arXiv subjects

Andrea Giuseppe Di Francesco

Publications and source records attributed to Andrea Giuseppe Di Francesco.

8 recordsLinked to original sources

arXiv2026

Differentiable Retrieval-Augmented Generation for Predicting Cellular Responses to Gene Perturbation

Predicting transcriptional responses to genetic perturbations is fundamental to functional genomics and therapeutic discovery. Recent deep learning models have shown promise in single-cell perturbation response prediction, but they typically generate each response in isolation, without explicitly leveraging related perturbations. We introduce PT-RAG (Perturbation-aware Two-stage Retrieval-Augmented Generation), a plug-in retrieval-and-conditioning module for generative cellular perturbation response. PT-RAG augments an existing perturbation-response backbone with learned access to related perturbation contexts. The key challenge is that relevance is not fixed in this setting: functionally related genes may elicit different effects across cell types. PT-RAG addresses this with a two-stage retrieval mechanism: GenePT-based semantic retrieval first identifies K candidate perturbations, after which a differentiable Gumbel-Softmax selector adaptively selects retrieved contexts conditioned on the control cell state, the query perturbation, and each candidate perturbation. We evaluate PT-RAG on two backbones, a STATE-style generator used as a frozen random reservoir and a fully trained scGPT, across cross-cell-type and cross-perturbation generalization tasks. PT-RAG consistently improves distributional similarity and often overall predictive quality; for example, on scGPT cross-cell-type results, the 2-Wasserstein distance drops by 5.9% relative to scGPT alone. The code to reproduce our experiments is available at https://github.com/difra100/PT-RAG_NIPS.

cs.LG↗

arXiv2026

Cross-Document Neural Re-Ranking via Query-Induced Subgraphs

Neural re-rankers typically score query-document pairs independently, neglecting cross-document context within the retrieved candidate set. We propose Graph Neural Re-Ranking (GNRR), a framework that extracts a sparse, query-induced subgraph from a pre-computed semantic corpus graph and applies Graph Neural Networks (GNN) to propagate cross-document signals. Unlike self-attention re-rankers, which scale quadratically with the number of candidates ($\mathcal{O}(K^2)$), GNRR achieves $\mathcal{O}(c \cdot K)$ online complexity, where $c$ is the fixed corpus graph degree and $K$ the candidate set size. We evaluate five GNN operators within this framework and find that architecture choice substantially affects generalization to harder queries: the GCN variant is the only one that consistently improves over TCT-ColBERT across all three TREC benchmarks. On TREC-DLHard, the most challenging evaluation benchmark, GNRR achieves $+5.2\%$ relative AP over TCT-ColBERT and $+9.0\%$ AP over a self-attention re-ranker. Notably, self-attention re-ranking degrades AP on DLHard ($-3.5\%$ versus TCT-ColBERT), suggesting that sparse corpus-graph structure provides a complementary re-ranking signal that dense self-attention fails to capture. Efficiency analysis shows that GNN models require fewer parameters and lower per-query latency at $K=1000$ than self-attention, with linear rather than quadratic scaling in candidate set size. Code to reproduce our experiment is available at https://github.com/difra100/Graph-Neural-Re-Ranking-via-Corpus-Graph

cs.IR↗

arXiv2026

Early-Exit Graph Neural Networks for Link Prediction

Graph Neural Networks are great for link prediction in various network-like structures; however, the question of their speed/quality tradeoff has been barely studied. While in practice the time it takes to do inference matters little for small benchmarks, the latency does limit applicability in large-scale domains. In this work, we explore early-exiting strategies that can be applied to Graph Neural Networks to solve the problem of link-prediction faster. We use no auxiliary losses to enforce early exiting, allowing it to emerge as an implicit property of the architecture. We show that our method enables early exiting in several setups, moving the Pareto frontier on the HeaRT benchmark for GCN and SAS-GNN backbones. Our findings show that inference speed of GNNs on many link-prediction problems can be improved, while losing little, or even winning in terms of prediction quality. The code is available in our repository: https://github.com/knyazer/link_prediction.

cs.LG↗

arXiv2026

A Standardized Framework For Evaluating Gene Expression Generative Models

The rapid development of generative models for single-cell gene expression data has created an urgent need for standardised evaluation frameworks. Current evaluation practices suffer from inconsistent metric implementations, incomparable hyperparameter choices, and a lack of biologically-grounded metrics. We present Generated Genetic Expression Evaluator (GGE), an open-source Python framework that addresses these challenges by providing a comprehensive suite of distributional metrics with explicit computation space options and biologically-motivated evaluation through differentially expressed gene (DEG)-focused analysis and perturbation-effect correlation, enabling standardized reporting and reproducible benchmarking. Through extensive analysis of the single-cell generative modeling literature, we identify that no standardized evaluation protocol exists. Methods report incomparable metrics computed in different spaces with different hyperparameters. We demonstrate that metric values vary substantially depending on implementation choices, highlighting the critical need for standardization. GGE enables fair comparison across generative approaches and accelerates progress in perturbation response prediction, cellular identity modeling, and counterfactual inference.

q-bio.GN↗

arXiv2026

Energy Guided smoothness to improve Robustness in Graph Classification

Graph Neural Networks (GNNs) are powerful at solving graph classification tasks, yet applied problems often contain noisy labels. In this work, we study GNN robustness to label noise, demonstrate GNN failure modes when models struggle to generalise on low-order graphs, low label coverage, or when a model is over-parameterized. We establish both empirical and theoretical links between GNN robustness and the reduction of the total Dirichlet Energy of learned node representations, which encapsulates the hypothesized GNN smoothness inductive bias. Finally, we introduce two training strategies to enhance GNN robustness: (1) by incorporating a novel inductive bias in the weight matrices through the removal of negative eigenvalues, connected to Dirichlet Energy minimization; (2) by extending to GNNs a loss penalty that promotes learned smoothness. Importantly, neither approach negatively impacts performance in noise-free settings, supporting our hypothesis that the source of GNNs robustness is their smoothness inductive bias.

cs.LG↗

arXiv2026

Early-Exit Graph Neural Networks

Early-exit mechanisms allow deep neural networks to stop inference once prediction confidence is high, reducing latency and energy on easy inputs while retaining full-depth accuracy on harder ones. Similarly, adding early exit mechanisms to Graph Neural Networks (GNNs), the go-to models for graph-structured data, allows for dynamic trading depth for confidence on simple graphs while maintaining full-depth accuracy on harder ones to capture intricate relationships. Yet, their potential in deep GNNs, where over-smoothing, over-squashing or more generally vanishing gradients prevent these model to properly learn, remains largely unexplored. To address this, we introduce Symmetric-Anti-Symmetric GNNs (SAS-GNN), whose symmetry-based inductive biases yield stable intermediate representations that support safe early exits. Building on this backbone, we propose Early-Exit GNNs (EEGNNs), which attach confidence-aware exit neural heads which are trainable end-to-end based on the task objective, enabling on-the-fly termination at node or graph level. Experiments show that EEGNNs learn task-driven exit strategies, while achieving competitive results on heterophilic graphs and long-range tasks. Even when not outperforming the strongest baselines, EEGNNs consistently deliver favorable accuracy-efficiency trade-offs thanks to their adaptive and parameter-efficient design. We plan to release the code to reproduce our experiments.

cs.LG↗

arXiv2025

GATSY: Graph Attention Network for Music Artist Similarity

The artist similarity quest has become a crucial subject in social and scientific contexts, driven by the desire to enhance music discovery according to user preferences. Modern research solutions facilitate music discovery according to user tastes. However, defining similarity among artists remains challenging due to its inherently subjective nature, which can impact recommendation accuracy. This paper introduces GATSY, a novel recommendation system built upon graph attention networks and driven by a clusterized embedding of artists. The proposed framework leverages the graph topology of the input data to achieve outstanding performance results without relying heavily on hand-crafted features. This flexibility allows us to include fictitious artists within a music dataset, facilitating connections between previously unlinked artists and enabling diverse recommendations from various and heterogeneous sources. Experimental results prove the effectiveness of the proposed method with respect to state-of-the-art solutions while maintaining flexibility. The code to reproduce these experiments is available at https://github.com/difra100/GATSY-Music_Artist_Similarity.

cs.IR↗

arXiv2025

Link Prediction with Physics-Inspired Graph Neural Networks

The message-passing mechanism underlying Graph Neural Networks (GNNs) is not naturally suited for heterophilic datasets, where adjacent nodes often have different labels. Most solutions to this problem remain confined to the task of node classification. In this article, we focus on the valuable task of link prediction under heterophily, an interesting problem for recommendation systems, social network analysis, and other applications. GNNs like GRAFF have improved node classification under heterophily by incorporating physics biases in the architecture. Similarly, we propose GRAFF-LP, an extension of GRAFF for link prediction. We show that GRAFF-LP effectively discriminates existing from non-existing edges by learning implicitly to separate the edge gradients. Based on this information, we propose a new readout function inspired by physics. Remarkably, this new function not only enhances the performance of GRAFF-LP but also improves that of other baseline models, leading us to reconsider how every link prediction experiment has been conducted so far. Finally, we provide evidence that even simple GNNs did not experience greater difficulty in predicting heterophilic links compared to homophilic ones. This leads us to believe in the necessity for heterophily measures specifically tailored for link prediction, distinct from those used in node classification. The code and appendix are available at https://github.com/difra100/Link_Prediction_with_PIGNN_IJCNN.

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