arXiv subjects

Pietro Liò

Publications and source records attributed to Pietro Liò.

At least 19 recordsLinked to original sources

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

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 no data-level defense reliably removes or detects it even when knowing what bias to look for. Aiming to shed light on the hidden traces of these biases, we show that a simple signature based on Sentence BERT embeddings can identify the topic of such a bias with a Matthews correlation coefficient of 0.83 if the teacher model used by the attacker is known and 0.46 if it is not. Additionally, we observe that different teacher models appear to express the same bias through different vocabulary.

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

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

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

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

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↗

arXiv2026

Data-driven Machine Learning Cannot Reach Symbolic-level Logical Reasoning -- The Limit of the Scaling Law

By promoting vectors to spheres and enabling explicit model construction, neural networks can perform symbolic-level syllogistic reasoning without training data. We identify two fundamental limitations that prevent conventional data-driven machine learning systems from achieving this capability: training data generated by the combination table cannot distinguish all 24 valid syllogism types, and end-to-end premise-to-conclusion mapping creates contradictory targets within neural components. Experiments with two representative conventional systems, GPT-5 using linguistic inputs and Euler Net using visual inputs, support this analysis. ChatGPT GPT-5 may reach 100% accuracy in syllogistic reasoning, but with hallucinations. Because the learning process terminates upon reaching 100% accuracy, the system cannot progress beyond empirical accuracy to symbolic level reasoning. Random test data reduced Euler Net's accuracy to 56%. Repeatedly expanding the training set increased its accuracy to 97%, with perfect performance on 8 syllogism types. However, because unintended inputs cannot be exhaustively covered, even 100% test accuracy does not imply symbolic-level reasoning. Since syllogistic reasoning underpins logical reasoning and human rationality, these results suggest that increasing data and training time alone cannot ensure symbolic level logical reasoning.

cs.AI↗

arXiv2026

Adaptive Depth in Looped Transformers: Diagnosing Learned Halting Gates and Trajectory Readouts

Looped Transformers increase test-time computation by repeatedly applying a shared recurrent block. Learned halting objectives in looped Transformers typically use a single exit distribution both as the inference-time stopping rule and as the training-time weighting of per-depth losses. This entangles exit selection with trajectory formation: the gate not only chooses which recurrent state to use, but also determines how strongly each intermediate state is supervised. Consequently, poor adaptive-compute performance can arise from the readout, the induced trajectory, or their interaction. We study adaptive depth in looped Transformers through this trajectory--readout lens, across controlled synthetic tasks (modular arithmetic and binary parity) and large-scale Ouro-1.4B and 2.6B checkpoints. We find that fixed-prior depth supervision, which shapes the trajectory without an input-dependent halting policy, produces difficulty-aware trajectories whose intermediate states expose useful stopping signals, and that simple post-hoc confidence readouts often match or outperform learned linear and MLP gates. Fitting gates on frozen trajectories localizes the failure: it appears to stem mainly from the trajectory induced by joint gate training rather than from limited gate expressivity. The same pattern is present in Ouro evaluations, where pretrained ponder gates are competitive but not uniformly Pareto-optimal, and measured latency confirms that the resulting reductions in average exit depth translate into practical inference-time savings. Our systematic diagnostic evaluation reframes adaptive depth in looped Transformers as a joint problem of trajectory formation and exit readout, rather than gate learning alone, highlighting a distinction that prior learned-halting work has often left implicit.

cs.LG↗

arXiv2026

Trajectory Inference of Human Aging from Cross-Sectional DNA Methylation Data

DNA methylation (DNAm) serves as one of the most robust molecular biomarkers of biological aging. While conventional epigenetic clocks accurately predict chronological age from high-dimensional CpG profiles, they treat aging as a static regression task, meaning they can only output a single score rather than simulating how an entire profile continuously changes over time. To reconstruct these continuous dynamics, we frame lifelong human epigenetic aging as a trajectory inference problem across discrete age snapshots derived from widely available cross-sectional data. We introduce a two-stage computational pipeline: first, an age-regularized Variational Autoencoder (VAE) maps high-dimensional CpG profiles onto a chronologically ordered latent manifold while preserving a generative decoder bridge back to the original methylation space. Second, we model the continuous movement across this latent space via Regularized Unbalanced Optimal Transport (RUOT) that unifies deterministic drift, random diffusion, and non-conservative mass changes. By resolving this RUOT formulation using the DeepRUOT framework, our model fluidly accommodates population-level density shifts like survivorship bias and cellular attrition without requiring rigid biological priors. Evaluated on a large-scale, 80-year pan-tissue dataset, our model demonstrates robust distribution interpolation and uncovers a prominent late-life surge in the learned growth field that mathematically captures the variance expansion driven by stochastic epigenetic drift. Finally, by decoding continuous latent paths back to individual CpG sites, we reconstruct and empirically verify distinct biological aging archetypes, offering a rigorous, generative paradigm for simulating human molecular aging.

q-bio.QM↗

arXiv2026

Communicability-Inspired Positional Encoding (CIPE)

Positional encodings (PEs) are essential for Transformers. Yet designing effective PEs for non-Euclidean graphs remains challenging. Such encodings should ideally induce an Attention-Compatible Geometry for self-attention: not merely describing graph structure, but defining a geometry whose inner products reflect meaningful structural relatedness. To realize this geometry, we propose Communicability-Inspired Positional Encoding (CIPE), built from communicability, a measure between pairs of nodes that aggregates contributions from paths of all lengths. By construction, CIPE inner products recover communicability, converting global multi-path connectivity into an attention-ready similarity geometry. For practical Transformer training, we introduce dimensionality alignment, mapping graph-size-dependent CIPE representations to prescribed dimensions while faithfully preserving the induced geometry. Empirically, CIPE improves structure-agnostic Transformers by 35.5% on average across seven benchmarks, outperforming representative PEs; it also consistently improves structure-biased graph Transformers, where competing PEs often yield only marginal benefits. These results position CIPE as a principled framework for attention-compatible graph positional encodings.

cs.LG↗