Georgios Paliouras

• National Centre of Scientific Research "Demokritos"

The work herein reviews the scientific literature on Machine Learning approaches for financial risk assessment using financial reports. We identify two prominent use cases that constitute fundamental risk factors for a company, namely misstatement detection and financial distress prediction. We further categorize the related work along four dimensi...

Complex diseases pose challenges in prediction due to their multifactorial and polygenic nature. This study employed machine learning (ML) to analyze genomic data from the UK Biobank, aiming to predict the genomic predisposition to complex diseases like multiple sclerosis (MS) and Alzheimer’s disease (AD). We tested logistic regression (LR), ensemb...

Neuro-Symbolic Artificial Intelligence (NeSy AI) has emerged as a promising direction for integrating neural learning with symbolic reasoning. In the probabilistic variant of such systems, a neural network first extracts a set of symbols from sub-symbolic input, which are then used by a symbolic component to reason in a probabilistic manner towards...

In this paper, we deal with the task of identifying the probability of misstatements in the annual financial reports of public companies. In particular, we improve the state-of-the-art for financial misstatement detection by training a TabTransformer model with a gated multi-layer perceptron, which encodes and exploits relationships between financi...

Multi-relational networks capture intricate relationships in data and have diverse applications across fields such as biomedical, financial, and social sciences. As networks derived from increasingly large datasets become more common, identifying efficient methods for representing and analyzing them becomes crucial. This work extends the Prime Adja...

In this work, we generalize the ideas of Kaiming initialization to Graph Neural Networks (GNNs) and propose a new scheme (G-Init) that reduces oversmoothing, leading to very good results in node and graph classification tasks. GNNs are commonly initialized using methods designed for other types of Neural Networks, overlooking the underlying graph t...

In this work we investigate an observation made by Kipf \& Welling, who suggested that untrained GCNs can generate meaningful node embeddings. In particular, we investigate the effect of training only a single layer of a GCN, while keeping the rest of the layers frozen. We propose a basis on which the effect of the untrained layers and their contri...

We address the need for focused retrieval and integration of biomedical literature, enabling improved subject annotation of documents with domain concepts for which no manual labels are available. To do so, we propose a novel zero-shot method, called PN Relabeler, that improves heuristic concept-level annotations by relabeling the documents Predict...

We present a system for Complex Event Recognition (CER) based on automata. While multiple such systems have been described in the literature, they typically suffer from a lack of clear and denotational semantics, a limitation which often leads to confusion with respect to their expressive power. In order to address this issue, our system is based o...

Objective This paper presents the novel BioASQ Synergy research process which aims to facilitate the interaction between biomedical experts and automated question answering systems. Materials and Methods The proposed research allows systems to provide answers to emerging questions, which in turn are assessed by experts. The assessment of the exper...

Tabular data is a way to structure, organize, and present information conveniently and effectively. Real-world tables present data in two dimensions by arranging cells in matrices that summarize information and facilitate side-by-side comparisons. Recent research efforts aim to train large models to understand structured tables, a process that enab...

We present a formalization of the Event Calculus (EC) in tensor spaces. The motivation for a tensor-based predicate calculus comes from the area of composite event recognition (CER). As a CER engine, we adopt a logic programming implementation of EC with optimizations for continuous narrative assimilation on data streams. We show how to evaluate EC...

We present a system for Complex Event Recognition (CER) based on automata. While multiple such systems have been described in the literature, they typically suffer from a lack of clear and denotational semantics, a limitation which often leads to confusion with respect to their expressive power. In order to address this issue, our system is based o...

We present the submission of team DICE for ML-ESG-3, the 3rd Shared Task on Multilingual ESG impact duration inference in the context of the joint FinNLP-KDF workshop series. The task provides news articles and seeks to determine the impact and duration of an event in the news article may have on a company. We experiment with various baselines and...

The large-scale biomedical semantic indexing and question-answering challenge (BioASQ) aims at the continuous advancement of methods and tools to meet the needs of biomedical researchers and practitioners for efficient and precise access to the ever-increasing resources of their domain. With this purpose, during the last eleven years, a series of a...

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, h...

In this work, we propose a novel representation of complex networks, which is compact and enables very efficient network analysis. Multi-relational networks capture complex data relationships and have a wide range of applications. As they get to be used with ever larger quantities of data, it is crucial to find efficient ways to represent and analy...

Symbolic event recognition systems detect event occurrences using first-order logic rules. Although existing online structure learning approaches ease the discovery of such rules in noisy data streams, they assume the existence of fully labelled training data. Splice is a recent online graph-based approach that estimates the labels of unlabelled da...

Biomedical experts are facing challenges in keeping up with the vast amount of biomedical knowledge published daily. With millions of citations added to databases like MEDLINE/PubMed each year, efficiently accessing relevant information becomes crucial. Traditional term-based searches may lead to irrelevant or missed documents due to homonyms, syno...

The performance of Graph Neural Networks (GNNs) deteriorates as the depth of the network increases. That performance drop is mainly attributed to oversmoothing, which leads to similar node representations through repeated graph convolutions. We show that in deep GNNs the activation function plays a crucial role in oversmoothing. We explain theoreti...

Complex Event Recognition (CER) systems detect event occurrences in streaming input using predefined event patterns. Techniques that learn event patterns from data are highly desirable in CER. Since such patterns are typically represented by symbolic automata, we propose a family of such automata where the transition-enabling conditions are defined...

In this paper, we propose a novel framework, called STAL, which makes use of unlabeled graph data, through a combination of Active Learning and Self-Training, in order to improve node labeling by Graph Neural Networks (GNNs). GNNs have been shown to perform well on many tasks, when sufficient labeled data are available. Such data, however, is often...

We present a system for online, incremental composite event recognition. In streaming environments, the usual case is for data to arrive with a (variable) delay from, and to be revised by, the underlying sources. We propose RTEC_inc, an incremental version of RTEC, a composite event recognition engine with formal, declarative semantics, that has be...

This is an overview of the eleventh edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2023. BioASQ is a series of international challenges promoting advances in large-scale biomedical semantic indexing and question answering. This year, BioASQ consisted of new editions of the two established ta...

This paper applies different link prediction methods on a knowledge graph generated from biomedical literature, with the aim to compare their ability to identify unknown drug-gene interactions and explain their predictions. Identifying novel drug–target interactions is a crucial step in drug discovery and repurposing. One approach to this problem i...

In this work, we examine the evaluation process for the task of detecting financial reports with a high risk of containing a misstatement. This task is often referred to, in the literature, as ``misstatement detection in financial reports''. We provide an extensive review of the related literature. We propose a new, realistic evaluation framework f...

Most phenomena related to biomedical tasks are inherently complex, and in many cases, are expressed as signals on biomedical Knowledge Graphs (KGs). In this work, we introduce the use of a new representation framework, the Prime Adjacency Matrix (PAM) for biomedical KGs, which allows for very efficient network analysis. PAM utilizes prime numbers t...

Tailoring personalized treatments demands the analysis of a patient’s characteristics, which may be scattered over a wide variety of sources. These features include family history, life habits, comorbidities, and potential treatment side effects. Moreover, the analysis of the services visited the most by a patient before a new diagnosis, as well as...

This paper applies different link prediction methods on a knowledge graphgenerated from biomedical literature, with the aim to compare their ability toidentify unknown drug-gene interactions and explain their predictions. Identifyingnovel drug-target interactions is a crucial step in drug discovery and repurposing.One approach to this problem is to...

The BioASQ question answering (QA) benchmark dataset contains questions in English, along with golden standard (reference) answers and related material. The dataset has been designed to reflect real information needs of biomedical experts and is therefore more realistic and challenging than most existing datasets. Furthermore, unlike most previous...

The large-scale biomedical semantic indexing and question-answering challenge (BioASQ) aims at the continuous advancement of methods and tools to meet the need of biomedical researchers and practitioners for efficient and precise access to the ever-increasing resources of their domain. With this purpose, during the last ten years a series of annual...

Semantic indexing of biomedical literature is usually done at the level of MeSH descriptors, representing topics of interest for the biomedical community. Several related but distinct biomedical concepts are often grouped together in a single coarse-grained descriptor and are treated as a single topic for semantic indexing. This study proposes a ne...

The BioASQ question answering (QA) benchmark dataset contains questions in English, along with golden standard (reference) answers and related material. The dataset has been designed to reflect real information needs of biomedical experts and is therefore more realistic and challenging than most existing datasets. Furthermore, unlike most previous...

Background Dementia develops as cognitive abilities deteriorate, and early detection is critical for effective preventive interventions. However, mainstream diagnostic tests and screening tools, such as CAMCOG and MMSE, often fail to detect dementia accurately. Various graph-based or feature-dependent prediction and progression models have been pro...

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...

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...

Multi-relational networks play an important role in today's world and are utilized to capture complex relationships between the data. Their applications span many domains such as biomedical, financial, social, etc., and because of their increasing usability, it becomes crucial to find efficient ways to deal with the added complexity of multiple lay...

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, h...

We present an open-source system that can optimize compressed trajectory representations for large fleets of vessels. We take into account the type of each vessel in order to choose a suitable configuration that can yield improved trajectory synopses, both in terms of approximation error and compression ratio. We employ a genetic algorithm that con...

There is a pressing need for advanced semantic annotation technologies of medical content, in particular medical publications, clinical trials and clinical records. Search engines and information retrieval systems require semantic annotation and indexing systems to support more advanced user search queries. Considering the relevance of disease conc...

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...

Early and precise prognosis of dementia is a critical medical challenge. The design of an optimal computational model that addresses this issue, and at the same time explains the underlying mechanisms that lead to output decisions, is an ongoing challenge. In this study, we focus on assessing the risk of an individual converting to Dementia in the...

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...

The development of the CRISPR-Cas9 technology has provided a simple yet powerful system for genome editing. Current gRNA design tools serve as an important platform for the efficient application of the CRISPR systems. However, most of the existing tools are black-box models that suffer from limitations, such as variable performance and unclear mech...

The development of the CRISPR-Cas9 technology has provided a simple yet powerful system for targeted genome editing. Compared with previous gene-editing tools, the CRISPR-Cas9 system identifies target sites by the complementarity between the guide RNA (gRNA) and the DNA sequence, which is less expensive and time-consuming, as well as more precise a...

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 inf...

The tenth version of the BioASQ Challenge will be held as an evaluation Lab within CLEF2022. The motivation driving BioASQ is the continuous advancement of approaches and tools to meet the need for efficient and precise access to the ever-increasing biomedical knowledge. In this direction, a series of annual challenges are organized, in the fields...

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become a successful and promising technology for gene-editing. To facilitate its effective application, various computational tools have been developed. These tools can assist researchers in the guide RNA (gRNA) design process by pred...

We present a system for online, incremental composite event recognition. In streaming environments, the usual case is for data to arrive with a (variable) delay from, and to be revised by, the underlying sources. We propose RTECinc, an incremental version of RTEC, a composite event recognition engine with formal, declarative semantics, that has bee...

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...

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 repr...

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 atte...

A focused crawler aims at discovering as many web pages relevant to a target topic as possible, while avoiding irrelevant ones; i.e. maximizing the harvest rate. Reinforcement Learning (RL) has been utilized to optimize the crawling process, yet it deals with huge state and action spaces, which can constitute a serious challenge. In this paper, we...

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 pr...

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 t...

INTRODUCTION Genome-wide association studies (GWAS) in late onset Alzheimer's disease (LOAD) provide lists of individual genetic determinants. However, GWAS are not good at capturing the synergistic effects among multiple genetic variants and lack good specificity. METHODS We applied tree-based machine learning algorithms (MLs) to discriminate LOAD...

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 atte...

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 pap...

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 e...

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 pap...

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 a...

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-structur...

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 e...

Computational systems and methods are being applied to solve biological problems for many years. Incorporating methods of this kind in the research for cancer treatment and related drug discovery in particular, is shown to be challenging due to the complexity and the dynamic nature of the related factors. Usually, there are two objectives in such s...

This paper describes the ninth edition of the BioASQ Challenge, which will run as an evaluation Lab in the context of CLEF2021. The aim of BioASQ is the promotion of systems and methods for highly precise biomedical information access. This is done through the organization of a series of challenges (shared tasks) on large-scale biomedical semantic...

Activity recognition refers to the detection of temporal combinations of ‘low-level’ or ‘short-term’ activities on sensor data. Various types of uncertainty exist in activity recognition systems and this often leads to erroneous detection. Typically, the frameworks aiming to handle uncertainty compute the probability of the occurrence of activities...

Knowledge Graphs provide insights from data extracted in various domains. In this paper, we present an approach discovering probable drug-to-drug interactions, through the generation of a Knowledge Graph from disease-specific literature. The Graph is generated using natural language processing and semantic indexing of biomedical publications and op...

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 s...

Activity recognition systems detect temporal combinations of 'low-level' or 'short-term' activities on sensor data. These systems exhibit various types of uncertainty, often leading to erroneous detection. We present an extension of an interval-based activity recognition system which operates on top of a probabilistic Event Calculus implementation....

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 t...

This paper describes the eighth edition of the BioASQ Challenge, which will run as an evaluation Lab in the context of CLEF2020. The aim of BioASQ is the promotion of systems and methods for highly precise biomedical information access. This is done through the organization of a series of challenges (shared tasks) on large-scale biomedical semantic...

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 t...

Biomedical researchers working on a specific disease need up-to-date and unified access to knowledge relevant to the disease of their interest. Knowledge is continuously accumulated in scientific literature and other resources such as biomedical ontologies. Identifying the specific information needed is a challenging task and computational tools ca...

Online structure learning approaches, such as those stemming from Statistical Relational Learning, enable the discovery of complex relations in noisy data streams. However, these methods assume the existence of fully-labelled training data, which is unrealistic for most real-world applications. We present a novel approach for completing the supervi...

We propose RTECinc, an incremental version of RTEC, a composite event recognition engine with formal, declarative semantics, that has been shown to scale to several real-world data streams. RTEC deals with delayed arrival of events by computing at each query time everything from scratch. This is often not efficient since it results to redundant com...

We present a system for online, incremental composite event recognition. In streaming environments, the usual case is for data to arrive with a (variable) delay from, and to be retracted/revised by the underlying sources. We propose RTECinc, an incremental version of RTEC, a composite event recognition engine with a formal, declarative semantics, t...

Systems for symbolic complex event recognition detect occurrences of events in time using a set of event definitions in the form of logical rules. The Event Calculus is a temporal logic that has been used as a basis in event recognition applications, providing among others, connections to techniques for learning such rules from data. We advance the...

Complex Event Processing (CEP) systems have appeared in abundance during the last two decades. Their purpose is to detect in real–time interesting patterns upon a stream of events and to inform an analyst for the occurrence of such patterns in a timely manner. However, there is a lack of methods for forecasting when a pattern might occur before suc...

Complex Event Processing (CEP) systems have appeared in abundance during the last two decades. Their purpose is to detect in real-time interesting patterns upon a stream of events and to inform an analyst for the occurrence of such patterns in a timely manner. However, there is a lack of methods for forecasting when a pattern might occur before suc...

Logic-based event recognition systems infer occurrences of events in time using a set of event definitions in the form of first-order rules. The Event Calculus is a temporal logic that has been used as a basis in event recognition applications, providing, among others, direct connections to machine learning, via Inductive Logic Programming (ILP). O...

In this paper we present a method to identify tweets that a user may find interesting enough to retweet. The method is based on a global, but personalized classifier, which is trained on data from several users, represented in terms of user-specific features. Thus, the method is trained on a sufficient volume of data, while also being able to make...

We approach the problem of human action recognition in videos by distinguishing between simple and complex actions. To recognize simple actions, we take advantage of the latest advances with 3D convolutional networks, which are able to offer a generic video snippet descriptor. For the complex ones, which involve interaction between more than one in...

We present a system for online probabilistic event forecasting. We assume that a user is interested in detecting and forecasting event patterns, given in the form of regular expressions. Our system can consume streams of events and forecast when the pattern is expected to be fully matched. As more events are consumed, the system revises its forecas...

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 Register Match Automata (RMA). RMA 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 m...

Online structure learning approaches, such as those stemming from Statistical Relational Learning, enable the discovery of complex relations in noisy data streams. However, these methods assume the existence of fully-labelled training data, which is unrealistic for most real-world applications. We present a novel approach for completing the supervi...