arXiv subjects

Pietro Liò

Publications and source records attributed to Pietro Liò.

At least 91 records · Page 5Linked to original sources

arXiv2025

Uncertainty Modeling in Graph Neural Networks via Stochastic Differential Equations

We propose a novel Stochastic Differential Equation (SDE) framework to address the problem of learning uncertainty-aware representations for graph-structured data. While Graph Neural Ordinary Differential Equations (GNODEs) have shown promise in learning node representations, they lack the ability to quantify uncertainty. To address this, we introduce Latent Graph Neural Stochastic Differential Equations (LGNSDE), which enhance GNODE by embedding randomness through a Bayesian prior-posterior mechanism for epistemic uncertainty and Brownian motion for aleatoric uncertainty. By leveraging the existence and uniqueness of solutions to graph-based SDEs, we prove that the variance of the latent space bounds the variance of model outputs, thereby providing theoretically sensible guarantees for the uncertainty estimates. Furthermore, we show mathematically that LGNSDEs are robust to small perturbations in the input, maintaining stability over time. Empirical results across several benchmarks demonstrate that our framework is competitive in out-of-distribution detection, robustness to noise, and active learning, underscoring the ability of LGNSDEs to quantify uncertainty reliably. Code is available at \href{https://github.com/Richard-Bergna/GraphNeuralSDE}{\texttt{github.com/Richard-Bergna/GraphNeuralSDE}}.

cs.LG↗

arXiv2025

Topotein: Topological Deep Learning for Protein Representation Learning

Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical organization inherent in protein structures. We introduce Topotein, a comprehensive framework that applies topological deep learning to PRL through the novel Protein Combinatorial Complex (PCC) and Topology-Complete Perceptron Network (TCPNet). Our PCC represents proteins at multiple hierarchical levels -- from residues to secondary structures to complete proteins -- while preserving geometric information at each level. TCPNet employs SE(3)-equivariant message passing across these hierarchical structures, enabling more effective capture of multi-scale structural patterns. Through extensive experiments on four PRL tasks, TCPNet consistently outperforms state-of-the-art geometric graph neural networks. Our approach demonstrates particular strength in tasks such as fold classification which require understanding of secondary structure arrangements, validating the importance of hierarchical topological features for protein analysis.

cs.LG↗

arXiv2025

RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design

We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for data preparation and evaluation to address unique challenges posed by RNA modeling. We formulate RNA structures as a set of rigid-body frames and associated loss functions which account for larger, more conformationally flexible RNA backbones (13 atoms per nucleotide) vs. proteins (4 atoms per residue). Toward tackling the lack of diversity in 3D RNA datasets, we explore training with structural clustering and cropping augmentations. Additionally, we define a suite of evaluation metrics to measure whether the generated RNA structures are globally self-consistent (via inverse folding followed by forward folding) and locally recover RNA-specific structural descriptors. The most performant version of RNA-FrameFlow generates locally realistic RNA backbones of 40-150 nucleotides, over 40% of which pass our validity criteria as measured by a self-consistency TM-score >= 0.45, at which two RNAs have the same global fold. Open-source code: https://github.com/rish-16/rna-backbone-design

q-bio.BM↗

arXiv2025

HealthBranches: Synthesizing Clinically-Grounded Question Answering Datasets via Decision Pathways

HealthBranches is a novel benchmark dataset for medical Question-Answering (Q&A), specifically designed to evaluate complex reasoning in Large Language Models (LLMs). This dataset is generated through a semi-automated pipeline that transforms explicit decision pathways from medical source into realistic patient cases with associated questions and answers. Covering 4,063 case studies across 17 healthcare topics, each data point is based on clinically validated reasoning chains. HealthBranches supports both open-ended and multiple-choice question formats and uniquely includes the full reasoning path for each Q&A. Its structured design enables robust evaluation of LLMs' multi-step inference capabilities, including their performance in structured Retrieval-Augmented Generation (RAG) contexts. HealthBranches establishes a foundation for the development of more trustworthy, interpretable, and clinically reliable LLMs in high-stakes domains while also serving as a valuable resource for educational purposes.

cs.CL↗

arXiv2025

Can LLMs effectively provide game-theoretic-based scenarios for cybersecurity?

Game theory has long served as a foundational tool in cybersecurity to test, predict, and design strategic interactions between attackers and defenders. The recent advent of Large Language Models (LLMs) offers new tools and challenges for the security of computer systems; In this work, we investigate whether classical game-theoretic frameworks can effectively capture the behaviours of LLM-driven actors and bots. Using a reproducible framework for game-theoretic LLM agents, we investigate two canonical scenarios -- the one-shot zero-sum game and the dynamic Prisoner's Dilemma -- and we test whether LLMs converge to expected outcomes or exhibit deviations due to embedded biases. Our experiments involve four state-of-the-art LLMs and span five natural languages, English, French, Arabic, Vietnamese, and Mandarin Chinese, to assess linguistic sensitivity. For both games, we observe that the final payoffs are influenced by agents characteristics such as personality traits or knowledge of repeated rounds. Moreover, we uncover an unexpected sensitivity of the final payoffs to the choice of languages, which should warn against indiscriminate application of LLMs in cybersecurity applications and call for in-depth studies, as LLMs may behave differently when deployed in different countries. We also employ quantitative metrics to evaluate the internal consistency and cross-language stability of LLM agents, to help guide the selection of the most stable LLMs and optimising models for secure applications.

cs.CR↗

arXiv2025

Multimodal Attention-Aware Fusion for Diagnosing Distal Myopathy: Evaluating Model Interpretability and Clinician Trust

Distal myopathy represents a genetically heterogeneous group of skeletal muscle disorders with broad clinical manifestations, posing diagnostic challenges in radiology. To address this, we propose a novel multimodal attention-aware fusion architecture that combines features extracted from two distinct deep learning models, one capturing global contextual information and the other focusing on local details, representing complementary aspects of the input data. Uniquely, our approach integrates these features through an attention gate mechanism, enhancing both predictive performance and interpretability. Our method achieves a high classification accuracy on the BUSI benchmark and a proprietary distal myopathy dataset, while also generating clinically relevant saliency maps that support transparent decision-making in medical diagnosis. We rigorously evaluated interpretability through (1) functionally grounded metrics, coherence scoring against reference masks and incremental deletion analysis, and (2) application-grounded validation with seven expert radiologists. While our fusion strategy boosts predictive performance relative to single-stream and alternative fusion strategies, both quantitative and qualitative evaluations reveal persistent gaps in anatomical specificity and clinical usefulness of the interpretability. These findings highlight the need for richer, context-aware interpretability methods and human-in-the-loop feedback to meet clinicians' expectations in real-world diagnostic settings.

cs.CV↗

arXiv2025

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.

cs.LG↗

arXiv2025

Challenges and Guidelines in Deep Generative Protein Design: Four Case Studies

Deep generative models show promise for $\textit{de novo}$ protein design, yet reliably producing designs that are geometrically plausible, evolutionarily consistent, functionally relevant, and dynamically stable remains challenging. We present a deep generative modeling pipeline for early $\textit{de novo}$ design of monomeric proteins, based on Score Matching and Flow Matching. We apply this pipeline to four diverse protein families with an adaptable evaluation protocol. Generated structures display realistic, clash-free conformations enriched with family-specific features, while the designed sequences preserve essential functional residues while retaining variability. Molecular dynamics and binding simulations show dynamic stability, with wild-type-like binding pockets that interact favorably with family-specific ligands. These results provide practical guidelines for integrating generative models into protein design workflows.

q-bio.BM↗

arXiv2025

TABASCO: A Fast, Simplified Model for Molecular Generation with Improved Physical Quality

State-of-the-art models for 3D molecular generation are based on significant inductive biases, SE(3), permutation equivariance to respect symmetry and graph message-passing networks to capture local chemistry, yet the generated molecules still struggle with physical plausibility. We introduce TABASCO which relaxes these assumptions: The model has a standard non-equivariant transformer architecture, treats atoms in a molecule as sequences and reconstructs bonds deterministically after generation. The absence of equivariant layers and message passing allows us to significantly simplify the model architecture and scale data throughput. On the GEOM-Drugs benchmark TABASCO achieves state-of-the-art PoseBusters validity and delivers inference roughly 10x faster than the strongest baseline, while exhibiting emergent rotational equivariance despite symmetry not being hard-coded. Our work offers a blueprint for training minimalist, high-throughput generative models suited to specialised tasks such as structure- and pharmacophore-based drug design. We provide a link to our implementation at github.com/carlosinator/tabasco.

cs.LG↗

arXiv2025

G-Adaptivity: optimised graph-based mesh relocation for finite element methods

We present a novel, and effective, approach to achieve optimal mesh relocation in finite element methods (FEMs). The cost and accuracy of FEMs is critically dependent on the choice of mesh points. Mesh relocation (r-adaptivity) seeks to optimise the mesh geometry to obtain the best solution accuracy at given computational budget. Classical r-adaptivity relies on the solution of a separate nonlinear "meshing" PDE to determine mesh point locations. This incurs significant cost at remeshing, and relies on estimates that relate interpolation- and FEM-error. Recent machine learning approaches have focused on the construction of fast surrogates for such classical methods. Instead, our new approach trains a graph neural network (GNN) to determine mesh point locations by directly minimising the FE solution error from the PDE system Firedrake to achieve higher solution accuracy. Our GNN architecture closely aligns the mesh solution space to that of classical meshing methodologies, thus replacing classical estimates for optimality with a learnable strategy. This allows for rapid and robust training and results in an extremely efficient and effective GNN approach to online r-adaptivity. Our method outperforms both classical, and prior ML, approaches to r-adaptive meshing. In particular, it achieves lower FE solution error, whilst retaining the significant speed-up over classical methods observed in prior ML work.

cs.LG↗

arXiv2025

Sheaf Hypergraph Networks

Higher-order relations are widespread in nature, with numerous phenomena involving complex interactions that extend beyond simple pairwise connections. As a result, advancements in higher-order processing can accelerate the growth of various fields requiring structured data. Current approaches typically represent these interactions using hypergraphs. We enhance this representation by introducing cellular sheaves for hypergraphs, a mathematical construction that adds extra structure to the conventional hypergraph while maintaining their local, higherorder connectivity. Drawing inspiration from existing Laplacians in the literature, we develop two unique formulations of sheaf hypergraph Laplacians: linear and non-linear. Our theoretical analysis demonstrates that incorporating sheaves into the hypergraph Laplacian provides a more expressive inductive bias than standard hypergraph diffusion, creating a powerful instrument for effectively modelling complex data structures. We employ these sheaf hypergraph Laplacians to design two categories of models: Sheaf Hypergraph Neural Networks and Sheaf Hypergraph Convolutional Networks. These models generalize classical Hypergraph Networks often found in the literature. Through extensive experimentation, we show that this generalization significantly improves performance, achieving top results on multiple benchmark datasets for hypergraph node classification.

cs.LG↗

arXiv2025

Wasserstein Hypergraph Neural Network

The ability to model relational information using machine learning has driven advancements across various domains, from medicine to social science. While graph representation learning has become mainstream over the past decade, representing higher-order relationships through hypergraphs is rapidly gaining momentum. In the last few years, numerous hypergraph neural networks have emerged, most of them falling under a two-stage, set-based framework. The messages are sent from nodes to edges and then from edges to nodes. However, most of the advancement still takes inspiration from the graph counterpart, often simplifying the aggregations to basic pooling operations. In this paper we are introducing Wasserstein Hypergraph Neural Network, a model that treats the nodes and hyperedge neighbourhood as distributions and aggregate the information using Sliced Wasserstein Pooling. Unlike conventional aggregators such as mean or sum, which only capture first-order statistics, our approach has the ability to preserve geometric properties like the shape and spread of distributions. This enables the learned embeddings to reflect how easily one hyperedge distribution can be transformed into another, following principles of optimal transport. Experimental results demonstrate that applying Wasserstein pooling in a hypergraph setting significantly benefits node classification tasks, achieving top performance on several real-world datasets.

cs.LG↗

arXiv2025

SPHINX: Structural Prediction using Hypergraph Inference Network

The importance of higher-order relations is widely recognized in a large number of real-world systems. However, annotating them is a tedious and sometimes impossible task. Consequently, current approaches for data modelling either ignore the higher-order interactions altogether or simplify them into pairwise connections. In order to facilitate higher-order processing, even when a hypergraph structure is not available, we introduce Structural Prediction using Hypergraph Inference Network (SPHINX), a model that learns to infer a latent hypergraph structure in an unsupervised way, solely from the final node-level signal. The model consists of a soft, differentiable clustering method used to sequentially predict, for each hyperedge, the probability distribution over the nodes and a sampling algorithm that converts them into an explicit hypergraph structure. We show that the recent advancement in $k$-subset sampling represents a suitable tool for producing discrete hypergraph structures, addressing some of the training instabilities exhibited by prior works. The resulting model can generate the higher-order structure necessary for any modern hypergraph neural network, facilitating the capture of higher-order interaction in domains where annotating them is difficult. Through extensive ablation studies and experiments conducted on two challenging datasets for trajectory prediction, we demonstrate that our model is capable of inferring suitable latent hypergraphs, that are interpretable and enhance the final performance.

cs.LG↗

arXiv2025

Sheaves Reloaded: A Directional Awakening

Sheaf Neural Networks (SNNs) represent a powerful generalization of Graph Neural Networks (GNNs) that significantly improve our ability to model complex relational data. While directionality has been shown to substantially boost performance in graph learning tasks and is key to many real-world applications, existing SNNs fall short in representing it. To address this limitation, we introduce the Directed Cellular Sheaf, a special type of cellular sheaf designed to explicitly account for edge orientation. Building on this structure, we define a new sheaf Laplacian, the Directed Sheaf Laplacian, which captures both the graph's topology and its directional information. This operator serves as the backbone of the Directed Sheaf Neural Network (DSNN), the first SNN model to embed a directional bias into its architecture. Extensive experiments on nine real-world benchmarks show that DSNN consistently outperforms baseline methods.

cs.LG↗

arXiv2025

Neural Algorithmic Reasoning with Multiple Correct Solutions

Neural Algorithmic Reasoning (NAR) extends classical algorithms to higher dimensional data. However, canonical implementations of NAR train neural networks to return only a single solution, even when there are multiple correct solutions to a problem, such as single-source shortest paths. For some applications, it is desirable to recover more than one correct solution. To that end, we give the first method for NAR with multiple solutions. We demonstrate our method on two classical algorithms: Bellman-Ford (BF) and Depth-First Search (DFS), favouring deeper insight into two algorithms over a broader survey of algorithms. This method involves generating appropriate training data as well as sampling and validating solutions from model output. Each step of our method, which can serve as a framework for neural algorithmic reasoning beyond the tasks presented in this paper, might be of independent interest to the field and our results represent the first attempt at this task in the NAR literature.

cs.LG↗

arXiv2025

Sparsity is All You Need: Rethinking Biological Pathway-Informed Approaches in Deep Learning

Biologically-informed neural networks typically leverage pathway annotations to enhance performance in biomedical applications. We hypothesized that the benefits of pathway integration does not arise from its biological relevance, but rather from the sparsity it introduces. We conducted a comprehensive analysis of all relevant pathway-based neural network models for predictive tasks, critically evaluating each study's contributions. From this review, we curated a subset of methods for which the source code was publicly available. The comparison of the biologically informed state-of-the-art deep learning models and their randomized counterparts showed that models based on randomized information performed equally well as biologically informed ones across different metrics and datasets. Notably, in 3 out of the 15 analyzed models, the randomized versions even outperformed their biologically informed counterparts. Moreover, pathway-informed models did not show any clear advantage in interpretability, as randomized models were still able to identify relevant disease biomarkers despite lacking explicit pathway information. Our findings suggest that pathway annotations may be too noisy or inadequately explored by current methods. Therefore, we propose a methodology that can be applied to different domains and can serve as a robust benchmark for systematically comparing novel pathway-informed models against their randomized counterparts. This approach enables researchers to rigorously determine whether observed performance improvements can be attributed to biological insights.

q-bio.QM↗

arXiv2025

Enhancing Surgical Documentation through Multimodal Visual-Temporal Transformers and Generative AI

The automatic summarization of surgical videos is essential for enhancing procedural documentation, supporting surgical training, and facilitating post-operative analysis. This paper presents a novel method at the intersection of artificial intelligence and medicine, aiming to develop machine learning models with direct real-world applications in surgical contexts. We propose a multi-modal framework that leverages recent advancements in computer vision and large language models to generate comprehensive video summaries. % The approach is structured in three key stages. First, surgical videos are divided into clips, and visual features are extracted at the frame level using visual transformers. This step focuses on detecting tools, tissues, organs, and surgical actions. Second, the extracted features are transformed into frame-level captions via large language models. These are then combined with temporal features, captured using a ViViT-based encoder, to produce clip-level summaries that reflect the broader context of each video segment. Finally, the clip-level descriptions are aggregated into a full surgical report using a dedicated LLM tailored for the summarization task. % We evaluate our method on the CholecT50 dataset, using instrument and action annotations from 50 laparoscopic videos. The results show strong performance, achieving 96\% precision in tool detection and a BERT score of 0.74 for temporal context summarization. This work contributes to the advancement of AI-assisted tools for surgical reporting, offering a step toward more intelligent and reliable clinical documentation.

cs.CV↗

arXiv2025

Renormalized Graph Representations for Node Classification

Graph neural networks process information on graphs represented at a given resolution scale. We analyze the effect of using different coarse-grained graph resolutions, obtained through the Laplacian renormalization group theory, on node classification tasks. At the theory's core is grouping nodes connected by significant information flow at a given time scale. Representations of the graph at different scales encode interaction information at different ranges. We specifically experiment using representations at the characteristic scale of the graph's mesoscopic structures. We provide the models with the original graph and the graph represented at the characteristic resolution scale and compare them to models that can only access the original graph. Our results showed that models with access to both the original graph and the characteristic scale graph can achieve statistically significant improvements in test accuracy.

cs.LG↗