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Pietro Liò

Publications and source records attributed to Pietro Liò.

At least 37 records · Page 2Linked to original sources
arXiv2026

Answer-Distribution Trajectories: A Stochastic-Dynamics View of LLM Reasoning

Chain-of-thought reasoning provides a structured computation between a model's input and final answer. Yet it is often evaluated through endpoint accuracy, which ignores the path taken to reach that answer. An emerging line of work addresses this limitation using entropy profiles, which track how uncertainty evolves over the reasoning process but do not reveal which competing hypotheses account for that uncertainty. We introduce answer-distribution trajectories, a stochastic-dynamics-inspired representation that tracks the model's full predictive distribution over answers as reasoning unfolds. As a strictly finer representation than endpoint and entropy summaries, answer-distribution trajectories enable us to characterize a trace through a dynamical reasoning profile spanning exploration, revision, motion, and commitment, and to distinguish different dynamical mechanisms of reasoning success and failure. Across sixteen open-weight language models and four reasoning benchmarks, we show that traces with the same endpoint and similar entropy profiles can exhibit substantially different reasoning dynamics. We further find substantial variation in these dynamics both within and across models and tasks, with different objectives favoring different dynamical profiles. Additionally, we show that training and inference choices systematically reshape these profiles. Our results suggest that answer-distribution trajectories provide a rich framework for analysing and evaluating the dynamics of LLM reasoning.

cs.AI↗
arXiv2026

ARO: Aligned Representation learning for multi-Omics data

The high cost of functional molecular assays, and prevalence of missing modalities and unmatched samples in computational biology, create significant barriers to comprehensive multi-omic profiling, essential for capturing and reasoning over molecules, cells, tissues, and organisms. This work proposes a model that learns meaningful representations from multi-omics cancer data supporting the reconstruction of missing and unpaired modalities. Contrary to increasingly complex, larger models, e.g. Foundation Models (FMs), ARO prioritizes practical applicability in limited or incomplete data settings. ARO optimally reconstructs missing modalities (MSE of $0.15$ on the validation and test data in the Unmasked settings), with its learned latent embeddings enabling a downstream cancer classification task. Our findings indicate that analyzing diverse molecular layers as a single integrated system offers a reliable and cost-efficient approach, reducing dependence on large-scale experimental testing, while still supporting multi-omic exploration in limited data settings.

cs.LG↗
arXiv2026

Towards Identifying the Dataset Biases Causing Phantom Transfer

Recent work has shown that a teacher model can transfer a bias to a student through a dataset from which every explicit reference to that bias has been filtered out, and that none of the tested data-level defenses reliably removes or detects such a bias, even when the defender knows what to look for. To shed light on the hidden traces these biases leave, we embed a dataset's completions with Sentence-BERT, subtract the embeddings of clean reference completions, and compare the result to an open vocabulary of candidate topics. This simple signature identifies the topic of the bias with a Matthews correlation coefficient of 0.83 when the attacker's teacher model is known, and 0.46 when it is not. We also observe that different teacher models appear to express the same bias through different vocabulary.

cs.LG↗
arXiv2026

When Numbers Start Talking: Numerical Signalling and Strategic Behaviour Among LLMs

Large language model (LLM)-based agents increasingly operate in multi-agent systems (MAS) characterised by strategic interaction. However, little is known about whether, and to what extent, different types of messages affect the outcomes of strategic games. By investigating AI agents based on four popular LLMs, playing four games with different cooperation equilibria, we study whether messages of different kinds (natural language, numerical signals, or random sequences) significantly modify the levels of cooperation in each game, also depending on the agents' assigned personalities. We observe that structured messages alter the final payoffs for most games and LLMs, but without a predictable pattern; this challenges the assumption that AI agents can converge to stable equilibria regardless of additional capabilities. Moreover, we observe that agent-generated numerical messages depart from randomness, most strongly and consistently when agents are explicitly instructed to communicate; however, they introduce an additional interpretability challenge, as their symbol distributions are mostly associated with the payoff structure and typically become more concentrated with repetition, but are overall difficult for humans to interpret. Monitoring for coordination of AI agents through restricted channels should thus prioritise message-level fingerprints, which generalise across models, over behavioural decisions, which do not.

cs.AI↗
arXiv2026

Get a GRIP, this will be a long TRIP: A Quantifiable Long-Range Framework for Verifying Over-squashing

Empirical claims about the connection between over-squashing and long-range interactions in GNNs, can only be trusted if the benchmarks used to validate them genuinely require long-range interactions. The de-facto standard, the Long Range Graph Benchmark, has been repeatedly shown to be saturated by tuned short-range models, with existing synthetic alternatives being tied to specific topologies. As such, there is a lack of principled certificate of long-rangedness on arbitrary graphs. This state reflects the absence of a precise characterization of long-ranged benchmarks. We address this fundamental gap by introducing four verifiable axioms: Predictability, Tightness, Strictly $k$-Range, and Topology-Invariance, that any task claiming to test $k$-hop interactions must satisfy. We formally prove that violating any one of them admits failure modes that undermine conclusions drawn from the task. Based on these axioms, we introduce TRIP (Truly Ranged Interactions Problem) and its generalisation GRIP (Generally Ranged Interactions Problem), constructive procedures that turn any graph into a provably long-ranged task by drawing features from stable distributions. Moreover, by construction, GRIP admits a closed-form, per-range Maximum-Likelihood oracle that yields the first a priori per-range lower bound on test error available on any benchmark. Using our framework, we: (i) audit 4 common long-range benchmarks and identify their failures modes with respect to our axioms; (ii) on TRIP-instantiated topologies, we find a popular notion of curvature is uncorrelated with GNN performance, supporting topological-vs-computational bottleneck distinction; and (iii) we show that a novel benchmark's over-squashing measures factors beyond pure long-rangedness. Code to use the framework and reproduce experiments is released https://github.com/ferranhernandezc/graph-grip.

cs.LG↗
arXiv2026

Equivariant Sheaf Neural Networks: Learning Geometric Transport on Graphs

Equivariant graph neural networks provide a principled way to model geometric systems, but efficient first-order architectures remain limited in how vector information can be transformed as it moves across a graph. We introduce \textsc{ESNN}, an Equivariant Sheaf Neural Network that enriches this interaction by learning directed, matrix-valued transport between neighboring vector features while preserving exact Euclidean equivariance. Rather than increasing the order of the representation, ESNN keeps scalar and vector features first-order and places the additional geometric flexibility in the edge transport itself. We characterize this transport theoretically, showing that when relative displacement is the only covariant geometric input, every linear $O(n)$-equivariant map decomposes into independent radial and tangential components, while learned covariant features enable richer feature-conditioned transformations. We also introduce controlled symmetry relaxation for systems with a preferred ambient direction, which may be prescribed or inferred from data while recovering full $E(n)$-equivariance when the directional pathway is inactive. Across particle dynamics, mesh-based simulation, point-cloud classification, and molecular property prediction, ESNN improves dynamics prediction, recovers the gravity axis when symmetry is broken, yields substantial gains on selected mesh tasks and long-horizon rollouts, and remains robust to unseen rotations. These results show that learning how geometric information is transported across edges offers a complementary route to expressive equivariant message passing without requiring higher-order representations.

cs.LG↗
arXiv2026

Let the Heads Talk: Beyond Diagonal Graph Attention

Sheaf Neural Networks generalize scalar-weighted message passing by replacing scalar edge weights with linear transport maps between local feature spaces. Yet the role of this matrix-valued transport is entangled with the broader sheaf-diffusion construction. We isolate the transport primitive through quiver representations and establish a direct connection with multi-head attention. Treating attention heads as coordinates of a local transport space reveals that standard multi-head attention implements diagonal edge maps: along each directed interaction, a source head can contribute only to the corresponding receiver head. Allowing off-diagonal entries instead enables edge-conditioned communication across heads before neighborhood aggregation. We show that this operation cannot, in general, be absorbed into a single shared linear map applied after aggregation. Building on this characterization, we introduce Topological Attention (Top-A), a multi-head attention that learns edge-dependent off-diagonal routes while preserving the original same-head paths and exactly recovering vanilla attention when the additional routing vanishes. We evaluate Top-A on relational reasoning, heterogeneous graph learning, and algorithmic reasoning, including out-of-distribution generalization, with heterophilic node classification as a contrast setting. The results show that cross-head transport is most useful when the task benefits from interaction-dependent transformations, while heterophily alone provides no systematic advantage. These findings identify edge-conditioned cross-head communication as a distinct computational primitive of matrix-valued transport.

cs.LG↗
arXiv2026

T-MoXAI: A Hierarchical Explainability Framework for Temporal Multimodal Data

Artificial Intelligence (AI) models for temporal multimodal data have potential in healthcare and agriculture, but their opacity can limit trust and adoption. We introduce T-MoXAI (Temporal Multimodal eXplainable AI), a hierarchical framework explaining (1) when timepoints influence predictions, using temporal Shapley values; (2) which modalities contribute at those moments, using attention analysis; and (3) what features or image regions drive decisions, using gradient based attribution. A transformer based architecture handles irregular temporal sequences and heterogeneous data, generating all three explanation levels in under one second for interactive decision support. We evaluate the framework on two real world tasks: predicting IVF treatment outcomes from ultrasound sequences and clinical measurements (AUC 0.660 despite significant class imbalance), and forecasting wheat yield from temporal RGB imagery and phenotypic traits ($R^2$ 0.265 amid substantial environmental variability). Ablation studies indicate that temporal modelling is critical in both domains: removing it reduces performance to the equivalent of random guessing. Temporal ROAR experiments provide evidence that the explanations reflect the model's reasoning process. With a unified, domain agnostic architecture and open source implementation, T-MoXAI provides a baseline for temporal multimodal XAI, addressing fragmentation in the field and supporting applications where understanding decisions is as important as predictive accuracy.

cs.LG↗
arXiv2026

Transfer Dynamics and Spectral Cascades in Graph-Coupled Kuramoto Networks

This work introduces a spectral transfer formalism for nonlinear synchronisation dynamics to resolve how internal dynamical activity redistributes across network scales, moving beyond traditional global observables like the Kuramoto order parameter. By projecting Kuramoto phase dynamics onto the eigenbasis of the graph Laplacian, we construct a time-dependent transfer matrix and derive novel network metrics, including the spectral flux, which quantifies directional redistribution between structural dynamical scales rather than physical transport across nodes. Numerical simulations on modular and hierarchical networks reveal highly structured, intermittent spectral transfer episodes characterised by forward and inverse spectral cascades, directional reversals, and complex interaction geometries. Crucially, we demonstrate a clear separation between macroscopic coherence and microscopic spectral interactions, showing that highly organised, fluctuating internal redistribution dynamics persist even beneath nearly stationary and featureless global synchronisation states. This framework extends conventional synchronisation analysis and establishes a multiscale approach for interpreting network dynamics as an evolving process of spectral reorganisation.

physics.soc-ph↗
arXiv2026

VLM-CAD: VLM-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing

Vision Language Models (VLMs) have demonstrated remarkable potential in multimodal reasoning. However, they can have spatial blindness and logical hallucinations when interpreting densely structured engineering content, such as analog circuit schematics. To address these challenges, we propose a Vision Language Model-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing (VLM-CAD) designed to support step-by-step reasoning over multimodal evidence. VLM-CAD bridges the modality gap by integrating a neuro-symbolic structural parsing module, Image2Net, which transforms raw pixels into explicit topological graphs and structured JSON representations to anchor VLM interpretation in deterministic facts. To ensure the reliability required for engineering decisions, we further propose ExTuRBO, an Explainable Trust Region Bayesian Optimization method. ExTuRBO employs agent-generated semantic seeds to warm-start local searches and uses Automatic Relevance Determination to provide sensitivity evidence for the final design report. Experimental results on 12 sizing tasks covering six circuits and four technology platforms show that VLM-CAD achieves a pooled Strict Pass@1 of 23.3% and a Relaxed Pass@1 of 91.7%, while providing sensitivity evidence for final design reports.

cs.MA↗
arXiv2026

ProtoGuide: Prototype-Driven Guidance for Class-Conditional Graph Generation

Discrete diffusion models are a prominent family for graph generation, but standard class-conditional mechanisms embed the class signal in the denoiser during training, tying the conditioning mechanism to the trained model. Classifier guidance avoids this coupling in continuous domains by steering a frozen model with a classifier's gradient, but discrete graph diffusion samples discrete edge states, so gradients cannot propagate through the sampled graph. We introduce ProtoGuide, a post-hoc, backbone-agnostic framework that recovers an analogous mechanism. At each reverse step the denoiser's per-edge output is relaxed into a differentiable soft adjacency, embedded by a frozen Siamese graph neural network, and scored against a target-class prototype and its nearest competitor; the resulting per-edge gradient, damped by a cosine schedule, is injected back into the denoiser output. All components stay frozen, so guidance is retargeted by supplying a different prototype. On five classes of real-world networks and two architecturally different backbones, EDGE and DiGress, ProtoGuide raises macro classification accuracy from 50.7% to 73.5% and from 73.6% to 83.8%, and outperforms DiGress's built-in conditional training under our configuration. Gains are largest where the unguided models are weakest, and are not uniform across classes. Per-graph coverage remains high in most settings, while distributional effects are class-dependent. A Best-of-N selection baseline matches this accuracy given enough oversampling, but at a substantial cost in graph diversity. An independently initialized classifier, a directionality test, and a few-shot analysis support target-directed steering and robustness to very small support sets.

cs.LG↗
arXiv2026

DynSHAP: Towards Explainable Dynamic Survival Analysis

Deep learning models for dynamic survival analysis (DSA) achieve strong predictive performance by incorporating longitudinal patient data, but their black box nature limits clinical trust and adoption. Existing explainability methods cannot handle longitudinal, irregular inputs and functional survival outputs simultaneously, which limits their usability in DSA. We propose DynSHAP, a SHAP framework suited specifically for dynamic survival analysis. It extends common marginal SHAP estimators to this setting by treating time--feature pairs as players in the Shapley game. We further introduce Temporal DynSHAP, which learns linear dependencies in features over time and uses conditional sampling to address them in explanations. When applied to synthetic data with known ground-truth attributions, Temporal DynSHAP recovers temporally dependent features more accurately than marginal estimators for a given state-of-the-art model. Applied to two real-world clinical datasets and two DSA architectures, DynSHAP produces attributions faithful to model learning, allowing medical experts to see which patient information drove the prediction and when.

cs.LG↗
arXiv2026

Orthogonal Polynomial Approximation for Matrix Log Normalization in Global Covariance Pooling

Global Covariance Pooling (GCP) improves deep networks by capturing second-order feature statistics, and is especially effective for fine-grained recognition. Because covariance matrices live on the Symmetric Positive Definite (SPD) manifold, a normalization step is required before the Euclidean classifier. The faithful choice is the matrix logarithm (MLN-COV), which maps the SPD manifold to its tangent space; in practice it was abandoned in favour of the matrix square root because its eigendecomposition-based gradient is numerically unstable. We show that this instability is an artifact of computing the logarithm spectrally, not of the logarithm itself. Approximating the logarithm with finite polynomials in the covariance matrix removes the eigendecomposition from both passes: every operation becomes a General Matrix Multiplication (GEMM), the gradient stays bounded on the spectral support of the pre-normalized covariance, and the unstable 1/(lambda_i-lambda_j) term never appears. The key ingredient is a mean-eigenvalue pre-normalization that centres the spectrum near 1, away from the singularity of log, with a scalar post-compensation that returns the singular part of log(A) in closed form. Our recommended normalizer is a degree-8 Chebyshev expansion evaluated by a three-term matrix recurrence, with a matching reverse recurrence for the backward pass; Legendre, Laguerre, Taylor and Pade expansions are studied as controls that isolate the roles of the basis and of the target function. On three fine-grained benchmarks and ImageNet-1k the decomposition-free logarithm is both faster and more accurate than the spectral logarithm and than the square-root approximations it replaces, and at matched basis and degree the log target beats the square-root target, confirming that the gain comes from the faithful Riemannian map rather than from a better polynomial family.

cs.CV↗
arXiv2026

GENIE: Generative Neural Inference for Epidemics

The SARS-CoV-2 pandemic highlighted the ongoing risk infectious diseases pose to society and the value of reliable information on the likely future burden. When forecasting an epidemic at fine spatial resolution, traditionally used mechanistic compartmental model struggle to capture highly complex granular transmission dynamics, resulting in inaccurate and overconfident forecasts. However, detailed Agent-Based Models (ABMs), are challenging to calibrate and are too computationally expensive to use in real-time. Amortized simulation-based inference promises to overcome this difficulty by exploiting the power of machine learning (ML) to perform approximate forecasting at near-real-time using arbitrarily complex models of epidemics. In this work we introduce Generative Neural Inference for Epidemics (GENIE), a spatio-temporal ML-based framework for high-resolution forecasting of the burden of respiratory pathogens. GENIE is designed to reflect two key characteristics of outbreaks: (i) shared biological mechanisms across locations and (ii) location-specific characteristics affecting transmission dynamics. This results in the model architecture having two modules: (i) a Local Infection Encoder - which learns to represent disease dynamics shared across all locations and (ii) a Local Profile Encoder - which learns location-specific representations. Using simulations from a high-resolution spatio-temporal ABM, GENIE is trained to generate samples from an approximate posterior predictive distribution of future epidemic trajectories. Benchmarked against established statistical and ML models, GENIE demonstrates superior performance across a range of measures including the timing and magnitude of peak hospitalisations.

stat.ME↗
arXiv2026

Looped Language Models Improve Compositional Tool Calling

Looped language models have shown promising results on reasoning benchmarks, yet their potential for agentic tool use remains largely unexplored. We study this question in compositional tool-calling settings, where models must coordinate multiple API calls, maintain intermediate state, and preserve dependencies across tool interactions. We evaluate native and retrofitted looped language models on API-Bank, BFCL, and NESTful, comparing looped and non-looped models trained under matched supervised fine-tuning recipes and varying recurrent depth at inference time. In controlled experiments, recurrent computation generally benefits compositional and dependency-aware tool use, while providing smaller and more model-dependent gains on isolated API invocation. Accuracy on multi-step tool use generally increases with recurrent depth; adaptive inference, however, achieves a more favorable compute-performance trade-off by allocating additional computation only when needed. Our results suggest that looped language models are a promising architecture for agentic systems that require reliable planning, coordination, and execution of compositional tool use workflows.

cs.AI↗
arXiv2026

LAEF: A Lead-Agnostic ECG Foundation Model Towards Point-of-Care Diagnostics

Point-of-care cardiac devices such as smartwatches and handheld ECG recorders typically capture 1--2 leads, yet existing ECG foundation models are architecturally constrained to fixed 12-lead inputs, degrading or failing under these reduced configurations. We introduce LAEF (Lead-Agnostic ECG Foundation), a 7M-parameter ECG foundation model that can natively process any lead subset without zero-padding or architectural modification. LAEF represents ECGs as variable-size spatiotemporal graphs with physiologically motivated intra- and inter-lead connectivity, processed by a Graph Attention Network that scales naturally with active lead count.Pre-trained on 9.2M 12-lead ECGs via masked node modelling with stochastic lead sampling, LAEF learns representations robust to lead configuration. Across 18 downstream datasets, LAEF is on par with specialized 12-lead baselines over 12$\times$ larger at full lead availability. Under direct point-of-care-oriented diagnostics (1--2 leads), it outperforms all zero-padded alternatives on 17 out of 18 datasets with with a single randomly sampled lead and on 14 out of 18 with 2 leads, with an average AUROC gain of +3.2 points. Representation analysis links this advantage to architectural lead-agnosticism, and a lead-importance study across 164 cardiovascular conditions shows population-level performance is stable across single standard input leads while still recovering established clinically lead-condition associations.

cs.LG↗
arXiv2026

Benchmarking Sheaf Neural Networks for Inductive Tasks

Sheaf Neural Networks (SNNs) generalize message passing by replacing scalar edge weights of standard Graph Neural Networks (GNNs) with learnable, edge-dependent restriction maps between node stalks. Despite their strong theoretical foundations and promising transductive results, SNNs have been evaluated almost exclusively on transductive node classification, leaving their behaviour under inductive protocols unknown. We address this gap through the first systematic benchmark of the sheaf design space, evaluating three diffusion mechanisms (neural sheaf diffusion, sheaf attention, and sheaf attention with Graph Attention Network v2), three restriction-map parameterizations, three stalk dimensions, and six modern GNN architectural components, within a message-passing reformulation that never assembles the heavy sheaf Laplacian, making the full design space trainable under cross-graph batching. Across $1{,}890$ controlled experiments on 14 inductive datasets, multiple insights emerge: restriction maps are the dominant design choice and general maps are preferable, larger stalks add capacity but not long-range reach, architectural components explain more performance variation than the entire sheaf-specific design space itself. Under a matched protocol, SNNs transfer to inductive settings but do not reach the strongest baselines, with gaps being dataset-dependent. Practically, a single sheaf configuration can generalize across datasets, so effort is better spent tuning the surrounding architectural recipe than the sheaf operator itself.

cs.LG↗
arXiv2026

DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models

Designing small molecule ligands that bind with high affinity to specific protein pockets is a fundamental goal in drug discovery, as small molecules constitute a major fraction of approved therapeutics. Recent breakthroughs in structure prediction, such as AlphaFold-3 and Boltz-2, enable accurate biomolecular interaction prediction and show promise as foundation models for downstream tasks, including binding affinity prediction. We propose to leverage these models and introduce DBMol, a new structure predictor-guided framework for de novo small molecule design. DBMol formulates an alternating optimization and projection process. In the optimization stage, DBMol starts from an initial molecule and uses gradient-based optimization to improve pocket-specific interactions and predicted binding affinity using a structure prediction model. In the projection stage, a flow-matching model maps the optimized molecular graph to discrete and chemically valid molecules. Experiments show that DBMol effectively optimizes the Boltz-2 affinity proxy and generates molecules with strong predicted affinity and specificity under Boltz-2 evaluation. To reduce self-confirmation bias, we further evaluate generated molecules using held-out metrics, including AF3-based evaluation. DBMol substantially improves pocket coverage while maintaining molecular diversity over unconditional generation, and is competitive under held-out metrics despite the absence of reference-ligand supervision. These results support the promise of structure prediction models as effective optimization signals for de novo molecular design.

cs.LG↗