arXiv subjects

Moein Khajehnejad

Publications and source records attributed to Moein Khajehnejad.

13 recordsLinked to original sources

arXiv2026

Many Brains, One Geometry: A Shared Visual-Semantic Space for Cross-Dataset fMRI Decoding

Visual decoding from fMRI is typically siloed by participant and experiment, obscuring whether heterogeneous neural measurements can be organized within a common computational geometry. Here we introduce BRAID-fMRI (Brain Representation Alignment across Individuals and Datasets), a shared CLIP-supervised decoding framework. BRAID-fMRI uses a single ROI-wise Transformer with optional participant conditioning across eight visual-fMRI datasets comprising 93 dataset-specific participant entries, 430,007 single-trial responses and 162,839 unique stimuli. Regional brain activity is aligned with 512-dimensional CLIP ViT-B/32 representations using a multi-positive contrastive objective that treats repeated stimuli across participants and datasets as positives. BRAID-fMRI supports retrieval across seven evaluation datasets. On eight matched participant entries, it achieves 35.0 +/- 11.1% Top-10 accuracy, exceeding the observed mean accuracy of the two evaluated baselines - the MindEye-style pooled-CLIP decoder (27.1 +/- 5.1%) and ridge regression (21.1 +/- 9.1%) - and attaining the highest observed accuracy for seven of eight entries. In separately trained participant-agnostic models, expanding the source pool increased target-dataset holdout accuracy by up to 92.1% relative to the initial source-training condition. The learned space preserves graded semantic structure, while ablations and saliency highlight ventral and early visual cortex and category-specific motion and attentional systems. These results support scalable cross-dataset decoding into a common CLIP-aligned space, with model sensitivity concentrated in ventral and early visual inputs.

cs.HC↗

arXiv2026

A memory-based active inference model of DishBrain-like adaptive behaviour

Recent and rapid advances in artificial intelligence (AI) make it increasingly important to understand the foundations of adaptive behaviour in autonomous agents, especially for building safe and efficient systems. While artificial neural networks have dominated the development of AI, recent work has begun to explore living biological neuronal networks as an alternative substrate for computation. These systems promise remarkable data and sample efficiency and rich dynamics, and may also inspire explainable and biologically plausible models. Here, we develop an experiment-informed active inference framework to model decision-making in closed-loop agents that mirror experimental setups using biological neurons. Using a generative model whose dimensions are matched to an experiment protocol, we systematically compare three decision-making schemes within this common generative model. Under matched episode counts (i.e. total data available for learning) to the in-vitro experiment, our simulations show that agents with short memory horizons reach a level of performance close to that of mouse and human cortical cultures (DishBrain platform), whereas longer memory horizons depart from it substantially. Increasing the planning horizon, by contrast, confers no comparable benefit. Because all model parameters are explicit, we can also track the quantities in our generative model that accompany this improvement, such as the risk term and the entropy of the transition and state-action mappings. Together, these results illustrate how active inference offers a formal language for comparing decision-making schemes in similar closed-loop control environments.

cs.AI↗

arXiv2026

From Neurons to Conversation: Speech Brain-Computer Interfaces

Speech brain-computer interfaces (BCIs) aim to restore communication by transforming neural activity related to speech, language, or communicative intent into external outputs such as text, synthesized voice, or avatar control. Recent advances in intracortical and electrocorticographic recording, deep sequence models, and language-model-assisted decoding have enabled rapid progress, including high-performance attempted-speech decoding and increasingly naturalistic speech synthesis. Yet these achievements also reveal that speech BCIs are not simply neural-to-text decoders. They are adaptive clinical systems in which neural representations, recording hardware, decoding architectures, language priors, feedback, and user learning interact over time. Here, we synthesize speech BCI research from a system-level perspective. We first examine the neural substrates of speech and language, emphasizing their hierarchical, distributed, temporally structured, and non-stationary organization. We then examine recording and decoding choices, closed-loop adaptation, evaluation, clinical translation, and ethics. Across these domains, we highlight recurring trade-offs between signal resolution and invasiveness, low-level motor and high-level semantic targets, decoder accuracy and user agency, and language-model fluency and faithful neural evidence. We argue the next generation of speech BCIs should be evaluated not only by offline accuracy, but also by robustness across sessions, calibration burden, latency, uncertainty, usability, and safeguards against unintended decoding. By reframing speech BCIs as adaptive, user-centred systems, we outline the interdisciplinary priorities spanning speech neuroscience, neural engineering, machine learning, clinical practice, and neuroethics needed to move from proof-of-concept decoding toward reliable, expressive, and controllable communication neuroprostheses.

cs.HC↗

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

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↗

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

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↗

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↗

arXiv2022

CrossWalk: Fairness-enhanced Node Representation Learning

The potential for machine learning systems to amplify social inequities and unfairness is receiving increasing popular and academic attention. Much recent work has focused on developing algorithmic tools to assess and mitigate such unfairness. However, there is little work on enhancing fairness in graph algorithms. Here, we develop a simple, effective and general method, CrossWalk, that enhances fairness of various graph algorithms, including influence maximization, link prediction and node classification, applied to node embeddings. CrossWalk is applicable to any random walk based node representation learning algorithm, such as DeepWalk and Node2Vec. The key idea is to bias random walks to cross group boundaries, by upweighting edges which (1) are closer to the groups' peripheries or (2) connect different groups in the network. CrossWalk pulls nodes that are near groups' peripheries towards their neighbors from other groups in the embedding space, while preserving the necessary structural properties of the graph. Extensive experiments show the effectiveness of our algorithm to enhance fairness in various graph algorithms, including influence maximization, link prediction and node classification in synthetic and real networks, with only a very small decrease in performance.

cs.LG↗

arXiv2020

Optimal Decision Making Under Strategic Behavior

We are witnessing an increasing use of data-driven predictive models to inform decisions. As decisions have implications for individuals and society, there is increasing pressure on decision makers to be transparent about their decision policies. At the same time, individuals may use knowledge, gained by transparency, to invest effort strategically in order to maximize their chances of receiving a beneficial decision. Our goal is to find decision policies that are optimal in terms of utility in such a strategic setting. To this end, we first characterize how strategic investment of effort by individuals leads to a change in the feature distribution. Using this characterization, we first show that, in general, we cannot expect to find optimal decision policies in polynomial time and there are cases in which deterministic policies are suboptimal. Then, we demonstrate that, if the cost individuals pay to change their features satisfies a natural monotonicity assumption, we can narrow down the search for the optimal policy to a particular family of decision policies with a set of desirable properties, which allow for a highly effective polynomial time heuristic search algorithm using dynamic programming. Finally, under no assumptions on the cost individuals pay to change their features, we develop an iterative search algorithm that is guaranteed to find locally optimal decision policies also in polynomial time. Experiments on synthetic and real credit card data illustrate our theoretical findings and show that the decision policies found by our algorithms achieve higher utility than those that do not account for strategic behavior.

cs.LG↗

arXiv2020

Adversarial Graph Embeddings for Fair Influence Maximization over Social Networks

Influence maximization is a widely studied topic in network science, where the aim is to reach the maximum possible number of nodes, while only targeting a small initial set of individuals. It has critical applications in many fields, including viral marketing, information propagation, news dissemination, and vaccinations. However, the objective does not usually take into account whether the final set of influenced nodes is fair with respect to sensitive attributes, such as race or gender. Here we address fair influence maximization, aiming to reach minorities more equitably. We introduce Adversarial Graph Embeddings: we co-train an auto-encoder for graph embedding and a discriminator to discern sensitive attributes. This leads to embeddings which are similarly distributed across sensitive attributes. We then find a good initial set by clustering the embeddings. We believe we are the first to use embeddings for the task of fair influence maximization. While there are typically trade-offs between fairness and influence maximization objectives, our experiments on synthetic and real-world datasets show that our approach dramatically reduces disparity while remaining competitive with state-of-the-art influence maximization methods.

cs.LG↗

arXiv2016

Navigation by anomalous random walks on complex networks

Anomalous random walks having long-range jumps are a critical branch of dynamical processes on networks, which can model a number of search and transport processes. However, traditional measurements based on mean first passage time are not useful as they fail to characterize the cost associated with each jump. Here we introduce a new concept of mean first traverse distance (MFTD) to characterize anomalous random walks that represents the expected traverse distance taken by walkers searching from source node to target node, and we provide a procedure for calculating the MFTD between two nodes. We use Levy walks on networks as an example, and demonstrate that the proposed approach can unravel the interplay between diffusion dynamics of Levy walks and the underlying network structure. Interestingly, applying our framework to the famous PageRank search, we can explain why its damping factor empirically chosen to be around 0.85. The framework for analyzing anomalous random walks on complex networks offers a new useful paradigm to understand the dynamics of anomalous diffusion processes, and provides a unified scheme to characterize search and transport processes on networks.

physics.soc-ph↗