-cases: the Digital Health
Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment
Evaluation Initiative (OAEI).Comment: under review at Semantic Web Journa
Seamless Multimodal Biometrics for Continuous Personalised Wellbeing Monitoring
Artificially intelligent perception is increasingly present in the lives of
every one of us. Vehicles are no exception, (...) In the near future, pattern
recognition will have an even stronger role in vehicles, as self-driving cars
will require automated ways to understand what is happening around (and within)
them and act accordingly. (...) This doctoral work focused on advancing
in-vehicle sensing through the research of novel computer vision and pattern
recognition methodologies for both biometrics and wellbeing monitoring. The
main focus has been on electrocardiogram (ECG) biometrics, a trait well-known
for its potential for seamless driver monitoring. Major efforts were devoted to
achieving improved performance in identification and identity verification in
off-the-person scenarios, well-known for increased noise and variability. Here,
end-to-end deep learning ECG biometric solutions were proposed and important
topics were addressed such as cross-database and long-term performance,
waveform relevance through explainability, and interlead conversion. Face
biometrics, a natural complement to the ECG in seamless unconstrained
scenarios, was also studied in this work. The open challenges of masked face
recognition and interpretability in biometrics were tackled in an effort to
evolve towards algorithms that are more transparent, trustworthy, and robust to
significant occlusions. Within the topic of wellbeing monitoring, improved
solutions to multimodal emotion recognition in groups of people and
activity/violence recognition in in-vehicle scenarios were proposed. At last,
we also proposed a novel way to learn template security within end-to-end
models, dismissing additional separate encryption processes, and a
self-supervised learning approach tailored to sequential data, in order to
ensure data security and optimal performance. (...)Comment: Doctoral thesis presented and approved on the 21st of December 2022
to the University of Port
Semantics-based privacy by design for Internet of Things applications
As Internet of Things (IoT) technologies become more widespread in everyday life, privacy issues are becoming more prominent. The aim of this research is to develop a personal assistant that can answer software engineers’ questions about Privacy by Design (PbD) practices during the design phase of IoT system development. Semantic web technologies are used to model the knowledge underlying PbD measurements, their intersections with privacy patterns, IoT system requirements and the privacy patterns that should be applied across IoT systems. This is achieved through the development of the PARROT ontology, developed through a set of representative IoT use cases relevant for software developers. This was supported by gathering Competency Questions (CQs) through a series of workshops, resulting in 81 curated CQs. These CQs were then recorded as SPARQL queries, and the developed ontology was evaluated using the Common Pitfalls model with the help of the Protégé HermiT Reasoner and the Ontology Pitfall Scanner (OOPS!), as well as evaluation by external experts. The ontology was assessed within a user study that identified that the PARROT ontology can answer up to 58% of privacy-related questions from software engineers
Sketch Beautification: Learning Part Beautification and Structure Refinement for Sketches of Man-made Objects
We present a novel freehand sketch beautification method, which takes as
input a freely drawn sketch of a man-made object and automatically beautifies
it both geometrically and structurally. Beautifying a sketch is challenging
because of its highly abstract and heavily diverse drawing manner. Existing
methods are usually confined to the distribution of their limited training
samples and thus cannot beautify freely drawn sketches with rich variations. To
address this challenge, we adopt a divide-and-combine strategy. Specifically,
we first parse an input sketch into semantic components, beautify individual
components by a learned part beautification module based on part-level implicit
manifolds, and then reassemble the beautified components through a structure
beautification module. With this strategy, our method can go beyond the
training samples and handle novel freehand sketches. We demonstrate the
effectiveness of our system with extensive experiments and a perceptive study.Comment: 13 figure
Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria
Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases
Collective moderation of hate, toxicity, and extremity in online discussions
How can citizens moderate hate, toxicity, and extremism in online discourse?
We analyze a large corpus of more than 130,000 discussions on German Twitter
over the turbulent four years marked by the migrant crisis and political
upheavals. With a help of human annotators, language models, machine learning
classifiers, and longitudinal statistical analyses, we discern the dynamics of
different dimensions of discourse. We find that expressing simple opinions, not
necessarily supported by facts but also without insults, relates to the least
hate, toxicity, and extremity of speech and speakers in subsequent discussions.
Sarcasm also helps in achieving those outcomes, in particular in the presence
of organized extreme groups. More constructive comments such as providing facts
or exposing contradictions can backfire and attract more extremity. Mentioning
either outgroups or ingroups is typically related to a deterioration of
discourse in the long run. A pronounced emotional tone, either negative such as
anger or fear, or positive such as enthusiasm and pride, also leads to worse
outcomes. Going beyond one-shot analyses on smaller samples of discourse, our
findings have implications for the successful management of online commons
through collective civic moderation
Interdisciplinarity in the Age of the Triple Helix: a Film Practitioner's Perspective
This integrative chapter contextualises my research including articles I have published as well as one of the creative artefacts developed from it, the feature film The Knife That Killed Me. I review my work considering the ways in which technology, industry methods and academic practice have evolved as well as how attitudes to interdisciplinarity have changed, linking these to Etzkowitz and Leydesdorff’s ‘Triple Helix’ model (1995). I explore my own experiences and observations of opportunities and challenges that have been posed by the intersection of different stakeholder needs and expectations, both from industry and academic perspectives, and argue that my work provides novel examples of the applicability of the ‘Triple Helix’ to the creative industries. The chapter concludes with a reflection on the evolution and direction of my work, the relevance of the ‘Triple Helix’ to creative practice, and ways in which this relationship could be investigated further
Development and application of methodologies and infrastructures for cancer genome analysis within Personalized Medicine
[eng] Next-generation sequencing (NGS) has revolutionized biomedical sciences, especially in the area of cancer. It has nourished genomic research with extensive collections of sequenced genomes that are investigated to untangle the molecular bases of disease, as well as to identify potential targets for the design of new treatments. To exploit all this information, several initiatives have emerged worldwide, among which the Pan-Cancer project of the ICGC (International Cancer Genome Consortium) stands out. This project has jointly analyzed thousands of tumor genomes of different cancer types in order to elucidate the molecular bases of the origin and progression of cancer. To accomplish this task, new emerging technologies, including virtualization systems such as virtual machines or software containers, were used and had to be adapted to various computing centers. The portability of this system to the supercomputing infrastructure of the BSC (Barcelona Supercomputing Center) has been carried out during the first phase of the thesis. In parallel, other projects promote the application of genomics discoveries into the clinics. This is the case of MedPerCan, a national initiative to design a pilot project for the implementation of personalized medicine in oncology in Catalonia. In this context, we have centered our efforts on the methodological side, focusing on the detection and characterization of somatic variants in tumors. This step is a challenging action, due to the heterogeneity of the different methods, and an essential part, as it lays at the basis of all downstream analyses.
On top of the methodological section of the thesis, we got into the biological interpretation of the results to study the evolution of chronic lymphocytic leukemia (CLL) in a close collaboration with the group of Dr. ElÃas Campo from the Hospital ClÃnic/IDIBAPS. In the first study, we have focused on the Richter transformation (RT), a transformation of CLL into a high-grade lymphoma that
leads to a very poor prognosis and with unmet clinical needs. We found that RT has greater genomic, epigenomic and transcriptomic complexity than CLL. Its genome may reflect the imprint of therapies that the patients received prior to RT, indicating the presence of cells exposed to these mutagenic treatments which later expand giving rise to the clinical manifestation of the disease. Multiple NGS- based techniques, including whole-genome sequencing and single-cell DNA and RNA sequencing, among others, confirmed the pre-existence of cells with the RT characteristics years before their manifestation, up to the time of CLL diagnosis. The transcriptomic profile of RT is remarkably different from that of CLL. Of particular importance is the overexpression of the OXPHOS pathway, which could be used as a therapeutic vulnerability. Finally, in a second study, the analysis of a case of CLL in a young adult, based on whole genome and single-cell sequencing at different times of the disease, revealed that the founder clone of CLL did not present any somatic driver mutations and was characterized by germline variants in ATM, suggesting its role in the origin of the disease, and highlighting the possible contribution of germline variants or other non-genetic mechanisms in the initiation of CLL
A survey, review, and future trends of skin lesion segmentation and classification
The Computer-aided Diagnosis or Detection (CAD) approach for skin lesion analysis is an emerging field of research that has the potential to alleviate the burden and cost of skin cancer screening. Researchers have recently indicated increasing interest in developing such CAD systems, with the intention of providing a user-friendly tool to dermatologists to reduce the challenges encountered or associated with manual inspection. This article aims to provide a comprehensive literature survey and review of a total of 594 publications (356 for skin lesion segmentation and 238 for skin lesion classification) published between 2011 and 2022. These articles are analyzed and summarized in a number of different ways to contribute vital information regarding the methods for the development of CAD systems. These ways include: relevant and essential definitions and theories, input data (dataset utilization, preprocessing, augmentations, and fixing imbalance problems), method configuration (techniques, architectures, module frameworks, and losses), training tactics (hyperparameter settings), and evaluation criteria. We intend to investigate a variety of performance-enhancing approaches, including ensemble and post-processing. We also discuss these dimensions to reveal their current trends based on utilization frequencies. In addition, we highlight the primary difficulties associated with evaluating skin lesion segmentation and classification systems using minimal datasets, as well as the potential solutions to these difficulties. Findings, recommendations, and trends are disclosed to inform future research on developing an automated and robust CAD system for skin lesion analysis
A Survey of Large Language Models
Language is essentially a complex, intricate system of human expressions
governed by grammatical rules. It poses a significant challenge to develop
capable AI algorithms for comprehending and grasping a language. As a major
approach, language modeling has been widely studied for language understanding
and generation in the past two decades, evolving from statistical language
models to neural language models. Recently, pre-trained language models (PLMs)
have been proposed by pre-training Transformer models over large-scale corpora,
showing strong capabilities in solving various NLP tasks. Since researchers
have found that model scaling can lead to performance improvement, they further
study the scaling effect by increasing the model size to an even larger size.
Interestingly, when the parameter scale exceeds a certain level, these enlarged
language models not only achieve a significant performance improvement but also
show some special abilities that are not present in small-scale language
models. To discriminate the difference in parameter scale, the research
community has coined the term large language models (LLM) for the PLMs of
significant size. Recently, the research on LLMs has been largely advanced by
both academia and industry, and a remarkable progress is the launch of ChatGPT,
which has attracted widespread attention from society. The technical evolution
of LLMs has been making an important impact on the entire AI community, which
would revolutionize the way how we develop and use AI algorithms. In this
survey, we review the recent advances of LLMs by introducing the background,
key findings, and mainstream techniques. In particular, we focus on four major
aspects of LLMs, namely pre-training, adaptation tuning, utilization, and
capacity evaluation. Besides, we also summarize the available resources for
developing LLMs and discuss the remaining issues for future directions.Comment: ongoing work; 51 page
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