Andrea Giuseppe Di Francesco

Andrea Rubbi, Andrea Giuseppe Di Francesco, Mohammad Lotfollahi et al.

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.

Andrea Giuseppe Di Francesco, Andrea Rubbi, Pietro Liò

Predicting how cells respond to genetic perturbations is fundamental to understanding gene function, disease mechanisms, and therapeutic development. While recent deep learning approaches have shown promise in modeling single-cell perturbation responses, they struggle to generalize across cell types and perturbation contexts due to limited contextual information during generation. We introduce PT-RAG (Perturbation-aware Two-stage Retrieval-Augmented Generation), a novel framework that extends Retrieval-Augmented Generation beyond traditional language-model applications to cellular biology. Unlike standard RAG systems designed for text retrieval with pre-trained LLMs, perturbation retrieval lacks established similarity metrics and requires learning what constitutes relevant context, making differentiable retrieval essential. PT-RAG addresses this through a two-stage pipeline: first, retrieving candidate perturbations $K$ using GenePT embeddings, then adaptively refining the selection through Gumbel-Softmax discrete sampling conditioned on both the cell state and the input perturbation. This cell-type-aware differentiable retrieval enables end-to-end optimization of the retrieval objective jointly with generation. On the Replogle-Nadig single-gene perturbation dataset, we demonstrate that PT-RAG outperforms both STATE and vanilla RAG under identical experimental conditions, with the strongest gains in distributional similarity metrics ($W_1$, $W_2$). Notably, vanilla RAG's dramatic failure is itself a key finding: it demonstrates that differentiable, cell-type-aware retrieval is essential in this domain, and that naive retrieval can actively harm performance. Our results establish retrieval-augmented generation as a promising paradigm for modelling cellular responses to gene perturbation. The code to reproduce our experiments is available at https://github.com/difra100/PT-RAG_ICLR.

Andrea Giuseppe Di Francesco, Francesco Caso, Maria Sofia Bucarelli et al.

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.

Farooq Ahmad Wani, Maria Sofia Bucarelli, Andrea Giuseppe Di Francesco et al.

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.

Andrea Giuseppe Di Francesco, Maria Sofia Bucarelli, Franco Maria Nardini et al.

Early-exit mechanisms allow deep neural networks to halt inference as soon as classification confidence is high enough, adaptively trading depth for confidence, and thereby cutting latency and energy on easy inputs while retaining full-depth accuracy for 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 and more complex graphs to capture intricate relationships. Although early exits have proven effective across various deep learning domains, their potential within GNNs in scenarios that require deep architectures while resisting over-smoothing and over-squashing remains largely unexplored. We unlock that potential by first introducing Symmetric-Anti-Symmetric Graph Neural Networks (SAS-GNN), whose symmetry-based inductive biases mitigate these issues and yield stable intermediate representations that can be useful to allow early exiting in GNNs. Building on this backbone, we present Early-Exit Graph Neural Networks (EEGNNs), which append confidence-aware exit heads that allow on-the-fly termination of propagation based on each node or the entire graph. Experiments show that EEGNNs preserve robust performance as depth grows and deliver competitive accuracy on heterophilic and long-range benchmarks, matching attention-based and asynchronous message-passing models while substantially reducing computation and latency. We plan to release the code to reproduce our experiments.