arXiv subjects

Georgios Paliouras

Publications and source records attributed to Georgios Paliouras.

At least 37 records · Page 2Linked to original sources

arXiv2022

Overview of BioASQ 2022: The tenth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

This paper presents an overview of the tenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2022. BioASQ is an ongoing series of challenges that promotes advances in the domain of large-scale biomedical semantic indexing and question answering. In this edition, the challenge was composed of the three established tasks a, b, and Synergy, and a new task named DisTEMIST for automatic semantic annotation and grounding of diseases from clinical content in Spanish, a key concept for semantic indexing and search engines of literature and clinical records. This year, BioASQ received more than 170 distinct systems from 38 teams in total for the four different tasks of the challenge. As in previous years, the majority of the competing systems outperformed the strong baselines, indicating the continuous advancement of the state-of-the-art in this domain.

cs.CL↗

arXiv2022

Knowledge4COVID-19: A Semantic-based Approach for Constructing a COVID-19 related Knowledge Graph from Various Sources and Analysing Treatments' Toxicities

In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug-drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the declarative definition of mapping rules using the RDF Mapping Language. Since valuable information about drug treatments, drug-drug interactions, and side effects is present in textual descriptions in scientific databases (e.g., DrugBank) or in scientific literature (e.g., the CORD-19, the Covid-19 Open Research Dataset), the Knowledge4COVID-19 framework implements Natural Language Processing. The Knowledge4COVID-19 framework extracts relevant entities and predicates that enable the fine-grained description of COVID-19 treatments and the potential adverse events that may occur when these treatments are combined with treatments of common comorbidities, e.g., hypertension, diabetes, or asthma. Moreover, on top of the KG, several techniques for the discovery and prediction of interactions and potential adverse effects of drugs have been developed with the aim of suggesting more accurate treatments for treating the virus. We provide services to traverse the KG and visualize the effects that a group of drugs may have on a treatment outcome. Knowledge4COVID-19 was part of the Pan-European hackathon#EUvsVirus in April 2020 and is publicly available as a resource through a GitHub repository (https://github.com/SDM-TIB/Knowledge4COVID-19) and a DOI (https://zenodo.org/record/4701817#.YH336-8zbol).

cs.DB↗

arXiv2022

Learning Automata-Based Complex Event Patterns in Answer Set Programming

Complex Event Recognition and Forecasting (CER/F) techniques attempt to detect, or even forecast ahead of time, event occurrences in streaming input using predefined event patterns. Such patterns are not always known in advance, or they frequently change over time, making machine learning techniques, capable of extracting such patterns from data, highly desirable in CER/F. Since many CER/F systems use symbolic automata to represent such patterns, we propose a family of such automata where the transition-enabling conditions are defined by Answer Set Programming (ASP) rules, and which, thanks to the strong connections of ASP to symbolic learning, are directly learnable from data. We present such a learning approach in ASP and an incremental version thereof that trades optimality for efficiency and is capable to scale to large datasets. We evaluate our approach on two CER datasets and compare it to state-of-the-art automata learning techniques, demonstrating empirically a superior performance, both in terms of predictive accuracy and scalability.

cs.AI↗

arXiv2022

FiNER: Financial Numeric Entity Recognition for XBRL Tagging

Publicly traded companies are required to submit periodic reports with eXtensive Business Reporting Language (XBRL) word-level tags. Manually tagging the reports is tedious and costly. We, therefore, introduce XBRL tagging as a new entity extraction task for the financial domain and release FiNER-139, a dataset of 1.1M sentences with gold XBRL tags. Unlike typical entity extraction datasets, FiNER-139 uses a much larger label set of 139 entity types. Most annotated tokens are numeric, with the correct tag per token depending mostly on context, rather than the token itself. We show that subword fragmentation of numeric expressions harms BERT's performance, allowing word-level BILSTMs to perform better. To improve BERT's performance, we propose two simple and effective solutions that replace numeric expressions with pseudo-tokens reflecting original token shapes and numeric magnitudes. We also experiment with FIN-BERT, an existing BERT model for the financial domain, and release our own BERT (SEC-BERT), pre-trained on financial filings, which performs best. Through data and error analysis, we finally identify possible limitations to inspire future work on XBRL tagging.

cs.CL↗

arXiv2022

Predicting Intervention Approval in Clinical Trials through Multi-Document Summarization

Clinical trials offer a fundamental opportunity to discover new treatments and advance the medical knowledge. However, the uncertainty of the outcome of a trial can lead to unforeseen costs and setbacks. In this study, we propose a new method to predict the effectiveness of an intervention in a clinical trial. Our method relies on generating an informative summary from multiple documents available in the literature about the intervention under study. Specifically, our method first gathers all the abstracts of PubMed articles related to the intervention. Then, an evidence sentence, which conveys information about the effectiveness of the intervention, is extracted automatically from each abstract. Based on the set of evidence sentences extracted from the abstracts, a short summary about the intervention is constructed. Finally, the produced summaries are used to train a BERT-based classifier, in order to infer the effectiveness of an intervention. To evaluate our proposed method, we introduce a new dataset which is a collection of clinical trials together with their associated PubMed articles. Our experiments, demonstrate the effectiveness of producing short informative summaries and using them to predict the effectiveness of an intervention.

cs.CL↗

arXiv2022

Parallel Model Exploration for Tumor Treatment Simulations

Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth and its response to different drugs are of particular importance, but also challenging complexity. The main challenges are first to calibrate the simulators so as to reproduce real-world cases, and second, to search for specific values of the parameter space concerning effective drug treatments. In this work, we combine a multi-scale simulator for tumor cell growth and a Genetic Algorithm (GA) as a heuristic search method for finding good parameter configurations in reasonable time. The two modules are integrated into a single workflow that can be executed in parallel on high performance computing infrastructures. In effect, the GA is used to calibrate the simulator, and then to explore different drug delivery schemes. Among these schemes, we aim to find those that minimize tumor cell size and the probability of emergence of drug resistant cells in the future. Experimental results illustrate the effectiveness and computational efficiency of the approach.

q-bio.QM↗

arXiv2021

Symbolic Register Automata for Complex Event Recognition and Forecasting

We propose an automaton model which is a combination of symbolic and register automata, i.e., we enrich symbolic automata with memory. We call such automata Symbolic Register Automata (SRA). SRA extend the expressive power of symbolic automata, by allowing Boolean formulas to be applied not only to the last element read from the input string, but to multiple elements, stored in their registers. SRA also extend register automata, by allowing arbitrary Boolean formulas, besides equality predicates. We study the closure properties of SRA under union, intersection, concatenation, Kleene closure, complement and determinization and show that SRA, contrary to symbolic automata, are not in general closed under complement and they are not determinizable. However, they are closed under these operations when a window operator, quintessential in Complex Event Recognition, is used. We show how SRA can be used in Complex Event Recognition in order to detect patterns upon streams of events, using our framework that provides declarative and compositional semantics, and that allows for a systematic treatment of such automata. We also show how the behavior of SRA, as they consume streams of events, can be given a probabilistic description with the help of prediction suffix trees. This allows us to go one step beyond Complex Event Recognition to Complex Event Forecasting, where, besides detecting complex patterns, we can also efficiently forecast their occurrence.

cs.FL↗

arXiv2021

Complex Event Forecasting with Prediction Suffix Trees: Extended Technical Report

Complex Event Recognition (CER) systems have become popular in the past two decades due to their ability to "instantly" detect patterns on real-time streams of events. However, there is a lack of methods for forecasting when a pattern might occur before such an occurrence is actually detected by a CER engine. We present a formal framework that attempts to address the issue of Complex Event Forecasting (CEF). Our framework combines two formalisms: a) symbolic automata which are used to encode complex event patterns; and b) prediction suffix trees which can provide a succinct probabilistic description of an automaton's behavior. We compare our proposed approach against state-of-the-art methods and show its advantage in terms of accuracy and efficiency. In particular, prediction suffix trees, being variable-order Markov models, have the ability to capture long-term dependencies in a stream by remembering only those past sequences that are informative enough. Our experimental results demonstrate the benefits, in terms of accuracy, of being able to capture such long-term dependencies. This is achieved by increasing the order of our model beyond what is possible with full-order Markov models that need to perform an exhaustive enumeration of all possible past sequences of a given order. We also discuss extensively how CEF solutions should be best evaluated on the quality of their forecasts.

cs.DB↗

arXiv2021

What is all this new MeSH about? Exploring the semantic provenance of new descriptors in the MeSH thesaurus

The Medical Subject Headings (MeSH) thesaurus is a controlled vocabulary widely used in biomedical knowledge systems, particularly for semantic indexing of scientific literature. As the MeSH hierarchy evolves through annual version updates, some new descriptors are introduced that were not previously available. This paper explores the conceptual provenance of these new descriptors. In particular, we investigate whether such new descriptors have been previously covered by older descriptors and what is their current relation to them. To this end, we propose a framework to categorize new descriptors based on their current relation to older descriptors. Based on the proposed classification scheme, we quantify, analyse and present the different types of new descriptors introduced in MeSH during the last fifteen years. The results show that only about 25% of new MeSH descriptors correspond to new emerging concepts, whereas the rest were previously covered by one or more existing descriptors, either implicitly or explicitly. Most of them were covered by a single existing descriptor and they usually end up as descendants of it in the current hierarchy, gradually leading towards a more fine-grained MeSH vocabulary. These insights about the dynamics of the thesaurus are useful for the retrospective study of scientific articles annotated with MeSH, but could also be used to inform the policy of updating the thesaurus in the future.

cs.DL↗

arXiv2021

Overview of BioASQ 2020: The eighth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

In this paper, we present an overview of the eighth edition of the BioASQ challenge, which ran as a lab in the Conference and Labs of the Evaluation Forum (CLEF) 2020. BioASQ is a series of challenges aiming at the promotion of systems and methodologies for large-scale biomedical semantic indexing and question answering. To this end, shared tasks are organized yearly since 2012, where different teams develop systems that compete on the same demanding benchmark datasets that represent the real information needs of experts in the biomedical domain. This year, the challenge has been extended with the introduction of a new task on medical semantic indexing in Spanish. In total, 34 teams with more than 100 systems participated in the three tasks of the challenge. As in previous years, the results of the evaluation reveal that the top-performing systems managed to outperform the strong baselines, which suggests that state-of-the-art systems keep pushing the frontier of research through continuous improvements.

cs.CL↗

arXiv2021

Overview of BioASQ 2021: The ninth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

Advancing the state-of-the-art in large-scale biomedical semantic indexing and question answering is the main focus of the BioASQ challenge. BioASQ organizes respective tasks where different teams develop systems that are evaluated on the same benchmark datasets that represent the real information needs of experts in the biomedical domain. This paper presents an overview of the ninth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2021. In this year, a new question answering task, named Synergy, is introduced to support researchers studying the COVID-19 disease and measure the ability of the participating teams to discern information while the problem is still developing. In total, 42 teams with more than 170 systems were registered to participate in the four tasks of the challenge. The evaluation results, similarly to previous years, show a performance gain against the baselines which indicates the continuous improvement of the state-of-the-art in this field.

cs.CL↗

arXiv2021

Harvesting the Public MeSH Note field

In this document, we report an analysis of the Public MeSH Note field of the new descriptors introduced in the MeSH thesaurus between 2006 and 2020. The aim of this analysis was to extract information about the previous status of these new descriptors as Supplementary Concept Records. The Public MeSH Note field contains information in semi-structured text, meant to be read by humans. Therefore, we adopted a semi-automated approach, based on regular expressions, to extract information from it. In the large majority of cases, we managed to minimize the required manual effort for extracting the previous state of a new descriptor as a Supplementary Concept Record. The source code for this analysis is openly available on GitHub.

cs.DL↗

arXiv2021

Online Learning Probabilistic Event Calculus Theories in Answer Set Programming

Complex Event Recognition (CER) systems detect event occurrences in streaming time-stamped input using predefined event patterns. Logic-based approaches are of special interest in CER, since, via Statistical Relational AI, they combine uncertainty-resilient reasoning with time and change, with machine learning, thus alleviating the cost of manual event pattern authoring. We present a system based on Answer Set Programming (ASP), capable of probabilistic reasoning with complex event patterns in the form of weighted rules in the Event Calculus, whose structure and weights are learnt online. We compare our ASP-based implementation with a Markov Logic-based one and with a number of state-of-the-art batch learning algorithms on CER datasets for activity recognition, maritime surveillance and fleet management. Our results demonstrate the superiority of our novel approach, both in terms of efficiency and predictive performance. This paper is under consideration for publication in Theory and Practice of Logic Programming (TPLP).

cs.AI↗

arXiv2020

Results of the seventh edition of the BioASQ Challenge

The results of the seventh edition of the BioASQ challenge are presented in this paper. The aim of the BioASQ challenge is the promotion of systems and methodologies through the organization of a challenge on the tasks of large-scale biomedical semantic indexing and question answering. In total, 30 teams with more than 100 systems participated in the challenge this year. As in previous years, the best systems were able to outperform the strong baselines. This suggests that state-of-the-art systems are continuously improving, pushing the frontier of research.

cs.CL↗

arXiv2020

iASiS Open Data Graph: Automated Semantic Integration of Disease-Specific Knowledge

In biomedical research, unified access to up-to-date domain-specific knowledge is crucial, as such knowledge is continuously accumulated in scientific literature and structured resources. Identifying and extracting specific information is a challenging task and computational analysis of knowledge bases can be valuable in this direction. However, for disease-specific analyses researchers often need to compile their own datasets, integrating knowledge from different resources, or reuse existing datasets, that can be out-of-date. In this study, we propose a framework to automatically retrieve and integrate disease-specific knowledge into an up-to-date semantic graph, the iASiS Open Data Graph. This disease-specific semantic graph provides access to knowledge relevant to specific concepts and their individual aspects, in the form of concept relations and attributes. The proposed approach is implemented as an open-source framework and applied to three diseases (Lung Cancer, Dementia, and Duchenne Muscular Dystrophy). Exemplary queries are presented, investigating the potential of this automatically generated semantic graph as a basis for retrieval and analysis of disease-specific knowledge.

cs.IR↗

arXiv2020

Beyond MeSH: Fine-Grained Semantic Indexing of Biomedical Literature based on Weak Supervision

In this work, we propose a method for the automated refinement of subject annotations in biomedical literature at the level of concepts. Semantic indexing and search of biomedical articles in MEDLINE/PubMed are based on semantic subject annotations with MeSH descriptors that may correspond to several related but distinct biomedical concepts. Such semantic annotations do not adhere to the level of detail available in the domain knowledge and may not be sufficient to fulfil the information needs of experts in the domain. To this end, we propose a new method that uses weak supervision to train a concept annotator on the literature available for a particular disease. We test this method on the MeSH descriptors for two diseases: Alzheimer's Disease and Duchenne Muscular Dystrophy. The results indicate that concept-occurrence is a strong heuristic for automated subject annotation refinement and its use as weak supervision can lead to improved concept-level annotations. The fine-grained semantic annotations can enable more precise literature retrieval, sustain the semantic integration of subject annotations with other domain resources and ease the maintenance of consistent subject annotations, as new more detailed entries are added in the MeSH thesaurus over time.

cs.IR↗

arXiv2019

Tensor Factorization with Label Information for Fake News Detection

The buzz over the so-called "fake news" has created concerns about a degenerated media environment and led to the need for technological solutions. As the detection of fake news is increasingly considered a technological problem, it has attracted considerable research. Most of these studies primarily focus on utilizing information extracted from textual news content. In contrast, we focus on detecting fake news solely based on structural information of social networks. We suggest that the underlying network connections of users that share fake news are discriminative enough to support the detection of fake news. Thereupon, we model each post as a network of friendship interactions and represent a collection of posts as a multidimensional tensor. Taking into account the available labeled data, we propose a tensor factorization method which associates the class labels of data samples with their latent representations. Specifically, we combine a classification error term with the standard factorization in a unified optimization process. Results on real-world datasets demonstrate that our proposed method is competitive against state-of-the-art methods by implementing an arguably simpler approach.

cs.SI↗

arXiv2019

Semi-Supervised Tensor Factorization for Node Classification in Complex Social Networks

This paper proposes a method to guide tensor factorization, using class labels. Furthermore, it shows the advantages of using the proposed method in identifying nodes that play a special role in multi-relational networks, e.g. spammers. Most complex systems involve multiple types of relationships and interactions among entities. Combining information from different relationships may be crucial for various prediction tasks. Instead of creating distinct prediction models for each type of relationship, in this paper we present a tensor factorization approach based on RESCAL, which collectively exploits all existing relations. We extend RESCAL to produce a semi-supervised factorization method that combines a classification error term with the standard factor optimization process. The coupled optimization approach, models the tensorial data assimilating observed information from all the relations, while also taking into account classification performance. Our evaluation on real-world social network data shows that incorporating supervision, when available, leads to models that are more accurate.

cs.SI↗