arXiv subjects

Grigorios Tsoumakas

Publications and source records attributed to Grigorios Tsoumakas.

At least 19 recordsLinked to original sources

arXiv2026

Overview of BioASQ 2026: The fourteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

This paper presents an overview of the fourteenth edition of the BioASQ challenge, organized in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2026. BioASQ is an international challenge series that supports progress in biomedical language processing tasks ranging from semantic indexing and information extraction to question answering and summarization. In 2026, BioASQ included six shared tasks: a) Task 14b on biomedical semantic question answering. b) Task Synergy14 on question answering for developing biomedical top- ics. c) Task MultiClinSum-2 on multilingual clinical summarization. d) Task BioNNE-R on extracting relations between nested named entities in Russian and English. e) Task ELCardioCC on clinical coding in cardiology. f) Task GutBrainIE on gut-brain interplay information extrac- tion. Across these six tasks, 87 distinct teams participated, submitting more than 1000 runs overall. As in previous editions, several submissions reached competitive performance, reflecting the continued progress of state-of-the-art methods across biomedical language processing tasks.

cs.CL↗

arXiv2026

Architecting the Secure AI-SOC: A Neurosymbolic Framework for Pipeline Integrity and Threat Mitigation

The integration of Large Language Models (LLMs) into Security Operations Centers (SOCs) streamlines threat intelligence but introduces critical vulnerabilities, notably indirect prompt injection via log poisoning. Adversaries exploit this vector to execute multistep ``promptware'' kill chains by embedding malicious payloads within system logs to hijack the LLM's operational logic. Securing this pipeline presents a dichotomy: deterministic defenses are computationally efficient yet semantically blind, while purely neural evaluations introduce prohibitive latency and probabilistic flaws. To address this, we propose a novel neurosymbolic defense-in-depth architecture that ensures end-to-end pipeline integrity. The primary layer employs customized SIEM decoders as a deterministic pre-filter, performing immediate structural sanitization to neutralize volumetric padding and signature-based injections at the ingestion edge. The secondary layer leverages NeMo Guardrails to enforce strict semantic boundaries through self-checking validation on the structured SIEM alerts prior to LLM processing. Furthermore, the framework integrates a closed-loop telemetry system, providing critical Human-in-the-Loop (HITL) visibility into thwarted attacks directly within the SOC dashboard. We present a comprehensive experimental evaluation mapped to the MITRE ATLAS taxonomy, assessing the framework against diverse prompt injections. Our results demonstrate that this synergistic approach effectively dismantles the promptware kill chain - bounding LLM stochasticity with verifiable constraints, and delivering a resilient, highly observable defense mechanism for next-generation AI-SOCs.

cs.CR↗

arXiv2026

Loss-Based Active Learning for Neural Abstractive Summarization

Fine-tuning abstractive summarization models requires high-quality annotated data. However, obtaining such corpora is expensive and time-consuming, as it requires human annotators to read and comprehend long documents to create accurate summaries. Active learning mitigates this issue by selecting only the most informative instances for annotation, allowing models to achieve competitive results with significantly fewer labels. However, the application of active learning to summarization remains under-explored, and existing studies often suffer from instability and significant computational bottlenecks. To overcome these challenges, we propose LOBSTER (LOss-BaSed acTivE leaRning), a novel active learning framework designed specifically for abstractive summarization. LOBSTER improves performance by prioritizing unlabeled instances semantically similar to the model's current high-loss training examples, enabling the model to explicitly correct its specific weaknesses. Our empirical evaluation across three benchmark datasets and two summarization backbone models demonstrates that LOBSTER consistently matches or outperforms current state-of-the-art approaches while achieving a query selection speedup of up to 665x.

cs.CL↗

arXiv2026

Less is More: Quality-Aware Training Data Selection for Scientific Summarization

Scientific long-document summarization datasets commonly treat author-written abstracts as gold reference summaries, although their quality and alignment with the source article vary. At the same time, publicly available scientific summarization datasets remain limited in scale and structure for modern long-context models. In this work, we address both challenges by a) constructing and releasing one of the largest biomedical and life science datasets for long-document summarization, containing 1.88 million PMC articles, and b) analyzing the reference quality of author-written abstracts with source-grounded and model-based metrics. We show that author-written abstracts vary in their alignment with the full article and that these quality signals can guide training-data selection. Training on selected high-quality subsets outperforms random sampling at matched training sizes and can match or exceed larger random subsets on factuality-oriented metrics. Our findings suggest that reference quality is an important factor in scientific summarization and that quality-aware data selection can improve training efficiency.

cs.CL↗

arXiv2026

Sub-Billion, Super-Frontier: Small Language Models Rival Zero-Shot Frontier LLMs on General and Literary Relation Extraction

Large language models (LLMs) achieve strong relation extraction (RE), but their computational demands and reliance on proprietary APIs limit deployment in resource-constrained or privacy-sensitive settings. We investigate how far small language models (SLMs) can close this gap across general-domain and literary text. We evaluate five models from 360M to 3B parameters under three domain-composition regimes and two prompt-conditioned tuning styles (30 configurations), comparing them with zero-shot frontier LLMs and a discriminative RoBERTa baseline. Across nine benchmarks, the best sub-billion model, Qwen2.5-0.5B fine-tuned on pooled general-domain data, achieves a general-domain positive-class micro-F1 of 0.83, versus 0.69 for GPT-5.4 and 0.66 for Claude Sonnet 4.6 evaluated zero-shot. This does not imply that SLMs are intrinsically stronger; rather, targeted task adaptation enables 4-bit models deployable on a single consumer GPU to outperform general-purpose frontier systems under this protocol. An in-domain RoBERTa baseline also exceeds both frontier models, indicating that the gain stems from task adaptation rather than generative decoding. On literary RE, tuned SLMs reach 0.92 on the human-annotated Biographical benchmark versus 0.83 for GPT-5.4, and 0.833 versus 0.578 on the two-benchmark literary average. A targeted domain-adaptive pretraining case study yields no practically meaningful gain over supervised fine-tuning, while the cleanest within-family scale comparison shows only marginal improvement. These results show that, when task-specific data are available, compact task-adapted models can provide accurate, private, and hardware-efficient RE.

cs.CL↗

arXiv2026

Addressing Imbalance in Multi-Label Data via Label-Specific Distance-based Oversampling

The complex imbalanced label distribution poses a crucial challenge to multi-label classification, as most classifiers are biased towards the majority class and high-frequent labels. Oversampling is an efficient and flexible solution that augments instances to provide a more balanced training dataset for multi-label classifiers. Most existing oversampling methods create synthetic instances in a heuristic way that essentially relies on neighborhood information retrieved using Euclidean distance within the entire feature space. However, they fail to consider the varying semantic relevance of features to different labels, leading to label inconsistency among proximate neighbors and further introducing label confusion and overfitting to synthetic instances. To overcome the above issue, we propose a novel sampling approach called Label-Specific Distance-based Multi-Label Oversampling (LSDMLO) that creates more useful and well-labeled synthetic instances to address the imbalance in multi-label datasets. LSDMLO derives the label-specific distance to identify label-consistent neighbors based on the weighted pertinent feature space, which facilitates selecting seed instances that express more label correlations in boundary areas and generating synthetic instances aligned with the label distribution of original data. The comprehensive experiments verify that the proposed LSDMLO outperforms the state-of-the-art multi-label sampling approaches under various base classifiers.

cs.LG↗

arXiv2026

D2ACE: Multi-Label Batch Selection Guided by Dual Dynamics and Adaptive Correlation Enhancement

Batch selection is crucial for improving both training efficiency and predictive performance in deep multi-label classification (MLC). Existing batch selection methods typically rely on a single metric to assess instance importance and use static label weights to distinguish label significance, neglecting the dynamic evolution of metric utility and label significance during training. In addition, the method that explicitly exploits label correlations is largely affected by abundant irrelevant labels and insensitive to local label distributions. To address these issues, we propose D2ACE, a novel multi-label batch selection method guided by Dual Dynamics and Adaptive Correlation Enhancement. D2ACE explicitly captures metric and label-level training dynamics by combining stage-wise Bernoulli mixture sampling, which balances uncertainty and noise-resistant hardness, with dynamic label weighting to recalibrate label priorities at each epoch based on current metric statistics. Furthermore, D2ACE introduces a local context-aware correlation enhancement to focus on relevant labels with instance-adaptive dependencies. Extensive experiments on tabular and image benchmarks demonstrate that D2ACE outperforms existing batch selection approaches across various deep MLC models, achieving stronger predictive performance and more efficient correlation modeling.

cs.LG↗

arXiv2026

From Lengthy to Lucid: A Systematic Literature Review on NLP Techniques for Taming Long Sentences

Long sentences have been a persistent issue in written communication for many years since they make it challenging for readers to grasp the main points or follow the initial intention of the writer. This survey, conducted using the PRISMA guidelines, systematically reviews two main strategies for addressing the issue of long sentences: a) sentence compression and b) sentence splitting. An increased trend of interest in this area has been observed since 2005, with significant growth after 2017. Current research is dominated by supervised approaches for both sentence compression and splitting. Yet, there is a considerable gap in weakly and self-supervised techniques, suggesting an opportunity for further research, especially in domains with limited data. We also observe that despite their potential, Large Language Models (LLMs) have not yet been widely explored in this area. In this survey, we categorize and group the most representative methods into a comprehensive taxonomy. We also conduct a comparative evaluation analysis of these methods on common sentence compression and splitting datasets. Finally, we discuss the challenges and limitations of current methods, providing valuable insights for future research directions. This survey is meant to serve as a comprehensive resource for addressing the complexities of long sentences. We aim to enable researchers to make further advancements in the field until long sentences are no longer a barrier to effective communication.

cs.CL↗

arXiv2025

What's the Best Way to Retrieve Slides? A Comparative Study of Multimodal, Caption-Based, and Hybrid Retrieval Techniques

Slide decks, serving as digital reports that bridge the gap between presentation slides and written documents, are a prevalent medium for conveying information in both academic and corporate settings. Their multimodal nature, combining text, images, and charts, presents challenges for retrieval-augmented generation systems, where the quality of retrieval directly impacts downstream performance. Traditional approaches to slide retrieval often involve separate indexing of modalities, which can increase complexity and lose contextual information. This paper investigates various methodologies for effective slide retrieval, including visual late-interaction embedding models like ColPali, the use of visual rerankers, and hybrid retrieval techniques that combine dense retrieval with BM25, further enhanced by textual rerankers and fusion methods like Reciprocal Rank Fusion. A novel Vision-Language Models-based captioning pipeline is also evaluated, demonstrating significantly reduced embedding storage requirements compared to visual late-interaction techniques, alongside comparable retrieval performance. Our analysis extends to the practical aspects of these methods, evaluating their runtime performance and storage demands alongside retrieval efficacy, thus offering practical guidance for the selection and development of efficient and robust slide retrieval systems for real-world applications.

cs.CL↗

arXiv2025

Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

This is an overview of the thirteenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2025. 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 tasks, b and Synergy, and four new tasks: a) Task MultiClinSum on multilingual clinical summarization. b) Task BioNNE-L on nested named entity linking in Russian and English. c) Task ELCardioCC on clinical coding in cardiology. d) Task GutBrainIE on gut-brain interplay information extraction. In this edition of BioASQ, 83 competing teams participated with more than 1000 distinct submissions in total for the six different shared tasks of the challenge. Similar to previous editions, several participating systems achieved competitive performance, indicating the continuous advancement of the state-of-the-art in the field.

cs.CL↗

arXiv2025

DUAL: Diversity and Uncertainty Active Learning for Text Summarization

With the rise of large language models, neural text summarization has advanced significantly in recent years. However, even state-of-the-art models continue to rely heavily on high-quality human-annotated data for training and evaluation. Active learning is frequently used as an effective way to collect such datasets, especially when annotation resources are scarce. Active learning methods typically prioritize either uncertainty or diversity but have shown limited effectiveness in summarization, often being outperformed by random sampling. We present Diversity and Uncertainty Active Learning (DUAL), a novel algorithm that combines uncertainty and diversity to iteratively select and annotate samples that are both representative of the data distribution and challenging for the current model. DUAL addresses the selection of noisy samples in uncertainty-based methods and the limited exploration scope of diversity-based methods. Through extensive experiments with different summarization models and benchmark datasets, we demonstrate that DUAL consistently matches or outperforms the best performing strategies. Using visualizations and quantitative metrics, we provide valuable insights into the effectiveness and robustness of different active learning strategies, in an attempt to understand why these strategies haven't performed consistently in text summarization. Finally, we show that DUAL strikes a good balance between diversity and robustness.

cs.CL↗

arXiv2024

Batch Selection for Multi-Label Classification Guided by Uncertainty and Dynamic Label Correlations

The accuracy of deep neural networks is significantly influenced by the effectiveness of mini-batch construction during training. In single-label scenarios, such as binary and multi-class classification tasks, it has been demonstrated that batch selection algorithms preferring samples with higher uncertainty achieve better performance than difficulty-based methods. Although there are two batch selection methods tailored for multi-label data, none of them leverage important uncertainty information. Adapting the concept of uncertainty to multi-label data is not a trivial task, since there are two issues that should be tackled. First, traditional variance or entropy-based uncertainty measures ignore fluctuations of predictions within sliding windows and the importance of the current model state. Second, existing multi-label methods do not explicitly exploit the label correlations, particularly the uncertainty-based label correlations that evolve during the training process. In this paper, we propose an uncertainty-based multi-label batch selection algorithm. It assesses uncertainty for each label by considering differences between successive predictions and the confidence of current outputs, and further leverages dynamic uncertainty-based label correlations to emphasize instances whose uncertainty is synergistically expressed across multiple labels. Empirical studies demonstrate the effectiveness of our method in improving the performance and accelerating the convergence of various multi-label deep learning models.

cs.LG↗

arXiv2024

Topic-Controllable Summarization: Topic-Aware Evaluation and Transformer Methods

Topic-controllable summarization is an emerging research area with a wide range of potential applications. However, existing approaches suffer from significant limitations. For example, the majority of existing methods built upon recurrent architectures, which can significantly limit their performance compared to more recent Transformer-based architectures, while they also require modifications to the model's architecture for controlling the topic. At the same time, there is currently no established evaluation metric designed specifically for topic-controllable summarization. This work proposes a new topic-oriented evaluation measure to automatically evaluate the generated summaries based on the topic affinity between the generated summary and the desired topic. The reliability of the proposed measure is demonstrated through appropriately designed human evaluation. In addition, we adapt topic embeddings to work with powerful Transformer architectures and propose a novel and efficient approach for guiding the summary generation through control tokens. Experimental results reveal that control tokens can achieve better performance compared to more complicated embedding-based approaches while also being significantly faster.

cs.CL↗

arXiv2024

Multi-Label Adaptive Batch Selection by Highlighting Hard and Imbalanced Samples

Deep neural network models have demonstrated their effectiveness in classifying multi-label data from various domains. Typically, they employ a training mode that combines mini-batches with optimizers, where each sample is randomly selected with equal probability when constructing mini-batches. However, the intrinsic class imbalance in multi-label data may bias the model towards majority labels, since samples relevant to minority labels may be underrepresented in each mini-batch. Meanwhile, during the training process, we observe that instances associated with minority labels tend to induce greater losses. Existing heuristic batch selection methods, such as priority selection of samples with high contribution to the objective function, i.e., samples with high loss, have been proven to accelerate convergence while reducing the loss and test error in single-label data. However, batch selection methods have not yet been applied and validated in multi-label data. In this study, we introduce a simple yet effective adaptive batch selection algorithm tailored to multi-label deep learning models. It adaptively selects each batch by prioritizing hard samples related to minority labels. A variant of our method also takes informative label correlations into consideration. Comprehensive experiments combining five multi-label deep learning models on thirteen benchmark datasets show that our method converges faster and performs better than random batch selection.

cs.LG↗

arXiv2023

Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature

Objective: Semantic indexing of biomedical literature is usually done at the level of MeSH descriptors with several related but distinct biomedical concepts often grouped together and treated as a single topic. This study proposes a new method for the automated refinement of subject annotations at the level of MeSH concepts. Methods: Lacking labelled data, we rely on weak supervision based on concept occurrence in the abstract of an article, which is also enhanced by dictionary-based heuristics. In addition, we investigate deep learning approaches, making design choices to tackle the particular challenges of this task. The new method is evaluated on a large-scale retrospective scenario, based on concepts that have been promoted to descriptors. Results: In our experiments concept occurrence was the strongest heuristic achieving a macro-F1 score of about 0.63 across several labels. The proposed method improved it further by more than 4pp. Conclusion: The results suggest that concept occurrence is a strong heuristic for refining the coarse-grained labels at the level of MeSH concepts and the proposed method improves it further.

cs.CL↗

arXiv2023

Local Interpretability of Random Forests for Multi-Target Regression

Multi-target regression is useful in a plethora of applications. Although random forest models perform well in these tasks, they are often difficult to interpret. Interpretability is crucial in machine learning, especially when it can directly impact human well-being. Although model-agnostic techniques exist for multi-target regression, specific techniques tailored to random forest models are not available. To address this issue, we propose a technique that provides rule-based interpretations for instances made by a random forest model for multi-target regression, influenced by a recent model-specific technique for random forest interpretability. The proposed technique was evaluated through extensive experiments and shown to offer competitive interpretations compared to state-of-the-art techniques.

cs.LG↗

arXiv2023

Fine-Grained Selective Similarity Integration for Drug-Target Interaction Prediction

The discovery of drug-target interactions (DTIs) is a pivotal process in pharmaceutical development. Computational approaches are a promising and efficient alternative to tedious and costly wet-lab experiments for predicting novel DTIs from numerous candidates. Recently, with the availability of abundant heterogeneous biological information from diverse data sources, computational methods have been able to leverage multiple drug and target similarities to boost the performance of DTI prediction. Similarity integration is an effective and flexible strategy to extract crucial information across complementary similarity views, providing a compressed input for any similarity-based DTI prediction model. However, existing similarity integration methods filter and fuse similarities from a global perspective, neglecting the utility of similarity views for each drug and target. In this study, we propose a Fine-Grained Selective similarity integration approach, called FGS, which employs a local interaction consistency-based weight matrix to capture and exploit the importance of similarities at a finer granularity in both similarity selection and combination steps. We evaluate FGS on five DTI prediction datasets under various prediction settings. Experimental results show that our method not only outperforms similarity integration competitors with comparable computational costs, but also achieves better prediction performance than state-of-the-art DTI prediction approaches by collaborating with conventional base models. Furthermore, case studies on the analysis of similarity weights and on the verification of novel predictions confirm the practical ability of FGS.

cs.AI↗

arXiv2023

Does Noise Affect Housing Prices? A Case Study in the Urban Area of Thessaloniki

Real estate markets depend on various methods to predict housing prices, including models that have been trained on datasets of residential or commercial properties. Most studies endeavor to create more accurate machine learning models by utilizing data such as basic property characteristics as well as urban features like distances from amenities and road accessibility. Even though environmental factors like noise pollution can potentially affect prices, the research around this topic is limited. One of the reasons is the lack of data. In this paper, we reconstruct and make publicly available a general purpose noise pollution dataset based on published studies conducted by the Hellenic Ministry of Environment and Energy for the city of Thessaloniki, Greece. Then, we train ensemble machine learning models, like XGBoost, on property data for different areas of Thessaloniki to investigate the way noise influences prices through interpretability evaluation techniques. Our study provides a new noise pollution dataset that not only demonstrates the impact noise has on housing prices, but also indicates that the influence of noise on prices significantly varies among different areas of the same city.

cs.LG↗