arXiv subjects

Valentina Giunchiglia

Publications and source records attributed to Valentina Giunchiglia.

5 recordsLinked to original sources

arXiv2025

Application of Whisper in Clinical Practice: the Post-Stroke Speech Assessment during a Naming Task

Detailed assessment of language impairment following stroke remains a cognitively complex and clinician-intensive task, limiting timely and scalable diagnosis. Automatic Speech Recognition (ASR) foundation models offer a promising pathway to augment human evaluation through intelligent systems, but their effectiveness in the context of speech and language impairment remains uncertain. In this study, we evaluate whether Whisper, a state-of-the-art ASR foundation model, can be applied to transcribe and analyze speech from patients with stroke during a commonly used picture-naming task. We assess both verbatim transcription accuracy and the model's ability to support downstream prediction of language function, which has major implications for outcomes after stroke. Our results show that the baseline Whisper model performs poorly on single-word speech utterances. Nevertheless, fine-tuning Whisper significantly improves transcription accuracy (reducing Word Error Rate by 87.72% in healthy speech and 71.22% in speech from patients). Further, learned representations from the model enable accurate prediction of speech quality (average F1 Macro of 0.74 for healthy, 0.75 for patients). However, evaluations on an unseen (TORGO) dataset reveal limited generalizability, highlighting the inability of Whisper to perform zero-shot transcription of single-word utterances on out-of-domain clinical speech and emphasizing the need to adapt models to specific clinical populations. While challenges remain in cross-domain generalization, these findings highlight the potential of foundation models, when appropriately fine-tuned, to advance automated speech and language assessment and rehabilitation for stroke-related impairments.

cs.SD↗

arXiv2025

KGARevion: An AI Agent for Knowledge-Intensive Biomedical QA

Biomedical reasoning integrates structured, codified knowledge with tacit, experience-driven insights. Depending on the context, quantity, and nature of available evidence, researchers and clinicians use diverse strategies, including rule-based, prototype-based, and case-based reasoning. Effective medical AI models must handle this complexity while ensuring reliability and adaptability. We introduce KGARevion, a knowledge graph-based agent that answers knowledge-intensive questions. Upon receiving a query, KGARevion generates relevant triplets by leveraging the latent knowledge embedded in a large language model. It then verifies these triplets against a grounded knowledge graph, filtering out errors and retaining only accurate, contextually relevant information for the final answer. This multi-step process strengthens reasoning, adapts to different models of medical inference, and outperforms retrieval-augmented generation-based approaches that lack effective verification mechanisms. Evaluations on medical QA benchmarks show that KGARevion improves accuracy by over 5.2% over 15 models in handling complex medical queries. To further assess its effectiveness, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion improved accuracy by 10.4%. The agent integrates with different LLMs and biomedical knowledge graphs for broad applicability across knowledge-intensive tasks. We evaluated KGARevion on AfriMed-QA, a newly introduced dataset focused on African healthcare, demonstrating its strong zero-shot generalization to underrepresented medical contexts.

cs.AI↗

arXiv2024

Empowering Biomedical Discovery with AI Agents

We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate AI models and biomedical tools with experimental platforms. Rather than taking humans out of the discovery process, biomedical AI agents combine human creativity and expertise with AI's ability to analyze large datasets, navigate hypothesis spaces, and execute repetitive tasks. AI agents are poised to be proficient in various tasks, planning discovery workflows and performing self-assessment to identify and mitigate gaps in their knowledge. These agents use large language models and generative models to feature structured memory for continual learning and use machine learning tools to incorporate scientific knowledge, biological principles, and theories. AI agents can impact areas ranging from virtual cell simulation, programmable control of phenotypes, and the design of cellular circuits to developing new therapies.

cs.AI↗

arXiv2023

Neural correlates of cognitive ability and visuo-motor speed: validation of IDoCT on UK Biobank Data

Automated online and App-based cognitive assessment tasks are becoming increasingly popular in large-scale cohorts and biobanks due to advantages in affordability, scalability and repeatability. However, the summary scores that such tasks generate typically conflate the cognitive processes that are the intended focus of assessment with basic visuomotor speeds, testing device latencies and speed-accuracy tradeoffs. This lack of precision presents a fundamental limitation when studying brain-behaviour associations. Previously, we developed a novel modelling approach that leverages continuous performance recordings from large-cohort studies to achieve an iterative decomposition of cognitive tasks (IDoCT), which outputs data-driven estimates of cognitive abilities, and device and visuomotor latencies, whilst recalibrating trial-difficulty scales. Here, we further validate the IDoCT approach with UK BioBank imaging data. First, we examine whether IDoCT can improve ability distributions and trial-difficulty scales from an adaptive picture-vocabulary task (PVT). Then, we confirm that the resultant visuomotor and cognitive estimates associate more robustly with age and education than the original PVT scores. Finally, we conduct a multimodal brain-wide association study with free-text analysis to test whether the brain regions that predict the IDoCT estimates have the expected differential relationships with visuomotor vs. language and memory labels within the broader imaging literature. Our results support the view that the rich performance timecourses recorded during computerised cognitive assessments can be leveraged with modelling frameworks like IDoCT to provide estimates of human cognitive abilities that have superior distributions, re-test reliabilities and brain-wide associations.

q-bio.NC↗

arXiv2022

Towards Training GNNs using Explanation Directed Message Passing

With the increasing use of Graph Neural Networks (GNNs) in critical real-world applications, several post hoc explanation methods have been proposed to understand their predictions. However, there has been no work in generating explanations on the fly during model training and utilizing them to improve the expressive power of the underlying GNN models. In this work, we introduce a novel explanation-directed neural message passing framework for GNNs, EXPASS (EXplainable message PASSing), which aggregates only embeddings from nodes and edges identified as important by a GNN explanation method. EXPASS can be used with any existing GNN architecture and subgraph-optimizing explainer to learn accurate graph embeddings. We theoretically show that EXPASS alleviates the oversmoothing problem in GNNs by slowing the layer wise loss of Dirichlet energy and that the embedding difference between the vanilla message passing and EXPASS framework can be upper bounded by the difference of their respective model weights. Our empirical results show that graph embeddings learned using EXPASS improve the predictive performance and alleviate the oversmoothing problems of GNNs, opening up new frontiers in graph machine learning to develop explanation-based training frameworks.

cs.LG↗