arXiv subjects

Adeel Razi

Publications and source records attributed to Adeel Razi.

At least 19 recordsLinked to original sources

arXiv2026

Hi-DREAM: Brain-Inspired Hierarchical Diffusion for fMRI-to-Image Reconstruction via ROI Encoder and VisuAl Mapping

Reconstructing natural images from fMRI requires bridging neural activity with both the structural and semantic representations used by modern generative models. Existing diffusion-based decoders often condition on a single global fMRI embedding, which limits their ability to exploit the hierarchical organization of the visual cortex and makes the contribution of different visual areas difficult to inspect. We propose Hi-DREAM, a brain-inspired hierarchical diffusion framework that structures fMRI conditioning according to early, middle, and late visual Regions of Interest (ROI) streams. A ROI adapter converts these streams into a multi-scale cortical pyramid, and a lightweight ROI-conditioned ControlNet injects the resulting anatomy-aware priors into matched U-Net depths during denoising. Experiments on the Natural Scenes Dataset (NSD) show that Hi-DREAM achieves state-of-the-art high-level semantic reconstruction while retaining strong low-level structure. Further ablation and attribution analyses show that the proposed hierarchy-aware conditioning is effective, and that different ROI streams provide complementary, inspectable contributions to reconstruction.

cs.CV↗

arXiv2026

Active Inference as the Test-Time Scaling Law for Physical AI Agents

In this paper, a novel test-time scaling law for physical artificial intelligence (AI) agents is introduced. This scaling law enables physical AI agents to reason with their world models to generalize in unforeseen scenarios at test time. The derived scaling law is grounded in the first principle of active inference, which equips agents with the general objective to survive in the real world, under which their specific task objectives are subsumed. Active inference achieves this by providing the reasoning to resolve prediction errors that arise when the agent encounters unforeseen situations outside its training distribution, enabling generalization in non-stationary environments. The proposed scaling law captures this by dynamically updating the agent's policy with this reasoning at test time. This policy update is modeled as a soft Bayesian inference process in which beliefs about the policy are updated using the reasoning that reduces expected prediction errors under allowable policies as a likelihood. The resulting posterior policy admits a biological interpretation, recovering the scaling mechanism that engages the brain's basal ganglia and prefrontal cortex at test time. To solve this analytically intractable problem, a variational inference solution minimizing free energy bounds is developed. This solution extends to enable learning beyond training by reinforcing new instances, resolved at test time, in both the policy and world model. Unlike existing scaling laws constrained by model size and training data, the derived solution scales with the continuous real-world experience of a physical AI agent. Simulation results on an autonomous driving task demonstrate that the proposed solution outperforms model-free Q-learning and model-based Bayesian reinforcement learning, achieving robust generalization to unforeseen scenarios while improving inference efficiency by over 36%.

cs.AI↗

arXiv2026

Hierarchical Bayesian inference for community detection and connectivity of functional brain networks

Most functional magnetic resonance imaging studies rely on estimates of hierarchically organized functional brain networks whose segregation and integration reflect the cognitive and behavioral changes in humans. However, most existing methods for estimating the community structure of networks from both individual and group-level analysis methods do not account for the variability between subjects. In this paper, we develop a new multilayer community detection method based on Bayesian latent block model (LBM). The method can robustly detect the community structure of weighted functional networks with an unknown number of communities at both individual and group levels and retain the variability of the individual networks. For validation, we propose a new community structure-based multivariate Gaussian generative model to simulate synthetic signal. Our simulation study shows that the community memberships estimated by hierarchical Bayesian inference are consistent with the predefined node labels in the generative model. The method is also tested via split-half reproducibility using working memory task fMRI data of 100 unrelated healthy subjects from the Human Connectome Project. Analyses using both synthetic and real data show that our proposed method is more accurate and reliable compared with the commonly used (multilayer) modularity models.

q-bio.NC↗

arXiv2026

Online Generalised Predictive Coding

This paper introduces an extension of generalised filtering for online applications. Generalised filtering refers to data assimilation schemes that jointly infer latent states, learn unknown model parameters, and estimate uncertainty in an integrated framework -- e.g., estimate state and observation noise -- at the same time (i.e., triple estimation). This framework appears across disciplines under different names, including variational Kalman-Bucy filtering in engineering, generalised predictive coding in neuroscience, and Dynamic Expectation Maximisation (DEM) in time-series analysis. Here, we specialise DEM for ``online'' data assimilation, through a separation of temporal scales. We describe the variational principles and procedures that allow one to assimilate data in a way that allows for a slow updating of parameters and precisions, which contextualise fast Bayesian belief updating about the dynamic hidden states. Using numerical studies, we demonstrate the validity of online DEM (ODEM) using a non-linear -- and potentially chaotic -- generative model, to show that the ODEM scheme can track the latent states of the generative process, even when its functional form differs fundamentally from the dynamics of the generative model. Framed from a neuro-mimetic predictive coding perspective, ODEM offers a biologically inspired solution to online inference, learning, and uncertainty estimation in dynamic environments.

stat.ML↗

arXiv2026

BrainSymphony: A parameter-efficient multimodal foundation model for brain dynamics with limited data

Foundation models are transforming neuroscience but are often prohibitively large, data-hungry, and difficult to deploy. Here, we introduce BrainSymphony, a lightweight and parameter-efficient foundation model with plug-and-play integration of fMRI time series and diffusion-derived structural connectivity, allowing unimodal or multimodal training and deployment without architectural changes while requiring substantially less data compared to the state-of-the-art. The model processes fMRI time series through parallel spatial and temporal transformer streams, distilled into compact embeddings by a Perceiver module, while a novel signed graph transformer encodes anatomical connectivity from diffusion MRI. These complementary representations are then combined through an adaptive fusion mechanism. Despite its compact design, BrainSymphony consistently outperforms larger models on benchmarks spanning prediction, classification, and unsupervised network discovery. Highlighting the model's generalizability and interpretability, attention maps reveal drug-induced context-dependent reorganization of cortical hierarchies in an independent psilocybin neuroimaging dataset. BrainSymphony delivers accessible, interpretable, and clinically meaningful results and demonstrates that architecturally informed, multimodal models can surpass much larger counterparts and advance applications of AI in neuroscience.

q-bio.QM↗

arXiv2026

A Quantifiable Information-Processing Hierarchy Provides a Necessary Condition for Detecting Agency

As intelligent systems are developed across diverse substrates - from machine learning models and neuromorphic hardware to in vitro neural cultures - understanding what gives a system agency has become increasingly important. Existing definitions, however, tend to rely on top-down descriptions that are difficult to quantify. We propose a bottom-up framework grounded in a system's information-processing order: the extent to which its transformation of input evolves over time. We identify three orders of information processing. Class I systems are reactive and memoryless, mapping inputs directly to outputs. Class II systems incorporate internal states that provide memory but follow fixed transformation rules. Class III systems are adaptive; their transformation rules themselves change as a function of prior activity. While not sufficient on their own, these dynamics represent necessary informational conditions for genuine agency. This hierarchy offers a measurable, substrate-independent way to identify the informational precursors of agency. We illustrate the framework with neurophysiological and computational examples, including thermostats and receptor-like memristors, and discuss its implications for the ethical and functional evaluation of systems that may exhibit agency.

q-bio.NC↗

arXiv2025

Brain-MGF: Multimodal Graph Fusion Network for EEG-fMRI Brain Connectivity Analysis Under Psilocybin

Psychedelics, such as psilocybin, reorganise large-scale brain connectivity, yet how these changes are reflected across electrophysiological (electroencephalogram, EEG) and haemodynamic (functional magnetic resonance imaging, fMRI) networks remains unclear. We present Brain-MGF, a multimodal graph fusion network for joint EEG-fMRI connectivity analysis. For each modality, we construct graphs with partial-correlation edges and Pearson-profile node features, and learn subject-level embeddings via graph convolution. An adaptive softmax gate then fuses modalities with sample-specific weights to capture context-dependent contributions. Using the world's largest single-site psilocybin dataset, PsiConnect, Brain-MGF distinguishes psilocybin from no-psilocybin conditions in meditation and rest. Fusion improves over unimodal and non-adaptive variants, achieving 74.0% accuracy and 76.5% F1 score on meditation, and 76.0% accuracy with 85.8% ROC-AUC on rest. UMAP visualisations reveal clearer class separation for fused embeddings. These results indicate that adaptive graph fusion effectively integrates complementary EEG-fMRI information, providing an interpretable framework for characterising psilocybin-induced alterations in large-scale neural organisation.

q-bio.NC↗

arXiv2025

Possible Principles for Aligned Structure Learning Agents

This paper offers a roadmap for the development of scalable aligned artificial intelligence (AI) from first principle descriptions of natural intelligence. In brief, a possible path toward scalable aligned AI rests upon enabling artificial agents to learn a good model of the world that includes a good model of our preferences. For this, the main objective is creating agents that learn to represent the world and other agents' world models; a problem that falls under structure learning (a.k.a. causal representation learning or model discovery). We expose the structure learning and alignment problems with this goal in mind, as well as principles to guide us forward, synthesizing various ideas across mathematics, statistics, and cognitive science. 1) We discuss the essential role of core knowledge, information geometry and model reduction in structure learning, and suggest core structural modules to learn a wide range of naturalistic worlds. 2) We outline a way toward aligned agents through structure learning and theory of mind. As an illustrative example, we mathematically sketch Asimov's Laws of Robotics, which prescribe agents to act cautiously to minimize the ill-being of other agents. We supplement this example by proposing refined approaches to alignment. These observations may guide the development of artificial intelligence in helping to scale existing -- or design new -- aligned structure learning systems.

cs.AI↗

arXiv2025

Simulating Biological Intelligence: Active Inference with Experiment-Informed Generative Model

With recent and rapid advancements in artificial intelligence (AI), understanding the foundation of purposeful behaviour in autonomous agents is crucial for developing safe and efficient systems. While artificial neural networks have dominated the path to AI, recent studies are exploring the potential of biologically based systems, such as networks of living biological neuronal networks. Along with promises of high power and data efficiency, these systems may also inform more explainable and biologically plausible models. In this work, we propose a framework rooted in active inference, a general theory of behaviour, to model decision-making in embodied agents. Using experiment-informed generative models, we simulate decision-making processes in a simulated game-play environment, mirroring experimental setups that use biological neurons. Our results demonstrate learning in these agents, providing insights into the role of memory-based learning and predictive planning in intelligent decision-making. This work contributes to the growing field of explainable AI by offering a biologically grounded and scalable approach to understanding purposeful behaviour in agents.

cs.AI↗

arXiv2025

Graph-Based Representation Learning of Neuronal Dynamics and Behavior

Understanding how neuronal networks reorganize in response to external stimuli and give rise to behavior is a central challenge in neuroscience and artificial intelligence. However, existing methods often fail to capture the evolving structure of neural connectivity in ways that capture its relationship to behavior, especially in dynamic, uncertain, or high-dimensional settings with sufficient resolution or interpretability. We introduce the Temporal Attention-enhanced Variational Graph Recurrent Neural Network (TAVRNN), a novel framework that models time-varying neuronal connectivity by integrating probabilistic graph learning with temporal attention mechanisms. TAVRNN learns latent dynamics at the single-unit level while maintaining interpretable population-level representations, to identify key connectivity patterns linked to behavior. TAVRNN generalizes across diverse neural systems and modalities, demonstrating state-of-the-art classification and clustering performance. We validate TAVRNN on three diverse datasets: (1) electrophysiological data from a freely behaving rat, (2) primate somatosensory cortex recordings during a reaching task, and (3) biological neurons in the DishBrain platform interacting with a virtual game environment. Our method outperforms state-of-the-art dynamic embedding techniques, revealing previously unreported relationships between adaptive behavior and the evolving topological organization of neural networks. These findings demonstrate that TAVRNN offers a powerful and generalizable approach for modeling neural dynamics across experimental and synthetic biological systems. Its architecture is modality-agnostic and scalable, making it applicable across a wide range of neural recording platforms and behavioral paradigms.

q-bio.NC↗

arXiv2025

A Principled Bayesian Framework for Training Binary and Spiking Neural Networks

We propose a Bayesian framework for training binary and spiking neural networks that achieves state-of-the-art performance without normalisation layers. Unlike commonly used surrogate gradient methods -- often heuristic and sensitive to hyperparameter choices -- our approach is grounded in a probabilistic model of noisy binary networks, enabling fully end-to-end gradient-based optimisation. We introduce importance-weighted straight-through (IW-ST) estimators, a unified class generalising straight-through and relaxation-based estimators. We characterise the bias-variance trade-off in this family and derive a bias-minimising objective implemented via an auxiliary loss. Building on this, we introduce Spiking Bayesian Neural Networks (SBNNs), a variational inference framework that uses posterior noise to train Binary and Spiking Neural Networks with IW-ST. This Bayesian approach minimises gradient bias, regularises parameters, and introduces dropout-like noise. By linking low-bias conditions, vanishing gradients, and the KL term, we enable training of deep residual networks without normalisation. Experiments on CIFAR-10, DVS Gesture, and SHD show our method matches or exceeds existing approaches without normalisation or hand-tuned gradients.

cs.LG↗

arXiv2025

SPM 25: open source neuroimaging analysis software

Statistical Parametric Mapping (SPM) is an integrated set of methods for testing hypotheses about the brain's structure and function, using data from imaging devices. These methods are implemented in an open source software package, SPM, which has been in continuous development for more than 30 years by an international community of developers. This paper reports the release of SPM 25.01, a major new version of the software that incorporates novel analysis methods, optimisations of existing methods, as well as improved practices for open science and software development.

q-bio.QM↗

arXiv2024

A Deep Probabilistic Spatiotemporal Framework for Dynamic Graph Representation Learning with Application to Brain Disorder Identification

Recent applications of pattern recognition techniques on brain connectome classification using functional connectivity (FC) are shifting towards acknowledging the non-Euclidean topology and dynamic aspects of brain connectivity across time. In this paper, a deep spatiotemporal variational Bayes (DSVB) framework is proposed to learn time-varying topological structures in dynamic FC networks for identifying autism spectrum disorder (ASD) in human participants. The framework incorporates a spatial-aware recurrent neural network with an attention-based message passing scheme to capture rich spatiotemporal patterns across dynamic FC networks. To overcome model overfitting on limited training datasets, an adversarial training strategy is introduced to learn graph embedding models that generalize well to unseen brain networks. Evaluation on the ABIDE resting-state functional magnetic resonance imaging dataset shows that our proposed framework substantially outperforms state-of-the-art methods in identifying patients with ASD. Dynamic FC analyses with DSVB-learned embeddings reveal apparent group differences between ASD and healthy controls in brain network connectivity patterns and switching dynamics of brain states. The code is available at https://github.com/Monash-NeuroAI/Deep-Spatiotemporal-Variational-Bayes.

cs.LG↗

arXiv2024

Evaluating the evolution and inter-individual variability of infant functional module development from 0 to 5 years old

The segregation and integration of infant brain networks undergo tremendous changes due to the rapid development of brain function and organization. Traditional methods for estimating brain modularity usually rely on group-averaged functional connectivity (FC), often overlooking individual variability. To address this, we introduce a novel approach utilizing Bayesian modeling to analyze the dynamic development of functional modules in infants over time. This method retains inter-individual variability and, in comparison to conventional group averaging techniques, more effectively detects modules, taking into account the stationarity of module evolution. Furthermore, we explore gender differences in module development under awake and sleep conditions by assessing modular similarities. Our results show that female infants demonstrate more distinct modular structures between these two conditions, possibly implying relative quiet and restful sleep compared with male infants.

q-bio.NC↗

arXiv2024

Biological Neurons Compete with Deep Reinforcement Learning in Sample Efficiency in a Simulated Gameworld

How do biological systems and machine learning algorithms compare in the number of samples required to show significant improvements in completing a task? We compared the learning efficiency of in vitro biological neural networks to the state-of-the-art deep reinforcement learning (RL) algorithms in a simplified simulation of the game `Pong'. Using DishBrain, a system that embodies in vitro neural networks with in silico computation using a high-density multi-electrode array, we contrasted the learning rate and the performance of these biological systems against time-matched learning from three state-of-the-art deep RL algorithms (i.e., DQN, A2C, and PPO) in the same game environment. This allowed a meaningful comparison between biological neural systems and deep RL. We find that when samples are limited to a real-world time course, even these very simple biological cultures outperformed deep RL algorithms across various game performance characteristics, implying a higher sample efficiency. Ultimately, even when tested across multiple types of information input to assess the impact of higher dimensional data input, biological neurons showcased faster learning than all deep reinforcement learning agents.

q-bio.NC↗

arXiv2024

Unsupervised Representation Learning for 3D MRI Super Resolution with Degradation Adaptation

High-resolution (HR) magnetic resonance imaging is critical in aiding doctors in their diagnoses and image-guided treatments. However, acquiring HR images can be time-consuming and costly. Consequently, deep learning-based super-resolution reconstruction (SRR) has emerged as a promising solution for generating super-resolution (SR) images from low-resolution (LR) images. Unfortunately, training such neural networks requires aligned authentic HR and LR image pairs, which are challenging to obtain due to patient movements during and between image acquisitions. While rigid movements of hard tissues can be corrected with image registration, aligning deformed soft tissues is complex, making it impractical to train neural networks with authentic HR and LR image pairs. Previous studies have focused on SRR using authentic HR images and down-sampled synthetic LR images. However, the difference in degradation representations between synthetic and authentic LR images suppresses the quality of SR images reconstructed from authentic LR images. To address this issue, we propose a novel Unsupervised Degradation Adaptation Network (UDEAN). Our network consists of a degradation learning network and an SRR network. The degradation learning network downsamples the HR images using the degradation representation learned from the misaligned or unpaired LR images. The SRR network then learns the mapping from the down-sampled HR images to the original ones. Experimental results show that our method outperforms state-of-the-art networks and is a promising solution to the challenges in clinical settings.

eess.IV↗

arXiv2024

On Predictive planning and counterfactual learning in active inference

Given the rapid advancement of artificial intelligence, understanding the foundations of intelligent behaviour is increasingly important. Active inference, regarded as a general theory of behaviour, offers a principled approach to probing the basis of sophistication in planning and decision-making. In this paper, we examine two decision-making schemes in active inference based on 'planning' and 'learning from experience'. Furthermore, we also introduce a mixed model that navigates the data-complexity trade-off between these strategies, leveraging the strengths of both to facilitate balanced decision-making. We evaluate our proposed model in a challenging grid-world scenario that requires adaptability from the agent. Additionally, our model provides the opportunity to analyze the evolution of various parameters, offering valuable insights and contributing to an explainable framework for intelligent decision-making.

cs.AI↗

arXiv2023

Active Inference and Intentional Behaviour

Recent advances in theoretical biology suggest that basal cognition and sentient behaviour are emergent properties of in vitro cell cultures and neuronal networks, respectively. Such neuronal networks spontaneously learn structured behaviours in the absence of reward or reinforcement. In this paper, we characterise this kind of self-organisation through the lens of the free energy principle, i.e., as self-evidencing. We do this by first discussing the definitions of reactive and sentient behaviour in the setting of active inference, which describes the behaviour of agents that model the consequences of their actions. We then introduce a formal account of intentional behaviour, that describes agents as driven by a preferred endpoint or goal in latent state-spaces. We then investigate these forms of (reactive, sentient, and intentional) behaviour using simulations. First, we simulate the aforementioned in vitro experiments, in which neuronal cultures spontaneously learn to play Pong, by implementing nested, free energy minimising processes. The simulations are then used to deconstruct the ensuing predictive behaviour, leading to the distinction between merely reactive, sentient, and intentional behaviour, with the latter formalised in terms of inductive planning. This distinction is further studied using simple machine learning benchmarks (navigation in a grid world and the Tower of Hanoi problem), that show how quickly and efficiently adaptive behaviour emerges under an inductive form of active inference.

q-bio.NC↗