Alessandro Crimi

Ahmed Abdeen Hamed, Byung Suk Lee, Alessandro Crimi et al.

Since the launch of various generative AI tools, scientists have been striving to evaluate their capabilities and contents, in the hope of establishing trust in their generative abilities. Regulations and guidelines are emerging to verify generated contents and identify novel uses. we aspire to demonstrate how ChatGPT claims are checked computationally using the rigor of network models. We aim to achieve fact-checking of the knowledge embedded in biological graphs that were contrived from ChatGPT contents at the aggregate level. We adopted a biological networks approach that enables the systematic interrogation of ChatGPT's linked entities. We designed an ontology-driven fact-checking algorithm that compares biological graphs constructed from approximately 200,000 PubMed abstracts with counterparts constructed from a dataset generated using the ChatGPT-3.5 Turbo model. In 10-samples of 250 randomly selected records a ChatGPT dataset of 1000 "simulated" articles , the fact-checking link accuracy ranged from 70% to 86%. This study demonstrated high accuracy of aggregate disease-gene links relationships found in ChatGPT-generated texts.

Wojciech Ciezobka, Joan Falco-Roget, Cemal Koba et al.

In this paper, we propose a reservoir computing-based and directed graph analysis pipeline. The goal of this pipeline is to define an efficient brain representation for connectivity in stroke data derived from magnetic resonance imaging. Ultimately, this representation is used within a directed graph convolutional architecture and investigated with explainable artificial intelligence (AI) tools. Stroke is one of the leading causes of mortality and morbidity worldwide, and it demands precise diagnostic tools for timely intervention and improved patient outcomes. Neuroimaging data, with their rich structural and functional information, provide a fertile ground for biomarker discovery. However, the complexity and variability of information flow in the brain requires advanced analysis, especially if we consider the case of disrupted networks as those given by the brain connectome of stroke patients. To address the needs given by this complex scenario we proposed an end-to-end pipeline. This pipeline begins with reservoir computing causality, to define effective connectivity of the brain. This allows directed graph network representations which have not been fully investigated so far by graph convolutional network classifiers. Indeed, the pipeline subsequently incorporates a classification module to categorize the effective connectivity (directed graphs) of brain networks of patients versus matched healthy control. The classification led to an area under the curve of 0.69 with the given heterogeneous dataset. Thanks to explainable tools, an interpretation of disrupted networks across the brain networks was possible. This elucidates the effective connectivity biomarker's contribution to stroke classification, fostering insights into disease mechanisms and treatment responses.

Szymon Mamoń, Max Talanov, Alessandro Crimi

As the prevalence of Alzheimer's disease (AD) rises, improving mechanistic insight from non-invasive biomarkers is increasingly critical. Recent work suggests that circuit-level brain alterations manifest as changes in electroencephalography (EEG) spectral features detectable by machine learning. However, conventional deep learning approaches for EEG-based AD detection are computationally intensive and mechanistically opaque. Spiking neural networks (SNNs) offer a biologically plausible and energy-efficient alternative, yet their application to AD diagnosis remains largely unexplored. We propose a neuro-bridge framework that links data-driven learning with minimal, biophysically grounded simulations, enabling bidirectional interpretation between machine learning signatures and circuit-level mechanisms in AD. Using resting-state clinical EEG, we train an SNN classifier that achieves competitive performance (AUC = 0.839) and identifies the aperiodic 1/f slope as a key discriminative marker. The 1/f slope reflects excitation-inhibition balance. To interpret this mechanistically, we construct spiking network simulations in which inhibitory-to-excitatory synaptic ratios are systematically varied to emulate healthy, mild cognitive impairment, and AD-like states. Using both membrane potential-based and synaptic current-based EEG proxies, we reproduce empirical spectral slowing and altered alpha organization. Incorporating empirical functional connectivity priors into multi-subnetwork simulations further enhances spectral differentiation, demonstrating that large-scale network topology constrains EEG signatures more strongly than excitation-inhibition balance alone. Overall, this neuro-bridge approach connects SNN-based classification with interpretable circuit simulations, advancing mechanistic understanding of EEG biomarkers while enabling scalable, explainable AD detection.

Monika Pytlarz, Adrian Onicas, Alessandro Crimi

Cross-modal augmentation of Magnetic Resonance Imaging (MRI) and microscopic imaging based on the same tissue samples is promising because it can allow histopathological analysis in the absence of an underlying invasive biopsy procedure. Here, we tested a method for generating microscopic histological images from MRI scans of the human corpus callosum using conditional generative adversarial network (cGAN) architecture. To our knowledge, this is the first multimodal translation of the brain MRI to histological volumetric representation of the same sample. The technique was assessed by training paired image translation models taking sets of images from MRI scans and microscopy. The use of cGAN for this purpose is challenging because microscopy images are large in size and typically have low sample availability. The current work demonstrates that the framework reliably synthesizes histology images from MRI scans of corpus callosum, emphasizing the network's ability to train on high resolution histologies paired with relatively lower-resolution MRI scans. With the ultimate goal of avoiding biopsies, the proposed tool can be used for educational purposes.

Ahmed Abdeen Hamed, Alessandro Crimi, Magdalena M. Misiak et al.

The generative capabilities of LLM models offer opportunities for accelerating tasks but raise concerns about the authenticity of the knowledge they produce. To address these concerns, we present a computational approach that evaluates the factual accuracy of biomedical knowledge generated by an LLM. Our approach consists of two processes: generating disease-centric associations and verifying these associations using the semantic framework of biomedical ontologies. Using ChatGPT as the selected LLM, we designed prompt-engineering processes to establish linkages between diseases and related drugs, symptoms, and genes, and assessed consistency across multiple ChatGPT models (e.g., GPT-turbo, GPT-4, etc.). Experimental results demonstrate high accuracy in identifying disease terms (88%-97%), drug names (90%-91%), and genetic information (88%-98%). However, symptom term identification was notably lower (49%-61%), due to the informal and verbose nature of symptom descriptions, which hindered effective semantic matching with the formal language of specialized ontologies. Verification of associations reveals literature coverage rates of 89%-91% for disease-drug and disease-gene pairs, while symptom-related associations exhibit lower coverage (49%-62%).

Szymon Mazurek, Monika Pytlarz, Sylwia Malec et al.

Artificial intelligence have contributed to advancements across various industries. However, the rapid growth of artificial intelligence technologies also raises concerns about their environmental impact, due to associated carbon footprints to train computational models. Fetal brain segmentation in medical imaging is challenging due to the small size of the fetal brain and the limited image quality of fast 2D sequences. Deep neural networks are a promising method to overcome this challenge. In this context, the construction of larger models requires extensive data and computing power, leading to high energy consumption. Our study aims to explore model architectures and compression techniques that promote energy efficiency by optimizing the trade-off between accuracy and energy consumption through various strategies such as lightweight network design, architecture search, and optimized distributed training tools. We have identified several effective strategies including optimization of data loading, modern optimizers, distributed training strategy implementation, and reduced floating point operations precision usage with light model architectures while tuning parameters according to available computer resources. Our findings demonstrate that these methods lead to satisfactory model performance with low energy consumption during deep neural network training for medical image segmentation.

Agus Hartoyo, Jan Argasiński, Aleksandra Trenk et al.

Covariance and Hessian matrices have been analyzed separately in the literature for classification problems. However, integrating these matrices has the potential to enhance their combined power in improving classification performance. We present a novel approach that combines the eigenanalysis of a covariance matrix evaluated on a training set with a Hessian matrix evaluated on a deep learning model to achieve optimal class separability in binary classification tasks. Our approach is substantiated by formal proofs that establish its capability to maximize between-class mean distance (the concept of \textit{separation}) and minimize within-class variances (the concept of \textit{compactness}), which together define the two linear discriminant analysis (LDA) criteria, particularly under ideal data conditions such as isotropy around class means and dominant leading eigenvalues. By projecting data into the combined space of the most relevant eigendirections from both matrices, we achieve optimal class separability as per these LDA criteria. Empirical validation across neural and health datasets consistently supports our theoretical framework and demonstrates that our method outperforms established methods. Our method stands out by addressing both separation and compactness criteria, unlike PCA and the Hessian method, which predominantly emphasize one criterion each. This comprehensive approach captures intricate patterns and relationships, enhancing classification performance. Furthermore, through the utilization of both LDA criteria, our method outperforms LDA itself by leveraging higher-dimensional feature spaces, in accordance with Cover's theorem, which favors linear separability in higher dimensions. Additionally, our approach sheds light on complex DNN decision-making, rendering them comprehensible within a 2D space.

Alessandro Crimi, Andrea Brovelli

Time-series forecasting and causal discovery are central in neuroscience, as predicting brain activity and identifying causal relationships between neural populations and circuits can shed light on the mechanisms underlying cognition and disease. With the rise of foundation models, an open question is how they compare to traditional methods for brain signal forecasting and causality analysis, and whether they can be applied in a zero-shot setting. In this work, we evaluate a foundation model against classical methods for inferring directional interactions from spontaneous brain activity measured with functional magnetic resonance imaging (fMRI) in humans. Traditional approaches often rely on Wiener-Granger causality. We tested the forecasting ability of the foundation model in both zero-shot and fine-tuned settings, and assessed causality by comparing Granger-like estimates from the model with standard Granger causality. We validated the approach using synthetic time series generated from ground-truth causal models, including logistic map coupling and Ornstein-Uhlenbeck processes. The foundation model achieved competitive zero-shot forecasting fMRI time series (mean absolute percentage error of 0.55 in controls and 0.27 in patients). Although standard Granger causality did not show clear quantitative differences between models, the foundation model provided a more precise detection of causal interactions. Overall, these findings suggest that foundation models offer versatility, strong zero-shot performance, and potential utility for forecasting and causal discovery in time-series data.

Ilerioluwakiiye Abolade, Emmanuel Idoko, Solomon Odelola et al.

Pediatric chest X-ray imaging is essential for early diagnosis, particularly in low-resource settings where advanced imaging modalities are often inaccessible. Low-dose protocols reduce radiation exposure in children but introduce substantial noise that can obscure critical anatomical details. Conventional denoising methods often degrade fine details, compromising diagnostic accuracy. In this paper, we present SharpXR, a structure-aware dual-decoder U-Net designed to denoise low-dose pediatric X-rays while preserving diagnostically relevant features. SharpXR combines a Laplacian-guided edge-preserving decoder with a learnable fusion module that adaptively balances noise suppression and structural detail retention. To address the scarcity of paired training data, we simulate realistic Poisson-Gaussian noise on the Pediatric Pneumonia Chest X-ray dataset. SharpXR outperforms state-of-the-art baselines across all evaluation metrics while maintaining computational efficiency suitable for resource-constrained settings. SharpXR-denoised images improved downstream pneumonia classification accuracy from 88.8% to 92.5%, underscoring its diagnostic value in low-resource pediatric care.

Szymon Mazurek, Stephen Moore, Alessandro Crimi

Goal: Epilepsy remains under-diagnosed in low-income countries due to scarce neurologists and costly diagnostic tools. We propose a graph-based deep learning framework to detect epilepsy from low-cost Electroencephalography (EEG) hardware, tested on recordings from Nigeria and Guinea-Bissau. Our focus is on fair, accessible automatic assessment and explainability to shed light on epilepsy biomarkers. Methods: We model EEG signals as spatio-temporal graphs, classify them, and identify interchannel relationships and temporal dynamics using graph attention networks (GAT). To emphasize connectivity biomarkers, we adapt the inherently node-focused GAT to analyze edges. We also designed signal preprocessing for low-fidelity recordings and a lightweight GAT architecture trained on Google Colab and deployed on RaspberryPi devices. Results: The approach achieves promising classification performance, outperforming a standard classifier based on random forest and graph convolutional networks in terms of accuracy and robustness over multiple sessions, but also highlighting specific connections in the fronto-temporal region. Conclusions: The results highlight the potential of GATs to provide insightful and scalable diagnostic support for epilepsy in underserved regions, paving the way for affordable and accessible neurodiagnostic tools.

Spyridon Bakas, Mauricio Reyes, Andras Jakab et al.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.