Publications

SpaTM: Topic Models for Inferring Spatially Informed Transcriptional Programs
Wenqi Dong
Qihuang Zhang
Robert Sladek
Yuemei Li
Spatial transcriptomics has revolutionized our ability to characterize tissues and diseases by contextualizing gene expression with spatial … (see more)organization. Available methods require researchers to either train a model using histology-based annotations or use annotation-free clustering approaches to uncover spatial domains. However, few methods provide researchers with a way to jointly analyze spatial data from both annotation-free and annotation-guided perspectives using consistent inductive biases and levels of interpretability. A single framework with consistent inductive biases ensures coherence and transferability across tasks, reducing the risks of conflicting assumptions. To this end, we propose the Spatial Topic Model (SpaTM), a topic-modeling framework capable of annotation-guided and annotation-free analysis of spatial transcriptomics data. SpaTM can be used to learn gene programs that represent histology-based annotations while providing researchers with the ability to infer spatial domains with an annotation-free approach if manual annotations are limited or noisy. We demonstrate SpaTM’s interpretability with its use of topic mixtures to represent cell states and transcriptional programs and how its intuitive framework facilitates the integration of annotation-guided and annotation-free analyses of spatial data with downstream analyses such as cell type deconvolution. Finally, we demonstrate how both approaches can be used to extend the analysis of large-scale snRNA-seq atlases with the inference of cell proximity and spatial annotations in human brains with Major Depressive Disorder.
International AI Safety Report Second Key Update: Technical Safeguards and Risk Management
Stephen Clare
Carina Prunkl
Maksym Andriushchenko
BEN BUCKNALL
Philip Fox
Nestor Maslej
Conor McGlynn
Malcolm Murray
Stephen Casper
Jessica Newman
Daniel Privitera
Daron Acemoglu
Thomas G. Dietterich
Fredrik Heintz
Geoffrey Hinton
Nick Jennings
Susan Leavy … (see 17 more)
Teresa Ludermir
Vidushi Marda
Helen Margetts
John McDermid
Jane Munga
Arvind Narayanan
Alondra Nelson
Clara Neppel
Sarvapali D. (Gopal) Ramchurn
Stuart Russell
Marietje Schaake
Bernhard Schölkopf
Alvaro Soto
Lee Tiedrich
Andrew Yao
Ya-Qin Zhang
This is the Second Key Update to the 2025 International AI Safety Report. The First Key Update (1) discussed developments in the capabilitie… (see more)s of general-purpose AI models and systems and associated risks. This Key Update covers how various actors, including researchers, companies, and governments, are approaching risk management and technical mitigations for AI. The past year has seen important developments in AI risk management, including better techniques for training safer models and monitoring their outputs. While this represents tangible progress, significant gaps remain. It is often uncertain how effective current measures are at preventing harms, and effectiveness varies across time and applications. There are many opportunities to further strengthen existing safeguard techniques and to develop new ones. This Key Update provides a concise overview of critical developments in risk management practices and technical risk mitigation since the publication of the 2025 AI Safety Report in January. It highlights where progress is being made and where gaps remain. Above all, it aims to support policymakers, researchers, and the public in navigating a rapidly changing environment, helping them to make informed and timely decisions about the governance of general-purpose AI. Professor Yoshua BengioUniversité de Montréal / LawZero /Mila – Quebec AI Institute & Chair
Large Language Model Applications in the Algebra Domain: A Systematic Review
Adsorption energies are necessary but not sufficient to identify good catalysts
Alexander Davis
Alexandre AGM Duval
Oleksandr Voznyy
Alex Hern'andez-Garcia
Evaluation and improvement of algorithmic fairness for COVID-19 severity classification using Explainable Artificial Intelligence-based bias mitigation
Charlene H. Chu
Katherine S. McGilton
Xiaoxiao Li
Charlene Ronquillo
The COVID-19 pandemic has highlighted the growing reliance on machine learning (ML) models for predicting disease severity, which is importa… (see more)nt for clinical decision-making and equitable resource allocation. While achieving high predictive accuracy is important, ensuring fairness in the prediction output of these models is equally important to prevent bias-driven disparities in healthcare. This study evaluates fairness in a machine learning-based COVID-19 severity classification model and proposes an Explainable AI (XAI)-based bias mitigation strategy to address sex-related bias. Using data from the Quebec Biobank, we developed an XGBoost-based multi-class classification model. Fairness was assessed using Subset Accuracy Parity Difference (SAPD) and Label-wise Equal Opportunity Difference (LEOD) metrics. Four bias mitigation strategies were implemented and evaluated: Fair Representation Learning, Fair Classifier Using Constraints, Adversarial Debiasing, and our proposed XAI-based method utilizing SHapley Additive exPlanations (SHAP) method for feature importance analysis. The study cohort included 1642 COVID-19 positive older adults (mean age: 77.5), balance equally between males and females. The baseline (unmitigated) classification model achieved 90.68% accuracy but exhibited a 10.11% Subset Accuracy Parity Difference between sexes, indicating a relatively large bias. The introduced XAI-based method demonstrated a better trade-off between model performance and fairness compared to existing bias mitigation methods by identifying sex-sensitive feature interactions and integrating them into the model re-training. Traditional fairness interventions often compromise accuracy to a greater extent. Our XAI-based method achieves the best balance between classification performance and bias, enhancing its clinical applicability. The XAI-driven bias mitigation intervention effectively reduces sex-based disparities in COVID-19 severity prediction without the significant accuracy loss observed in traditional methods. This approach provides a framework for developing fair and accurate clinical decision support systems for older adults, which ensures equitable care in clinical risk stratification and resource allocation.
Long-Horizon Model-Based Offline Reinforcement Learning Without Conservatism
Cognitive cartography of mammalian brains using meta-analysis of AI experts
Andrea I. Luppi
Hana Ali
Zhen-Qi Liu
Filip Milisav
Alessandro Gozzi
Bratislav Misic
The complexity of the brain is increasingly mirrored by the complexity of the neuroscientific literature, yet no individual mind can fully g… (see more)rasp the diversity of scales, methodologies and model organisms. Where human experts flag, the latest AI models excel: large language models can seamlessly integrate knowledge across scientific domains. Here we show how large language models can systematically and quantitatively synthesise literature-wide neuroscientific knowledge about the cognitive operations and dysfunctions associated with each brain region. Meta-analysis of AI experts reveals structure-function mappings to which existing meta-analytic frameworks are blind, demonstrated by lesions and direct intracranial stimulation. It also unlocks the possibility of extending quantitative literature meta-analysis and decoding of brain maps to other model organisms beyond human. As proof of concept, we integrate LLM meta-analysis with species-specific transcriptomics in human, macaque, and mouse, to discover an evolutionarily conserved molecular circuit for cognition. Altogether, meta-analysis of AI experts can fundamentally catalyze neuroscientific discovery by overcoming the barrier of data aggregation from heterogeneous studies, finally bringing together a scattered literature to identify emergent patterns and latent insights across disparate subfields, modalities, and species.
Curly Flow Matching for Learning Non-gradient Field Dynamics
Katarina Petrović
Viggo Moro
Kacper Kapuśniak
İsmail İlkan Ceylan
Michael Bronstein
Avishek Joey Bose
Modeling the transport dynamics of natural processes from population-level observations is a ubiquitous problem in the natural sciences. Suc… (see more)h models rely on key assumptions about the underlying process in order to enable faithful learning of governing dynamics that mimic the actual system behavior. The de facto assumption in current approaches relies on the principle of least action that results in gradient field dynamics and leads to trajectories minimizing an energy functional between two probability measures. However, many real-world systems, such as cell cycles in single-cell RNA, are known to exhibit non-gradient, periodic behavior, which fundamentally cannot be captured by current state-of-the-art methods such as flow and bridge matching. In this paper, we introduce Curly Flow Matching (Curly-FM), a novel approach that is capable of learning non-gradient field dynamics by designing and solving a Schrödinger bridge problem with a non-zero drift reference process---in stark contrast to typical zero-drift reference processes---which is constructed using inferred velocities in addition to population snapshot data. We showcase Curly-FM by solving the trajectory inference problems for single cells, computational fluid dynamics, and ocean currents with approximate velocities. We demonstrate that Curly-FM can learn trajectories that better match both the reference process and population marginals. Curly-FM expands flow matching models beyond the modeling of populations and towards the modeling of known periodic behavior in physical systems. Our code repository is accessibleat: https://github.com/kpetrovicc/curly-flow-matching.git
From Noise to Narrative: Tracing the Origins of Hallucinations in Transformers
As generative AI systems become competent and democratized in science, business, and government, deeper insight into their failure modes now… (see more) poses an acute need. The occasional volatility in their behavior, such as the propensity of transformer models to hallucinate, impedes trust and adoption of emerging AI solutions in high-stakes areas. In the present work, we establish how and when hallucinations arise in pre-trained transformer models through concept representations captured by sparse autoencoders, under scenarios with experimentally controlled uncertainty in the input space. Our systematic experiments reveal that the number of semantic concepts used by the transformer model grows as the input information becomes increasingly unstructured. In the face of growing uncertainty in the input space, the transformer model becomes prone to activate coherent yet input-insensitive semantic features, leading to hallucinated output. At its extreme, for pure-noise inputs, we identify a wide variety of robustly triggered and meaningful concepts in the intermediate activations of pre-trained transformer models, whose functional integrity we confirm through targeted steering. We also show that hallucinations in the output of a transformer model can be reliably predicted from the concept patterns embedded in transformer layer activations. This collection of insights on transformer internal processing mechanics has immediate consequences for aligning AI models with human values, AI safety, opening the attack surface for potential adversarial attacks, and providing a basis for automatic quantification of a model's hallucination risk.
Geometry-Aware Edge Pooling for Graph Neural Networks
Graph Neural Networks (GNNs) have shown significant success for graph-based tasks. Motivated by the prevalence of large datasets in real-wor… (see more)ld applications, pooling layers are crucial components of GNNs. By reducing the size of input graphs, pooling enables faster training and potentially better generalisation. However, existing pooling operations often optimise for the learning task at the expense of discarding fundamental graph structures, thus reducing interpretability. This leads to unreliable performance across dataset types, downstream tasks and pooling ratios. Addressing these concerns, we propose novel graph pooling layers for structure-aware pooling via edge collapses. Our methods leverage diffusion geometry and iteratively reduce a graph's size while preserving both its metric structure and its structural diversity. We guide pooling using magnitude, an isometry-invariant diversity measure, which permits us to control the fidelity of the pooling process. Further, we use the spread of a metric space as a faster and more stable alternative ensuring computational efficiency. Empirical results demonstrate that our methods (i) achieve top performance compared to alternative pooling layers across a range of diverse graph classification tasks, (ii) preserve key spectral properties of the input graphs, and (iii) retain high accuracy across varying pooling ratios.
PointMAC: Meta-Learned Adaptation for Robust Test-Time Point Cloud Completion
Rui Ma
Ziqiang Wang
Xinxin Zuo
Point cloud completion is essential for robust 3D perception in safety-critical applications such as robotics and augmented reality. However… (see more), existing models perform static inference and rely heavily on inductive biases learned during training, limiting their ability to adapt to novel structural patterns and sensor-induced distortions at test time. To address this limitation, we propose PointMAC, a meta-learned framework for robust test-time adaptation in point cloud completion. It enables sample-specific refinement without requiring additional supervision. Our method optimizes the completion model under two self-supervised auxiliary objectives that simulate structural and sensor-level incompleteness. A meta-auxiliary learning strategy based on Model-Agnostic Meta-Learning (MAML) ensures that adaptation driven by auxiliary objectives is consistently aligned with the primary completion task. During inference, we adapt the shared encoder on-the-fly by optimizing auxiliary losses, with the decoder kept fixed. To further stabilize adaptation, we introduce Adaptive
Understanding Softmax Attention Layers: Exact Mean-Field Analysis on a Toy Problem
Elvis Dohmatob
Self-attention has emerged as a fundamental component driving the success of modern transformer architectures, which power large language mo… (see more)dels and various applications. However, a theoretical understanding of how such models actually work is still under active development. The recent work of (Marion et al., 2025) introduced the so-called "single-location regression" problem, which can provably be solved by a simplified self-attention layer but not by linear models, thereby demonstrating a striking functional separation. A rigorous analysis of self-attention with softmax for this problem is challenging due to the coupled nature of the model. In the present work, we use ideas from the classical random energy model in statistical physics to analyze softmax self-attention on the single-location problem. Our analysis yields exact analytic expressions for the population risk in terms of the overlaps between the learned model parameters and those of an oracle. Moreover, we derive a detailed description of the gradient descent dynamics for these overlaps and prove that, under broad conditions, the dynamics converge to the unique oracle attractor. Our work not only advances our understanding of self-attention but also provides key theoretical ideas that are likely to find use in further analyses of even more complex transformer architectures.