arXiv subjects

Pietro Liò

Publications and source records attributed to Pietro Liò.

At least 73 records · Page 4Linked to original sources

arXiv2026

Shortest-Path Flow Matching with Mixture-Conditioned Bases for OOD Generalization to Unseen Conditions

Robust generalization under distribution shift remains a key challenge for conditional generative modeling: conditional flow-based methods often fit the training conditions well but fail to extrapolate to unseen ones. We introduce SP-FM, a shortest-path flow-matching framework that improves out-of-distribution (OOD) generalization by conditioning both the base distribution and the flow field on the condition. Specifically, SP-FM learns a condition-dependent base distribution parameterized as a flexible, learnable mixture, together with a condition-dependent vector field trained via shortest-path flow matching. Conditioning the base allows the model to adapt its starting distribution across conditions, enabling smooth interpolation and more reliable extrapolation beyond the observed training range. We provide theoretical insights into the resulting conditional transport and show how mixture-conditioned bases enhance robustness under shift. Empirically, SP-FM is effective across heterogeneous domains, including predicting responses to unseen perturbations in single-cell transcriptomics and modeling treatment effects in high-content microscopy--based drug screening. Overall, SP-FM provides a simple yet effective plug-in strategy for improving conditional generative modeling and OOD generalization across diverse domains.

cs.LG↗

arXiv2026

Entropy-Lens: Uncovering Decision Strategies in LLMs

In large language models (LLMs), each block operates on the residual stream to map input token sequences to output token distributions. However, most of the interpretability literature focuses on internal latent representations, leaving token-space dynamics underexplored. The high dimensionality and categoricity of token distributions hinder their analysis, as standard statistical descriptors are not suitable. We show that the entropy of logit-lens predictions overcomes these issues. In doing so, it provides a per-layer scalar, permutation-invariant metric. We introduce Entropy-Lens to distill the token-space dynamics of the residual stream into a low-dimensional signal. We call this signal the entropy profile. We apply our method to a variety of model sizes and families, showing that (i) entropy profiles uncover token prediction dynamics driven by expansion and pruning strategies; (ii) these dynamics are family-specific and invariant under depth rescaling; (iii) they are characteristic of task type and output format; (iv) these strategies have unequal impact on downstream performance, with the expansion strategy usually being more critical. Ultimately, our findings further enhance our understanding of the residual stream, enabling a granular assessment of how information is processed across model depth.

cs.LG↗

arXiv2026

SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling

Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D for geometry-based conditional generation remains largely unexplored. In this work, we present SynCoGen (Synthesizable Co-Generation), a single framework that combines simultaneous masked graph diffusion and flow matching for synthesizable 3D molecule generation. SynCoGen samples from the joint distribution of molecular building blocks, chemical reactions, and atomic coordinates. To train the model, we curated SynSpace, a dataset family containing over 1.2M synthesis-aware building block graphs and 7.5M conformers. SynCoGen achieves state-of-the-art performance in unconditional small molecule graph and conformer co-generation. For protein ligand generation in drug discovery, the amortized model delivers superior performance in both molecular linker design and pharmacophore-conditioned generation across diverse targets without relying on any scoring functions. Overall, this multimodal non-autoregressive formulation represents a foundation for a range of molecular design applications, including analog expansion, lead optimization, and direct de novo design.

cs.LG↗

arXiv2026

An Empirical Investigation of Neural ODEs and Symbolic Regression for Dynamical Systems

Accurately modelling the dynamics of complex systems and discovering their governing differential equations are critical tasks for accelerating scientific discovery. Using noisy, synthetic data from two damped oscillatory systems, we explore the extrapolation capabilities of Neural Ordinary Differential Equations (NODEs) and the ability of Symbolic Regression (SR) to recover the underlying equations. Our study yields three key insights. First, we demonstrate that NODEs can extrapolate effectively to new boundary conditions, provided the resulting trajectories share dynamic similarity with the training data. Second, SR successfully recovers the equations from noisy ground-truth data, though its performance is contingent on the correct selection of input variables. Finally, we find that SR recovers two out of the three governing equations, along with a good approximation for the third, when using data generated by a NODE trained on just 10% of the full simulation. While this last finding highlights an area for future work, our results suggest that using NODEs to enrich limited data and enable symbolic regression to infer physical laws represents a promising new approach for scientific discovery.

cs.LG↗

arXiv2026

Superposition in Graph Neural Networks

Interpreting graph neural networks (GNNs) is difficult because message passing mixes signals and internal channels rarely align with human concepts. We study superposition, the sharing of directions by multiple features, directly in the latent space of GNNs. Using controlled experiments with unambiguous graph concepts, we extract features as (i) class-conditional centroids at the graph level and (ii) linear-probe directions at the node level, and then analyze their geometry with simple basis-invariant diagnostics. Across GCN/GIN/GAT we find: increasing width produces a phase pattern in overlap; topology imprints overlap onto node-level features that pooling partially remixes into task-aligned graph axes; sharper pooling increases axis alignment and reduces channel sharing; and shallow models can settle into metastable low-rank embeddings. These results connect representational geometry with concrete design choices (width, pooling, and final-layer activations) and suggest practical approaches for more interpretable GNNs.

cs.LG↗

arXiv2026

How to make Medical AI Systems safer? Simulating Vulnerabilities, and Threats in Multimodal Medical RAG System

Large Vision-Language Models (LVLMs) augmented with Retrieval-Augmented Generation (RAG) are increasingly employed in medical AI to enhance factual grounding through external clinical image-text retrieval. However, this reliance creates a significant attack surface. We propose MedThreatRAG, a novel multimodal poisoning framework that systematically probes vulnerabilities in medical RAG systems by injecting adversarial image-text pairs. A key innovation of our approach is the construction of a simulated semi-open attack environment, mimicking real-world medical systems that permit periodic knowledge base updates via user or pipeline contributions. Within this setting, we introduce and emphasize Cross-Modal Conflict Injection (CMCI), which embeds subtle semantic contradictions between medical images and their paired reports. These mismatches degrade retrieval and generation by disrupting cross-modal alignment while remaining sufficiently plausible to evade conventional filters. While basic textual and visual attacks are included for completeness, CMCI demonstrates the most severe degradation. Evaluations on IU-Xray and MIMIC-CXR QA tasks show that MedThreatRAG reduces answer F1 scores by up to 27.66% and lowers LLaVA-Med-1.5 F1 rates to as low as 51.36%. Our findings expose fundamental security gaps in clinical RAG systems and highlight the urgent need for threat-aware design and robust multimodal consistency checks. Finally, we conclude with a concise set of guidelines to inform the safe development of future multimodal medical RAG systems.

cs.LG↗

arXiv2026

An AI Monkey Gets Grapes for Sure -- Sphere Neural Networks for Reliable Decision-Making

This paper compares three methodological categories of neural reasoning: LLM reasoning, supervised learning-based reasoning, and explicit model-based reasoning. LLMs remain unreliable and struggle with simple decision-making that animals can master without extensive corpora training. Through disjunctive syllogistic reasoning testing, we show that reasoning via supervised learning is less appealing than reasoning via explicit model construction. Concretely, we show that an Euler Net trained to achieve 100.00% in classic syllogistic reasoning can be trained to reach 100.00% accuracy in disjunctive syllogistic reasoning. However, the retrained Euler Net suffers severely from catastrophic forgetting (its performance drops to 6.25% on already-learned classic syllogistic reasoning), and its reasoning competence is limited to the pattern level. We propose a new version of Sphere Neural Networks that embeds concepts as circles on the surface of an n-dimensional sphere. These Sphere Neural Networks enable the representation of the negation operator via complement circles and achieve reliable decision-making by filtering out illogical statements that form unsatisfiable circular configurations. We demonstrate that the Sphere Neural Network can master 16 syllogistic reasoning tasks, including rigorous disjunctive syllogistic reasoning, while preserving the rigour of classical syllogistic reasoning. We conclude that neural reasoning with explicit model construction is the most reliable among the three methodological categories of neural reasoning.

cs.AI↗

arXiv2025

How Smoothing is N-simplicial Attention?

Going from pure Multilayer Perceptron (MLP) to a learnable graph message-passing mechanism at each layer has been foundational to state-of-the-art results, despite the computational trade-off (e.g. GATs or Transformers). To go a step further, in this work, we introduce N-simplicial attention, going from pairwise token similarity to higher-order interactions, and adapt it for Rotary Position Embeddings (RoPE). To help manage the increased complexity, we propose a cost-effective simplex selection enabling the model to focus its computation load onto the more task-sensitive interactions. Beyond these core mechanisms, we study how smoothing N-simplicial attention is by deriving a Lipschitz upper-bound and by demonstrating that by itself it also suffers from over-smoothing, despite opening the attention message-passing to higher-order interactions.

cs.LG↗

arXiv2025

Multi-Scale Protein Structure Modelling with Geometric Graph U-Nets

Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents them from capturing the hierarchical interactions that govern protein function, such as global domains and long-range allosteric regulation. In this work, we argue that the network architecture itself should mirror this biological hierarchy. We introduce Geometric Graph U-Nets, a new class of models that learn multi-scale representations by recursively coarsening and refining the protein graph. We prove that this hierarchical design can theoretically more expressive than standard Geometric GNNs. Empirically, on the task of protein fold classification, Geometric U-Nets substantially outperform invariant and equivariant baselines, demonstrating their ability to learn the global structural patterns that define protein folds. Our work provides a principled foundation for designing geometric deep learning architectures that can learn the multi-scale structure of biomolecules.

cs.LG↗

arXiv2025

DisentangleFormer: Spatial-Channel Decoupling for Multi-Channel Vision

Vision Transformers face a fundamental limitation: standard self-attention jointly processes spatial and channel dimensions, leading to entangled representations that prevent independent modeling of structural and semantic dependencies. This problem is especially pronounced in hyperspectral imaging, from satellite hyperspectral remote sensing to infrared pathology imaging, where channels capture distinct biophysical or biochemical cues. We propose DisentangleFormer, an architecture that achieves robust multi-channel vision representation through principled spatial-channel decoupling. Motivated by information-theoretic principles of decorrelated representation learning, our parallel design enables independent modeling of structural and semantic cues while minimizing redundancy between spatial and channel streams. Our design integrates three core components: (1) Parallel Disentanglement: Independently processes spatial-token and channel-token streams, enabling decorrelated feature learning across spatial and spectral dimensions, (2) Squeezed Token Enhancer: An adaptive calibration module that dynamically fuses spatial and channel streams, and (3) Multi-Scale FFN: complementing global attention with multi-scale local context to capture fine-grained structural and semantic dependencies. Extensive experiments on hyperspectral benchmarks demonstrate that DisentangleFormer achieves state-of-the-art performance, consistently outperforming existing models on Indian Pine, Pavia University, and Houston, the large-scale BigEarthNet remote sensing dataset, as well as an infrared pathology dataset. Moreover, it retains competitive accuracy on ImageNet while reducing computational cost by 17.8% in FLOPs. The code will be made publicly available upon acceptance.

cs.CV↗

arXiv2025

AutoHFormer: Efficient Hierarchical Autoregressive Transformer for Time Series Prediction

Time series forecasting requires architectures that simultaneously achieve three competing objectives: (1) strict temporal causality for reliable predictions, (2) sub-quadratic complexity for practical scalability, and (3) multi-scale pattern recognition for accurate long-horizon forecasting. We introduce AutoHFormer, a hierarchical autoregressive transformer that addresses these challenges through three key innovations: 1) Hierarchical Temporal Modeling: Our architecture decomposes predictions into segment-level blocks processed in parallel, followed by intra-segment sequential refinement. This dual-scale approach maintains temporal coherence while enabling efficient computation. 2) Dynamic Windowed Attention: The attention mechanism employs learnable causal windows with exponential decay, reducing complexity while preserving precise temporal relationships. This design avoids both the anti-causal violations of standard transformers and the sequential bottlenecks of RNN hybrids. 3) Adaptive Temporal Encoding: a novel position encoding system is adopted to capture time patterns at multiple scales. It combines fixed oscillating patterns for short-term variations with learnable decay rates for long-term trends. Comprehensive experiments demonstrate that AutoHFormer 10.76X faster training and 6.06X memory reduction compared to PatchTST on PEMS08, while maintaining consistent accuracy across 96-720 step horizons in most of cases. These breakthroughs establish new benchmarks for efficient and precise time series modeling. Implementations of our method and all baselines in hierarchical autoregressive mechanism are available at https://github.com/lizzyhku/Autotime.

cs.LG↗

arXiv2025

Graph Neural Networks Based Analog Circuit Link Prediction

Circuit link prediction, which identifies missing component connections from incomplete netlists, is crucial in analog circuit design automation. However, existing methods face three main challenges: 1) Insufficient use of topological patterns in circuit graphs reduces prediction accuracy; 2) Data scarcity due to the complexity of annotations hinders model generalization; 3) Limited adaptability to various netlist formats restricts model flexibility. We propose Graph Neural Networks Based Analog Circuit Link Prediction (GNN-ACLP), a graph neural networks (GNNs) based method featuring three innovations to tackle these challenges. First, we introduce the SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction) framework and achieve port-level accuracy in circuit link prediction. Second, we propose Netlist Babel Fish, a netlist format conversion tool that leverages retrieval-augmented generation (RAG) with a large language model (LLM) to enhance the compatibility of netlist formats. Finally, we build a comprehensive dataset, SpiceNetlist, comprising 775 annotated circuits of 7 different types across 10 component classes. Experiments demonstrate accuracy improvements of 16.08% on SpiceNetlist, 11.38% on Image2Net, and 16.01% on Masala-CHAI compared to the baseline in intra-dataset evaluation, while maintaining accuracy from 92.05% to 99.07% in cross-dataset evaluation, demonstrating robust feature transfer capabilities. However, its linear computational complexity makes processing large-scale netlists challenging and requires future addressing.

cs.AR↗

arXiv2025

Strategic Communication and Language Bias in Multi-Agent LLM Coordination

Large Language Model (LLM)-based agents are increasingly deployed in multi-agent scenarios where coordination is crucial but not always assured. Research shows that the way strategic scenarios are framed linguistically can affect cooperation. This paper explores whether allowing agents to communicate amplifies these language-driven effects. Leveraging FAIRGAME, we simulate one-shot and repeated games across different languages and models, both with and without communication. Our experiments, conducted with two advanced LLMs-GPT-4o and Llama 4 Maverick-reveal that communication significantly influences agent behavior, though its impact varies by language, personality, and game structure. These findings underscore the dual role of communication in fostering coordination and reinforcing biases.

cs.MA↗

arXiv2025

Symmetry and Generalisation in Neural Approximations of Renormalisation Transformations

Deep learning models have proven enormously successful at using multiple layers of representation to learn relevant features of structured data. Encoding physical symmetries into these models can improve performance on difficult tasks, and recent work has motivated the principle of parameter symmetry breaking and restoration as a unifying mechanism underlying their hierarchical learning dynamics. We evaluate the role of parameter symmetry and network expressivity in the generalisation behaviour of neural networks when learning a real-space renormalisation group (RG) transformation, using the central limit theorem (CLT) as a test case map. We consider simple multilayer perceptrons (MLPs) and graph neural networks (GNNs), and vary weight symmetries and activation functions across architectures. Our results reveal a competition between symmetry constraints and expressivity, with overly complex or overconstrained models generalising poorly. We analytically demonstrate this poor generalisation behaviour for certain constrained MLP architectures by recasting the CLT as a cumulant recursion relation and making use of an established framework to propagate cumulants through MLPs. We also empirically validate an extension of this framework from MLPs to GNNs, elucidating the internal information processing performed by these more complex models. These findings offer new insight into the learning dynamics of symmetric networks and their limitations in modelling structured physical transformations.

cs.LG↗

arXiv2025

Assessing the Geographic Generalization and Physical Consistency of Generative Models for Climate Downscaling

Kilometer-scale weather data is crucial for real-world applications but remains computationally intensive to produce using traditional weather simulations. An emerging solution is to use deep learning models, which offer a faster alternative for climate downscaling. However, their reliability is still in question, as they are often evaluated using standard machine learning metrics rather than insights from atmospheric and weather physics. This paper benchmarks recent state-of-the-art deep learning models and introduces physics-inspired diagnostics to evaluate their performance and reliability, with a particular focus on geographic generalization and physical consistency. Our experiments show that, despite the seemingly strong performance of models such as CorrDiff, when trained on a limited set of European geographies (e.g., central Europe), they struggle to generalize to other regions such as Iberia, Morocco in the south, or Scandinavia in the north. They also fail to accurately capture second-order variables such as divergence and vorticity derived from predicted velocity fields. These deficiencies appear even in in-distribution geographies, indicating challenges in producing physically consistent predictions. We propose a simple initial solution: introducing a power spectral density loss function that empirically improves geographic generalization by encouraging the reconstruction of small-scale physical structures. The code for reproducing the experimental results can be found at https://github.com/CarloSaccardi/PSD-Downscaling

cs.LG↗

arXiv2025

MoRE-GNN: Multi-omics Data Integration with a Heterogeneous Graph Autoencoder

The integration of multi-omics single-cell data remains challenging due to high-dimensionality and complex inter-modality relationships. To address this, we introduce MoRE-GNN (Multi-omics Relational Edge Graph Neural Network), a heterogeneous graph autoencoder that combines graph convolution and attention mechanisms to dynamically construct relational graphs directly from data. Evaluations on six publicly available datasets demonstrate that MoRE-GNN captures biologically meaningful relationships and outperforms existing methods, particularly in settings with strong inter-modality correlations. Furthermore, the learned representations allow for accurate downstream cross-modal predictions. While performance may vary with dataset complexity, MoRE-GNN offers an adaptive, scalable and interpretable framework for advancing multi-omics integration.

cs.LG↗

arXiv2025

GLANCE: Graph Logic Attention Network with Cluster Enhancement for Heterophilous Graph Representation Learning

Graph Neural Networks (GNNs) have demonstrated significant success in learning from graph-structured data but often struggle on heterophilous graphs, where connected nodes differ in features or class labels. This limitation arises from indiscriminate neighbor aggregation and insufficient incorporation of higher-order structural patterns. To address these challenges, we propose GLANCE (Graph Logic Attention Network with Cluster Enhancement), a novel framework that integrates logic-guided reasoning, dynamic graph refinement, and adaptive clustering to enhance graph representation learning. GLANCE combines a logic layer for interpretable and structured embeddings, multi-head attention-based edge pruning for denoising graph structures, and clustering mechanisms for capturing global patterns. Experimental results in benchmark datasets, including Cornell, Texas, and Wisconsin, demonstrate that GLANCE achieves competitive performance, offering robust and interpretable solutions for heterophilous graph scenarios. The proposed framework is lightweight, adaptable, and uniquely suited to the challenges of heterophilous graphs.

cs.LG↗

arXiv2025

On the Sheafification of Higher-Order Message Passing

Recent work in Topological Deep Learning (TDL) seeks to generalize graph learning's preeminent $message \ passing$ paradigm to more complex relational structures: simplicial complexes, cell complexes, hypergraphs, and combinations thereof. Many approaches to such ${higher\text{-}order \ message \ passing}$ (HOMP) admit formulation in terms of nonlinear diffusion with the Hodge (combinatorial) Laplacian, a graded operator which carries an inductive bias that dimension-$k$ data features correlate with dimension-$k$ topological features encoded in the (singular) cohomology of the underlying domain. For $k=0$ this recovers the graph Laplacian and its well-studied homophily bias. In higher gradings, however, the Hodge Laplacian's bias is more opaque and potentially even degenerate. In this essay, we position sheaf theory as a natural and principled formalism for modifying the Hodge Laplacian's diffusion-mediated interface between local and global descriptors toward more expressive message passing. The sheaf Laplacian's inductive bias correlates dimension-$k$ data features with dimension-$k$ $sheaf$ cohomology, a data-aware generalization of singular cohomology. We will contextualize and novelly extend prior theory on sheaf diffusion in graph learning ($k=0$) in such a light -- and explore how it fails to generalize to $k>0$ -- before developing novel theory and practice for the higher-order setting. Our exposition is accompanied by a self-contained introduction shepherding sheaves from the abstract to the applied.

cs.LG↗