Lorenzo Bini

Lorenzo Bini, Marco Sorbi, Stephane Marchand-Maillet

Graph Neural Networks (GNNs) have become increasingly popular for effectively modeling graph-structured data, and attention mechanisms have been pivotal in enabling these models to capture complex patterns. In our study, we reveal a critical yet underexplored consequence of integrating attention into edge-featured GNNs: the emergence of Massive Activations (MAs) within attention layers. By developing a novel method for detecting MAs on edge features, we show that these extreme activations are not only activation anomalies but encode domain-relevant signals. Our post-hoc interpretability analysis demonstrates that, in molecular graphs, MAs aggregate predominantly on common bond types (e.g., single and double bonds) while sparing more informative ones (e.g., triple bonds). Furthermore, our ablation studies confirm that MAs can serve as natural attribution indicators, reallocating to less informative edges. Our study assesses various edge-featured attention-based GNN models using benchmark datasets, including ZINC, TOX21, and PROTEINS. Key contributions include (1) establishing the direct link between attention mechanisms and MAs generation in edge-featured GNNs, (2) developing a robust definition and detection method for MAs enabling reliable post-hoc interpretability. Overall, our study reveals the complex interplay between attention mechanisms, edge-featured GNNs model, and MAs emergence, providing crucial insights for relating GNNs internals to domain knowledge.

Lorenzo Bini, Fatemeh Nassajian Mojarrad, Margarita Liarou et al.

This paper presents FlowCyt, the first comprehensive benchmark for multi-class single-cell classification in flow cytometry data. The dataset comprises bone marrow samples from 30 patients, with each cell characterized by twelve markers. Ground truth labels identify five hematological cell types: T lymphocytes, B lymphocytes, Monocytes, Mast cells, and Hematopoietic Stem/Progenitor Cells (HSPCs). Experiments utilize supervised inductive learning and semi-supervised transductive learning on up to 1 million cells per patient. Baseline methods include Gaussian Mixture Models, XGBoost, Random Forests, Deep Neural Networks, and Graph Neural Networks (GNNs). GNNs demonstrate superior performance by exploiting spatial relationships in graph-encoded data. The benchmark allows standardized evaluation of clinically relevant classification tasks, along with exploratory analyses to gain insights into hematological cell phenotypes. This represents the first public flow cytometry benchmark with a richly annotated, heterogeneous dataset. It will empower the development and rigorous assessment of novel methodologies for single-cell analysis.

Lorenzo Bini, Stephane Marchand-Maillet

We present LaplaceGNN, a novel self-supervised graph learning framework that bypasses the need for negative sampling by leveraging spectral bootstrapping techniques. Our method integrates Laplacian-based signals into the learning process, allowing the model to effectively capture rich structural representations without relying on contrastive objectives or handcrafted augmentations. By focusing on positive alignment, LaplaceGNN achieves linear scaling while offering a simpler, more efficient, self-supervised alternative for graph neural networks, applicable across diverse domains. Our contributions are twofold: we precompute spectral augmentations through max-min centrality-guided optimization, enabling rich structural supervision without relying on handcrafted augmentations, then we integrate an adversarial bootstrapped training scheme that further strengthens feature learning and robustness. Our extensive experiments on different benchmark datasets show that LaplaceGNN achieves superior performance compared to state-of-the-art self-supervised graph methods, offering a promising direction for efficiently learning expressive graph representations.

Lorenzo Bini, Stephane Marchand-Maillet

Generating high-fidelity and biologically plausible synthetic single-cell RNA sequencing (scRNA-seq) data, especially with conditional control, is challenging due to its high dimensionality, sparsity, and complex biological variations. Existing generative models often struggle to capture these unique characteristics and ensure robustness to structural noise in cellular networks. We introduce LapDDPM, a novel conditional Graph Diffusion Probabilistic Model for robust and high-fidelity scRNA-seq generation. LapDDPM uniquely integrates graph-based representations with a score-based diffusion model, enhanced by a novel spectral adversarial perturbation mechanism on graph edge weights. Our contributions are threefold: we leverage Laplacian Positional Encodings (LPEs) to enrich the latent space with crucial cellular relationship information; we develop a conditional score-based diffusion model for effective learning and generation from complex scRNA-seq distributions; and we employ a unique spectral adversarial training scheme on graph edge weights, boosting robustness against structural variations. Extensive experiments on diverse scRNA-seq datasets demonstrate LapDDPM's superior performance, achieving high fidelity and generating biologically-plausible, cell-type-specific samples. LapDDPM sets a new benchmark for conditional scRNA-seq data generation, offering a robust tool for various downstream biological applications.