Brain

Large brains are metabolically costly, and associations with changing environments do not imply they evolved there, as the Cognitive Buffer Hypothesis (CBH) would suggest. They may instead evolve in stable conditions and later facilitate colonization of changing environments. Using neuro-evolution in an artificial seasonal foraging task, we compared agents evolving exclusively in changing environments to agents first evolved in static environments before transitioning. Results show that larger neural networks in dynamic environments arise mainly from prior static evolution, achieving superior performance under unpredictable changes. Our results challenge strict CBH predictions, provide agent-based (computational) support for a colonization-based account and highlight the role of evolutionary history in brain size evolution.

The larval stage of Drosophila melanogaster is a compact model system for neuroscience whose genetic toolkit allows fluorescent markers to be expressed in defined neural populations, and comparing the resulting expression patterns across animals requires every brain to be registered into a shared anatomical reference space. Existing pipelines for this task are predominantly based on classical registration methods, which perform a new optimization for each volume, often require per-case parameter tuning, and can take minutes per brain, limiting their use as a routine preprocessing step. We present a trained deep registration pipeline that deformably aligns a larval brain to a reference template in a single forward pass at high spatial resolution, on volumes that hold several times more voxels than those learned 3D registration is normally reported on, together with the preprocessing and anatomy-anchored evaluation pipeline required to apply it. Against eleven classical and seven further learned baselines on a held-out collection acquired with different acquisition and quality strata, the proposed pipeline is the most accurate, improving on the strongest classical baseline by 23 percentage points of anatomical landmark-local mutual information. It registers a volume one to two orders of magnitude faster than the classical deformable pipelines, and it retains more of its accuracy than any other method as acquisition quality degrades. The network, its trained weights and the full pipeline are released as the open-source deep larval brain registration framework: https://github.com/agentdr1/deep-larval-brain-reg

Multimodal large language models predict brain activity, but brain alignment has been a measurement, not a design tool. We propose the Platonic brain bridge hypothesis: omni models, multimodal large language models that process video, audio and text jointly, converge on brain-like representations usable in both directions. From model to brain, brain-likeness of seven omni models is stable across participants, rises with every input channel in three bases, and our encoders lead the Algonauts 2025 out-of-distribution leaderboard. From brain to model, Brain-MoE fixes the expert partition of a frozen base to the seven networks of human cortex, trains experts on network-labelled Brain-AVQA questions, raises held-out accuracy in all 15 model-benchmark pairs by 6.42 percentage points on average and exceeds capacity-matched random experts in 14. Brain-Scope localizes the correspondence to sparse features whose removal weakens brain prediction. Human brain organization is therefore a usable architectural prior for multimodal large language models.

The ambition of the 2025 PNPL competition (Landau et al., 2025) was to launch a multi-year curriculum for non-invasive speech decoding. Designed to progress from foundational tasks toward the linguistic complexity required for a practical brain-computer interface (BCI), it set the stage with speech detection and phoneme classification tasks. Winning submissions reached F1-macro scores of 95.6% and 73.6% on the respective tasks (Elvers et al., 2026), highly significant advances. This success was built on the LibriBrain dataset (Özdogan et al., 2025), the largest within-subject MEG dataset recorded at the time with ${\sim}50$ hours of data for one subject. However, while within-subject scale drives strong decoding performance, a practical BCI must generalise to new users from minutes of data, not hours. The 2026 PNPL competition responds to this challenge with LibriBrain100 (Mantegna et al., 2026), an extended LibriBrain dataset with 32 additional subjects (${\sim}40$ minutes each) plus even more within-subject data (${\sim}80$ hours). Advancing the curriculum of tasks to focus on word classification, two complementary tracks are presented in this competition: the Deep track targets within-subject word classification at scale, aiming at the best possible performance; the Broad track targets cross-subject generalisation, progressively reducing the amount of subject-specific fine-tuning data from ${\sim}40$ to ${\sim}20$ to ${\sim}10$ minutes, a duration that falls within a clinically feasible range and brings us a step closer to a non-invasive BCI capable of restoring communication to people living with profound paralysis.

Neuroradiologists rarely read a brain MRI in isolation, yet automated brain-MRI report generation has been built almost entirely for single studies. Temporal analysis has been explored on chest radiography and chest CT, but to our knowledge, longitudinal reporting for brain MRI, where interval change is often subtle and spatially distributed, remains unaddressed. We present BrainDiff, the first longitudinal vision-language system for brain MRI. BrainDiff outperforms both frontier general-purpose and single-study neuroimaging models on the same patient pairs. Moreover, BrainDiff retains 91% of internal RadGraph-XL entity+relation F1 (rg_er) on an external, cross-hospital cohort. Beyond the system, we contribute three analyses. First, we identify two independent grounding levers: a counterfactual objective with prior-report dropout, which increases measured image reliance by ~47%, and a staged curriculum. Together, these interventions raise image reliance 2.5-fold from the baseline. Second, we provide a factorial over prior-report availability and image identity, isolating a visual contribution of +0.0387 rg_er, which grows when the prior report is withheld. Third, a cheap change-decodability test for candidate backbones shows that interval change is decodable far more weakly than single-study pathology (0.60 vs. 0.77 AUROC). Code is publicly available at https://github.com/jhuldr/BrainDiff.

Autonomous driving requires planning under both semantic constraints and predictive dynamics. Existing end-to-end driving approaches, however, typically emphasize only one side of this requirement: Vision-Language-Action (VLA) models exploit VLM priors for semantic reasoning, while World Action Models (WAMs) provide future-aware prediction through generative world modeling. This naturally motivates a unified planner that can leverage both semantic priors and predictive dynamics. However, we find that a naive combination through joint token-level attention suffers from an attention-allocation mismatch, where semantic shortcuts dominate the shared attention space and suppress predictive dynamics. Inspired by neuroscience evidence that complex behavior arises from coordination among functionally specialized systems, we propose BrainWAM, a structured action-space coordination framework that converts semantic reasoning and predictive world modeling into two specialized action-oriented pathways, and aligns them at the level of compact action representations. We further introduce an asynchronous rectified-flow inference strategy with decoupled video and action denoising, which shortens inference latency while preserving planning-relevant predictive context. BrainWAM reaches state-of-the-art performance on both NAVSIM v1 (89.5 PDMS) and NAVSIM v2 (89.6 EPDMS), consistently outperforming VLA-only or WAM-only methods, highlighting BrainWAM as a practical and promising direction for autonomous driving systems.

Brain magnetic resonance imaging (MRI) is central to neuroscience and clinical assessment, but models are commonly developed for individual diseases, populations or imaging protocols. Foundation models promise more general representations, yet they are usually pretrained once and can lose earlier capabilities when updated with new data. Here we show that Alcmaeon, a three-dimensional brain MRI foundation model pretrained without manual labels on more than 425,000 volumes and derived imaging maps, can be expanded sequentially across clinical domains. Alcmaeon combines volumetric encoding and latent diffusion generation with Graph-Blueprint Pruning (GBP), which protects network modules important to earlier domains while leaving the remaining capacity trainable. Across expansion from healthy ageing and neurodegeneration to developmental, psychiatric and tumour imaging, GBP showed less forgetting than sequential adaptation and elastic weight consolidation across voxel-level reconstruction measures, with its largest advantage after adaptation to tumour imaging. The blueprints provided an inspectable record of how model capacity was protected and reused. Representations from different model levels supported image synthesis, disease classification, survival modelling and postoperative prediction, although no single representation was optimal for every task. These findings provide a route towards brain MRI foundation models that can grow with emerging data while retaining earlier capabilities.

Reliable physical reasoning from video requires understanding how objects move, interact, and respond to interventions. Existing vision-language models (VLMs) often struggle to interpret these dynamics and reason reliably about future and counterfactual outcomes. We introduce PhysMind, a training-free agentic framework that constructs one reusable, question-agnostic executable world per video. PhysMind recovers a temporally consistent dynamic scene through object segmentation, mesh reconstruction, and 6D pose tracking, then fits analytic continuous-time dynamics and latent physical parameters without unrolling a time-stepped simulator. Given a question, it inspects, continues, or edits the world and answers from the resulting trajectories and interactions. Relative to direct chain-of-thought (CoT) reasoning with the same VLM, PhysMind improves accuracy by 38.23 points on CLEVRER and 8.08 points on Physion++. On counterfactual questions, it exceeds the strongest evaluated VLM baseline, GPT-5.5, by 19.25 points.

Collaborative music agents need internal representations rich enough to support both understanding and generation, yet flexible enough for a workflow where the human retains agency. We present a hierarchical self-supervised ``world model'' for symbolic music: a 2.55M-parameter Swin V2 encoder trained on MIDI piano-roll images with JEPA-style objectives (pitch- and time-shift equivariance, masked embedding prediction, and a distributional regularizer), using no labels and no music-theory vocabulary. Probing the frozen embeddings shows that the level at which a musical property becomes decodable tracks its musical time scale: phrase boundaries are read off the coarsest levels, note density and harmonic detail off the finest. Temporal and phrase structure emerge from the self-supervised objectives alone, while harmonic content must be asked for; a small chord-supervision head raises joint chord recovery from .18 to .54, and key detection, which is never supervised, from .16 to .70. Following the Representation AutoEncoder paradigm, a conditional flow-matching model stands in for a trained decoder, flowing in pixel space from PCA-reduced conditioning: it reproduces a target window at pixel F1 $0.996$, and the same per-level conditioning dropout that controls how far variations stray also enables graphical prompting for masked inpainting with no inpainting-specific sampler. The pipeline runs on CPU producing a suggestion in $2.8$ s, or $0.6$ s on Apple MPS, which we demonstrate in a live interactive demo. In concert with an LLM-based brain, these capabilities supply the core of a collaborative music creation agent in service of, rather than in place of, human agency.

Predictive coding offers a powerful framework for cortical computation, yet scalable implementations that respect both Bayesian exactness and neurobiological constraints remain scarce. We bridge this gap by formally connecting predictive coding to Recursive Gaussian Processes (RGPs). RGPs employ a single Gaussian process $g(t, \cdot)$ indexed by layer index and input value, preventing the representational collapse of standard deep Gaussian processes while allowing learnable cross-layer dependence via $r_{1g}$. We demonstrate that RGPs intrinsically implement hierarchical Bayesian inference, uncertainty propagation, and precision-weighted prediction error. Critically, we map RGP components---the shared GP, spike-and-slab variable selection, and MCMC dynamics---onto the canonical cortical microcircuit, providing a neurobiological substrate for these computations. Drawing on the free energy principle, we show that RGP inference minimizes variational free energy, formally linking Bayesian mechanics to neuronal dynamics. Our synthesis positions RGPs as both a principled computational tool and a candidate model for the brain's predictive machinery, generating testable predictions for laminar-specific dynamics and spectral asymmetries between feedforward and feedback processing.

Modern neuroscience relies on integrating multi-scale, multimodal datasets to uncover the neural principles underlying intelligence. However, analytical challenges posed by highly heterogeneous data and fragmented workflows increasingly constrain discoveries. Here we introduce SeekBrain, an autonomous multi-agent framework designed to accelerate neuroscience discovery through domain-grounded hierarchical planning and cross-modal data analysis. SeekBrain dynamically constructs a repertoire of analysis recipes extracted from code-paper pairs. By coupling this codified expertise with agentic planning and execution engines, the framework scalably generates hypotheses and analytical pipelines on demand. Systematic evaluation on the expert-annotated BrainArena benchmark demonstrates that SeekBrain substantially outperforms state-of-the-art agent baselines across various analysis tasks. Crucially, when deployed in real-world research, SeekBrain integrated behavioral, neural, and anatomical data to reveal structured, distributed neural representations of larval zebrafish behavior and a shared axis of regional decoding strength across the brain in a mouse decision-making task. These results establish SeekBrain as a scalable and practical tool for accelerating data-driven discoveries in neuroscience.

Medical foundation models (FMs) are increasingly used for brain MRI analysis. However, their evaluation remains dominated by high-resource datasets, leaving generalization to African cohorts underexplored. We assess whether FMs generalize equally to African and non-African brain MRI data across two tasks: dementia classification using a Nigerian dataset and brain tumor segmentation using BraTS-Africa. We evaluate two generalist FMs (BrainIAC, 3DINO) and two segmentation-specific FMs (MedSAM2, Medical-SAM2) against a from-scratch baseline. For classification, FMs provide limited gains (highest ROC-AUC of 0.86 with BrainIAC), whereas for segmentation they consistently improve performance, reaching up to 0.86 Dice with MedSAM2. Performance differences between African and non-African cohorts are inconsistent and appear more related to dataset size than data origin. These results suggest that FMs do not exhibit an inherent bias against African cohorts, and highlight the limited availability and diversity of African neuroimaging datasets as the main barrier to robust evaluation and deployment.

Predicting future structural MRI of a brain is challenging because longitudinal changes are often subtle and confined to specific anatomical regions, while most subject-specific brain structure remains stable over time. An effective model should therefore preserve global brain structural consistency while remaining sensitive to fine-grained disease progression. Existing latent-space-based methods improve computational efficiency, but suffer from information loss during their compression-reconstruction procedure. In contrast, direct voxel-space methods avoid latent reconstruction but commonly use a unified prediction pathway to model brain structure and progression-related changes. Subtle local changes may therefore be overshadowed by the dominant stable brain structure. To address these challenges, we propose ProgFormer, a hierarchical voxel-space Diffusion Transformer for longitudinal brain MRI prediction. ProgFormer uses a coarse pathway to perform the primary volumetric prediction from 3D patch tokens. This pathway models overall brain structure and longitudinal context. The fine pathway then uses the coarse representations as spatio-temporal grounding for voxel-level refinement within individual patches. The two pathways jointly estimate a velocity field directly in voxel space through conditional flow matching, enabling end-to-end prediction without a separately learned image autoencoder. The predicted future scan is then generated from Gaussian noise by integrating the estimated velocity field over a sequence of Euler steps. Extensive experimental results on three widely used benchmarks, ADNI, AIBL, and OASIS, under both pairwise and trajectory settings demonstrate favourable performance compared against several state-of-the-art methods.

Brains and large language models (LLMs) are fundamentally different memory systems, but they can be compared through shared functional questions: where memory-related information is represented, how partial cues recover broader associations, how new information is written or updated, and how memory-related states can be perturbed. In biological systems, these questions span synapses, neuronal ensembles, hippocampal-cortical interactions, and plasticity; in LLMs, they span weights, activations, context windows, retrieval systems, and external stores. The comparison is therefore functional and experimental rather than anatomical. Human studies reveal sparse concept responses, temporal binding, rapid association formation, episode-specific coding, and recall-related reactivation, but selective intervention remains limited. Rodent studies provide more selective causal access to learning-related ensembles, whereas human and macaque interventions usually affect broader circuits. LLMs lack lived episodic memory, yet they permit unusually direct and repeatable manipulation of internal states and stored information. We argue that this asymmetry creates a new opportunity. LLMs are not ahead in memory itself, but in experimental access. Their tools may help turn broad questions about retrieval, updating, persistence, reversibility, and unintended effects into sharper biological hypotheses. The productive bridge is to transfer experimental logic, not anatomical parts.

Large language models (LLMs) have demonstrated remarkable capabilities in language understanding, reasoning, and world knowledge. As embodied agents become increasingly capable, there is a growing demand for compact models that can serve as an on-device brain, preserving the broad general intelligence of LLMs while enabling effective high-level interaction with embodied environments. Existing approaches, however, often prioritize either general-purpose intelligence or specialized embodied capabilities, making it challenging to satisfy both requirements within a single model. We present \textbf{Athena-Brain-8B}, an 8B LLM designed to serve as an on-device brain for embodied intelligence for embodied intelligence. Through a multi-stage post-training pipeline consisting of General Supervised Fine-Tuning, General Reinforcement Learning, Embodied Expert training, and Model Merge, Athena-Brain-8B maintains strong general capabilities while acquiring strong high-level embodied interaction capabilities and generating concise responses for efficient embodied interaction. Experimental results demonstrate the effectiveness of Athena across both general and embodied evaluations. Compared with the corresponding Qwen3-8B thinking model, Athena-Brain-8B achieves comparable performance on general language and reasoning benchmarks while generating substantially shorter responses. On in-domain embodied benchmarks, Athena-Brain-8B consistently outperforms models of similar scale and surpasses several substantially larger frontier models evaluated zero-shot, demonstrating that compact language models can effectively integrate strong general intelligence with embodied capabilities.

A walking fly steers toward a goal direction, held as a bump of activity across the FC2 neurons of the fan-shaped body. These neurons also inhibit one another over distance, more strongly the farther apart they are, a feedback proposed to keep the fly on a single goal. We asked, from the connectome, what circuit produces this inhibition, and whether it lets FC2 actively choose one goal among competitors (a winner-take-all) or simply keeps a goal set elsewhere as one clean bump. Tracing the wiring in a single FlyWire brain, we find the inhibition is almost entirely global: four FB5A cells inhibit every FC2 neuron roughly equally, with a smaller, distance-dependent contribution from hDelta interneurons and a negligible direct component. A ring-attractor winner-take-all (the kind the compass uses) requires local recurrent excitation that the FC2 wiring lacks, so this geometry cannot build one; and across a range of dynamical models, including a spiking network, no version of the circuit locks onto a winner at the connectome-scaled reference coupling. FC2 therefore normalizes an externally set goal rather than selecting it, with FB5A likely acting as the global normalizer, much as the APL neuron does in the mushroom body. We are explicit about two open points: a different mechanism, mutual inhibition between two competing goals (which hDelta supplies), could in principle select at very strong coupling, and we bound rather than exclude it; and FB5A's inhibitory identity is a low-confidence prediction of the connectome's transmitter classifier, not yet measured, and likely not GABAergic. We then ask where the goal is actually set: the connectome nominates an upstream hDelta network and rules out the leading proposed alternative, whose neurons supply under 0.2% of FC2's input. Finally, we propose a direct experiment, silencing FB5A while imaging FC2, that would test the account.

Validating Explainable Artificial Intelligence (XAI) methods in medical imaging requires ground-truth data with known locations of informative features. However, current approaches rely on expert annotations, which are prone to labeling errors, or on hand-crafted artificial perturbations superimposed onto healthy images to mimic lesions or malignant features, which lack clinical realism. We present Local Label-Informed Feature Transfer (LLIFT), a framework for generating semi-synthetic brain magnetic resonance images with realistic lesions placed in user-controlled regions, which does not require pixel-level lesion annotations during training. We implement LLIFT with two generative paradigms: LLIFT-GAN, a custom GAN that learns pathological features from binary class labels alone, and LLIFT-DM, a diffusion-based inpainting pipeline conditioned on bounding-box masks via ControlNet. Both approaches are evaluated on brain magnetic resonance imaging data derived from the Human Connectome Project. In evaluations, both achieve Fréchet Inception Distance scores, with respect to the real pathological distribution, that are comparable to the inter-class reference between healthy and pathological images in the given dataset. Furthermore, qualitative inspection confirms the realism of lesion structures. The resulting benchmark datasets provide spatially controlled ground truth data for evaluating XAI methods in medical imaging.

Foundation models pretrained using self-supervised learning have transformed computer vision by learning transferable representations from large-scale unlabeled data. However, existing foundation models for neuroimaging remain limited by task-specific training, slice-based learning strategies, or relatively small pretraining datasets, restricting their generalizability across diverse brain MRI applications. In this work, we present BrainNext, a general-purpose self-supervised foundation model for volumetric brain MRI analysis. BrainNext combines masked autoencoder (MAE) pretraining with a native three-dimensional Bi-Directional xLSTM-UNet architecture to learn rich anatomical representations from 60,551 unlabeled brain MRI examinations spanning multiple MRI modalities. The pretrained model is subsequently adapted to downstream tasks through lightweight task-specific fine-tuning. We evaluate BrainNext on the Foundation Models for Medical Imaging (FOMO) 2025 Method Track, encompassing classification, segmentation, and brain-age estimation, where it achieved second place overall and ranked first in the meningioma segmentation task on the official FOMO 2025 challenge leaderboard, demonstrating strong transferability across heterogeneous neuroimaging tasks. These results highlight the potential of large-scale self-supervised pretraining to learn robust and transferable volumetric representations, establishing BrainNext as a scalable foundation model for diverse brain MRI applications.

This paper reports a convergence neither program was looking for. Marcus's The Algebraic Mind named three things any architecture needs -- operations over variables, recursive structure, and individuals distinct from kinds -- showed multilayer perceptrons have none, and left a register-and-treelet implementation as conjecture. Thagard's Brain-Mind ran it from the other end, making binding the mechanism from which the whole of mind is assembled, and circular convolution load-bearing. Marcus leaves his register algebra open; Thagard's is lossy, degrading under the very recursion his own account demands. VaCoAl is a hyperdimensional computing architecture built end-to-end on XOR-and-shift over GF(2) via primitive-polynomial LFSRs; PyVaCoAl is its extended software realization (all results here); the silicon substrate exists as CASRAM. Bind(R,F) = R XOR Shift(F) is exactly reversible and non-commutative: it supplies all three pillars at fixed dimension and removes convolution's depth degradation. Capability: exact reversible binding at O(N) yields compositional generalization with post-hoc auditability, which no lossy or learned substrate offers. Necessity: two independent architecture programs and the dentate gyrus-CA3 circuit require the same algebra -- convergence, not biomimicry. New here: discrimination and failure-tolerance are one. Repair every collision (RR = 1) and the system is bit-identical to a hash dictionary: candidates become indistinguishable and the confidence path-integral collapses; a memory that never fails keeps no record of which routes were hard. Position: we do not surpass large language models but supply the auditable, multi-hop relational reasoning embeddings lack. No consciousness is implemented and no cognitive experiment reported; bit-exactness holds in silicon, approximately under biological noise; speed and power remain unbenchmarked.

Understanding the brain increasingly depends on integrating evidence across scales, modalities, and disciplines. Addressing a single research question therefore requires a coordinated sequence of operations, from surveying prior work to executing analyses and interpreting results in light of domain knowledge. AI agents promise to accelerate this process, but current agents lack domain expertise in brain science, may fabricate claims, drift during multi-step reasoning, and offer few defined points for expert intervention. These failures are especially costly in brain science, where conclusions feed into downstream scientific claims and depend on laboratory-specific expertise and careful human judgment. We present \textbf{BrainPilot} a \textbf{fully open-source} multi-agent system that accelerates brain science research with traceable logs and agent-verified results. A principal investigator (PI) agent coordinates specialist agents grounded in curated domain knowledge: a unified brain science knowledge base containing 7{,}233 indexed items and a skill library of 72 reusable methodology units across seven research domains. Every major step is recorded in the Graph of Trace, an auditable record that links subgoals, tool use, evidence, and claims and allows researchers to follow and inspect the workflow. An Auditor agent further integrates fabrication checking into the workflow. For evaluation, we run three brain science tasks from Agents' Last Exam, introduce our own benchmark, \textbf{BrainPilotBench-v0}, and present additional end-to-end case studies. Across these evaluations, BrainPilot with an open-source backbone model attains performance comparable to state-of-the-art agent framework with less costs.

Embodied cognition requires agents to connect high-level task reasoning with the physical states to be achieved. We introduce Hy-Embodied-RxBrain, an embodied cognition foundation model with joint language-visual reasoning and imagination. Unlike vision-language models that emphasize scene understanding and textual decision making, or generative world models that mainly predict future visual states, RxBrain represents embodied plans in a single planning sequence where language and visual imagination play complementary roles. Language provides the abstract structure of a plan, including task decomposition, planning primitives, constraints, temporal order, and decision logic, while visual imagination grounds this structure through world state prediction and joint subgoal planning, associating each planning step with intermediate and final physical states. RxBrain adopts a unified multimodal Mixture-of-Transformers architecture that supports language, image, and video understanding and generation within one model. To train this capability, we build an automatic pipeline that converts embodied videos into joint text-visual planning supervision by decomposing videos into planning steps and aligning them with visual state transitions. We further introduce RxBrain-Bench to evaluate whether models can represent embodied plans through joint textual and visual components rather than separate understanding or generation. Experiments show that RxBrain maintains embodied understanding and generation abilities, and produces plans with coupled textual reasoning, world state prediction, and joint subgoal planning. We also extend RxBrain to continuous robot action generation, where it shows promising real-robot performance without large-scale action-data pretraining. These results provide an initial step toward foundation models for embodied cognition.

We model human motor cortex during a wrist-extension BCI task as a port-Hamiltonian system (pHS): a conservative interconnection (gyroscopic coupling between neural phasors) plus a dissipative port (power-law energy decay driven by a GNN surrogate). A metriplectic integrator evolves the phasor state; a Fluctuation--Dissipation-consistent noise channel produces stochastic trajectories at body temperature. Training on \FitTrainN\ real EEG cycles (PhysioNet EEGMMIDB, 3 held-out subjects) reaches a test MSE of \FitTestMSE\ and passes three scale-free criticality rungs: near-critical branching ratio ($σ\approx1$), $1/f$ power-law spectrum, and long-range DFA correlations. The model generates closed-loop neuromodulation signals that restore phase-locking in silico when applied to de-synchronised inputs, suggesting a path toward structure-preserving BCI decoders.

Financial markets are noisy, non-stationary, and high-dimensional, making it difficult to discover predictive and robust trading signals. Alpha discovery has evolved from manual factor design to machine learning, evolutionary search, and recent LLM-based frameworks, improving the efficiency of factor generation, search, and evaluation. However, existing methods still mostly automate isolated steps, rather than functioning as end-to-end quant researchers that can absorb external knowledge, close the hypothesis-to-code validation loop, and learn from accumulated discovery feedback. To fill this gap, we introduce XAlpha, a memory-driven AI Quant Researcher for continuous hypothesis-to-code alpha discovery. XAlpha maintains a multi-source research memory system that integrates report-grounded financial knowledge with discovery feedback from prior generations and research cycles. Guided by this memory system, a Macro Brain plans research themes and selects suitable Archetypes; a Micro Brain transforms the planned hypothesis pool into executable factor code and verifies ex-ante tri-alignment among the hypothesis idea, code logic, and financial plausibility; and a Cross Brain consolidates empirical outcomes into generation-level feedback, cycle-level summaries, and archetype-level research cues for future exploration. In this way, XAlpha turns alpha mining from isolated factor generation into a closed-loop research process that continuously reads, hypothesizes, implements, validates, reflects, and evolves. Experiments on CSI300 show that XAlpha achieves stronger overall alpha discovery performance than representative baselines.

Functional brain networks exhibit a hierarchical organization across ROI, community, and whole-brain levels, supporting local processing, inter-community coordination, and global integration. Recent studies have demonstrated that brain community-aware modeling is beneficial for both diagnosis and biomarker identification of brain networks. However, existing brain graph modeling methods often struggle to model ROI-community interactions, thereby failing to fully exploit the hierarchy across ROI, community, and whole-brain network levels. To address this issue, inspired by deep hyperbolic learning in modeling hierarchical structures, we propose a novel framework, termed Hyperbolic Learning on Brain Graphs (HLBG), for brain network analysis. The core idea of HLBG is to exploit the inherent hierarchical geometry of hyperbolic space to model the hierarchical relationships among ROIs, functional communities, and the whole-brain network, thereby learning hierarchy-aware and highly discriminative representations for brain network data. Specifically, HLBG first projects representations from ROIs, communities, and the whole-brain network into Lorentzian hyperbolic space. Then, the multi-level hierarchy is imposed via two geometric entailment constraints. In addition, we introduce a new Graph-aware Mamba (GaMamba) model, which incorporates topology-derived structural prompts into Mamba to capture long-range dependencies while preserving graph topological information. Experiments on ABIDE-I and REST-MDD demonstrate that HLBG outperforms state-of-the-art methods and identifies disorder-relevant functional biomarkers.

Embodied AI is moving from isolated perception or action modules toward physical agents that understand, plan under goals, act through robot bodies, monitor progress, and improve from experience. Existing systems address this loop only in parts: end-to-end policies generate actions but often lack spatial reasoning, planning, and execution assessment, while robot-agent systems orchestrate tools or specialists but do not learn a shared representation. This fragmentation limits general Physical Agentic AI. We present ACE-Brain-0.5, a unified embodied foundation model that organizes robot intelligence into five coupled functions: spatial perception, decision making, embodied interaction, self-monitoring, and self-improvement. Built on ACE-Brain-0, which established spatial intelligence as a shared scaffold across robot platforms, ACE-Brain-0.5 extends an understanding-centric model into a closed-loop foundation model. A single 8B backbone instantiates the first four functions: grounding objects and affordances, reasoning over 3D and egocentric spatial relations, decomposing instructions into subgoals, generating navigation and manipulation actions, and estimating progress for verification and recovery. To unify these capabilities without cross-task interference, we introduce SSR+, which extends Scaffold-Specialize-Reconcile with a Reactivate stage after task-vector merging. The fifth function, self-improvement, is realized by a companion framework that updates external execution state, including task schemas, spatial memory, and failure-recovery cases, from rollouts. Across fifteen benchmarks, ACE-Brain-0.5 improves over ACE-Brain-0 on 14 of 18 spatial perception and grounding benchmarks, achieves competitive navigation and manipulation performance, and provides strong progress estimation in ID and OOD settings. Together, these results mark an early step toward general Physical Agentic AI.

Brain decoding aims to uncover neural mechanisms by inferring stimulus-related representations from brain signals. In fMRI studies, this is typically achieved by mapping fMRI responses to the latent representations of computational models. Recently, CLIP has become a popular choice for brain decoding due to its rich vision--language embedding space. However, aligning fMRI signals with CLIP representations remains challenging. As CLIP is not explicitly optimized for neural alignment, its representations may capture statistically predictive cues that are only partially reflected in brain activity, limiting decoding performance. In this paper, we investigate whether adversarially robust representations improve neural decoding with CLIP. Adversarial training suppresses non-robust features and promotes more stable, perceptually structured representations, which may better align with brain activity. We evaluate this by fixing the fMRI decoder and varying only the target representation (standard CLIP vs. robust variants) on fMRI-image retrieval and zero-shot classification tasks across NSD and GOD datasets. Empirical results show that this simple change consistently improves task performance and yields stronger alignment across multiple metrics. Attribution analysis further reveals consistently low agreement between standard CLIP and its robust variants, suggesting that adversarial robustness reorganizes feature importance in the visual representation. These findings suggest that the choice of target representation influences neural decoding performance and that adversarial robustness may serve as a useful criterion for brain decoding.

Modeling the bidirectional correspondence between external sensory stimuli and internal neural activity has emerged as a critical frontier in neuroscience. However, existing approaches predominantly treat brain encoding and decoding as isolated tasks, relying heavily on unimodal alignment and external priors while overlooking the brain's intrinsic nature as a multimodal integration system. To address these limitations, we propose BrainJanus, the first unified brain model that integrates brain, vision, and language within a single framework. Specifically, we introduce a Unified Brain Tokenizer to quantize continuous neural dynamics into discrete tokens aligned with visual and linguistic representations in a shared Omni space. Building on this, we utilize an All-in-One autoregressive architecture that leverages next-token prediction to enable seamless any-to-any generation, which encompasses image-to-brain and text-to-brain encoding, and brain-to-image and brain-to-text decoding. Extensive experiments demonstrate that BrainJanus achieves superior performance across diverse benchmarks. Furthermore, our framework exhibits zero-shot generalization and preserves interpretable biological topography, highlighting its potential as a general-purpose brain modeling paradigm. The code is available at \href{https://github.com/HaitaoWuTJU/BrainJanus}{GitHub}.

While large language models have been dominating the research landscape recently, small language models remain highly relevant across various domains; yet, they receive far less attention. In this study, we investigate how smaller language models perform during the generation stage within a Retrieval-Augmented Generation (RAG) system. To benchmark these models effectively, we utilised both open-source and proprietary datasets covering diverse subject areas and question types. Our findings demonstrate that a RAG system with small language models can be executed directly on-device without requiring any GPU hardware within a reasonable time. The experimental code and links to the supplementary materials can be accessed through the GitHub repository: https://github.com/SibNN/SLM-RAG-EVAL.

Multi-site functional MRI (fMRI) studies are essential for robust neuropsychiatric diagnosis yet suffer severe domain shifts from scanner heterogeneity, demographics, and site-specific acquisition protocols. Traditional domain adaptation requires concurrent source and target data access, violating clinical privacy regulations. Moreover, functional connectivity matrices lie on the Symmetric Positive Definite (SPD) manifold, where Euclidean operations cause geometric distortions corrupting diagnostic patterns. We propose BrainRiem, a source-free domain adaptation framework learning compact Riemannian brain prototypes via manifold-aware bi-level optimization. It employs the Log-Euclidean Metric to ensure prototypes remain valid SPD matrices, while Dirichlet Energy spectral calibration aligns their frequency characteristics with real brain networks. Only anonymized prototypes are transmitted to target sites, serving as stable anchors for training local models without source data access and reducing leakage under the evaluated attacks. Comprehensive experiments on ABIDE and REST-meta-MDD show BrainRiem consistently outperforms state-of-the-art source-free, traditional, and graph domain adaptation methods across diverse scanners and demographics. Notably, learned prototypes exhibit biologically interpretable connectivity patterns aligning with established neuroscience findings, validating the necessity of Riemannian geometry for brain network analysis.

Medical vision-language models typically generate diagnoses through single-pass inference without indicating which image regions support their conclusions. This lack of spatial grounding limits clinical utility: outputs cannot be audited, and models may hallucinate findings on normal scans. We present BrReMark (Brain Rethink via ROI Marking), a framework that introduces explicit region marking into brain MRI diagnosis. The model first generates hypotheses about potential abnormalities and grounds them through explicit bounding box marking, then verifies conclusions by re-examining the marked evidence. Training combines supervised fine-tuning on structured reasoning trajectories with reinforcement learning using a composite reward over localization accuracy and diagnostic reasoning. Furthermore, we integrate a domain randomization-based pathology synthesis augmentation strategy to improve the model's generalizability to out-of-distribution (OOD) data. On internal benchmark, BrReMark improves mAP50 from 0.74% to 37.54% compared to the base model, while achieving 21.57% Clinical F1 and 45.26% diagnostic accuracy. On NOVA OOD benchmark, it also achieves competitive overall performance with a 45.7% reduction in false positives compared to the state-of-the-art, indicating reduced hallucination on rare pathologies. These findings suggest that explicit hypothesis-verification grounding is a practical path toward trustworthy open-ended brain MRI diagnosis across both in-distribution and OOD settings.

Zero-shot visual decoding from electroencephalography (EEG) aims to infer visual semantics from non-invasive neural recordings, but remains challenging due to the low signal-to-noise ratio, non-stationarity, and limited spatial resolution of EEG. Existing EEG-vision alignment methods often rely on holistic EEG embeddings, which can obscure the complementary temporal, spectral, and spatial structure underlying visual perception. We introduce a unified multiview EEG representation learning framework for aligning brain responses with visual semantic embeddings. Our method builds an EEG encoder that jointly models three complementary views: input-conditioned state-space temporal dynamics, learnable wavelet-based spectral decomposition for sample-adaptive frequency modeling, and attention-modulated graph learning for structured electrode interactions. The resulting multiview EEG embeddings are fused and aligned with pretrained visual representations in a shared semantic space using contrastive learning with EEG-specific regularization, enabling 200-way zero-shot visual classification. Experiments on THINGS-EEG benchmark show that our method achieves state-of-the-art performance, with 54.8% Top-1 and 85.6% Top-5 accuracy in the within-subject setting and 15.3% Top-1 and 45.4% Top-5 accuracy in the cross-subject setting. We further present the first systematic cross-session EEG-image decoding evaluation, achieving 40.8% Top-1 and 78.0% Top-5 accuracy. These results suggest that explicitly modeling multiview neural structure improves both semantic alignment and generalization in EEG-based visual decoding.

Brain-Computer Interfaces (BCIs) and brain signal understanding are pivotal for clinical health and next-generation interactions. Despite this significance, its widespread adoption in real-world scenarios remains restricted, primarily because current analytical paradigms lack sufficient agentic intelligence. First, existing methodologies impose prohibitive technical barriers, requiring extensive specialized expertise. Second, they remain inherently static and task-specific, failing to execute the complex, long-horizon workflows essential for real-world deployment. To accelerate the democratization of brain signal understanding, we draw inspiration from Large Language Models (LLMs) to introduce BrainAgent, an LLM-driven multi-agent framework designed to ground abstract natural language intent into rigorous, executable, and end-to-end processing pipelines. BrainAgent employs a hierarchical architecture where a central supervisor orchestrates specialized sub-agents for adaptive task decomposition and execution. Furthermore, we establish a comprehensive, systematic benchmark for evaluating agentic systems in brain signal analysis. Empirical results demonstrate that BrainAgent effectively automates complex workflows with superior reliability, marking a paradigm shift toward democratized brain signal understanding.

Automated diagnosis of 3D brain CT scans is essential for critical care, yet it remains challenging due to the heavy reliance on manual annotations and the limited semantic understanding of conventional models. While 2D foundation vision-language models (VLMs) have shown remarkable generalization, effectively transferring their representational power to 3D volumes remains an open problem. In this paper, we propose Brain-Adapter, a novel dual-stream multiple instance learning (MIL) framework that leverages pre-trained 2D biomedical VLMs and raw diagnostic reports for robust scan-level multi-label classification. Specifically, we introduce a Text-Conditioned Attention (TCA) mechanism, utilizing raw diagnostic sentences as semantic queries to dynamically align visual cues with specific disease concepts. Concurrently, a parallel visual MIL stream captures global scan characteristics, supervised by structured labels extracted via a Large Language Model (LLM). To ensure representation coherence, a consistency constraint enforces synergy between the two streams. During inference, an Uncertainty-Aware Refinement (UAR) module dynamically calibrates and fuses these dual-stream predictions to resolve ambiguous cases. Extensive experiments demonstrate that our method significantly outperforms state-of-the-art 3D models and standard MIL approaches. By eliminating the reliance on dense annotations, Brain-Adapter provides a highly scalable and clinically viable solution for 3D acute intracranial pathology analysis.

Robotic ultrasound scanning in real clinical environments requires both high-level clinical workflow reasoning and low-level closed-loop execution. Physicians natural-language instructions often contain implicit anatomical targets, procedural logic, image-quality requirements, and safety constraints, while execution is affected by patient motion, contact variations, and target drift. We propose a fast and slow hierarchical embodied ultrasound system for safe and interpretable robotic ultrasound assistance. The Slow Brain performs intent parsing and stage-wise task planning with knowledge augmentation from an API and handbook corpus, and generates executable plans through task-graph construction and structured plan verification. The Fast Brain fuses multimodal feedback, including ultrasound images, robot pose and force states, and patient-motion information, to refine local actions and perform image-quality-guided recovery behaviors. The system further integrates a Safety Shield and a hierarchical escalation policy to constrain risky actions and trigger replanning or human confirmation under persistent failures or safety-bound violations. Experiments on planning evaluation, closed-loop execution under dynamic perturbations, and safety-mechanism validation demonstrate that the proposed hierarchical design improves task success rates while reducing safety violations.

While deep learning models achieve state-of-the-art performance in complex tasks, they remain brittle when faced with new environments or sensory deprivation. In contrast, biological systems exhibit remarkable tolerance to these challenges. We address this vulnerability by developing a recurrent neural network (RNN) whose architecture is directly derived from the synaptic-resolution brain connectome of the fruit fly Drosophila melanogaster. We demonstrate the feasibility of training the fly connectome neural network (FLYNN) to perform vision-based navigation in MuJoCo, achieving performance comparable to modern hand-crafted networks of similar parameter counts. Crucially, FLYNN exhibits superior resistance to out-of-distribution (OOD) data and tolerance to sensory loss without further training. It remained functional even under total vision loss while hand-crafted networks largely failed, even when specifically trained with camera dropout. Principal Component Analysis (PCA) of the internal state of FLYNN suggests that it exhibits a particularly high degree of representational modularity, which might be related to its robustness. Our work provides a new direction for designing resilient artificial agents following the topology of biological brains.

Learning-based planners for sidewalk navigation can generate diverse candidate trajectories in real time, yet their scoring functions often fail to select the best trajectory in challenging situations, outputting trajectories that make the mobile robot drive onto grass, toward pedestrians, or in the wrong direction, even when better candidates exist in the same set. We call this the trajectory scoring gap: in real-world sidewalk navigation, the gap between an anchor-based planner's top choice and the best possible candidate is substantial, likely due to limited high-level scene understanding capability of the planner. Rather than replacing the planner with an end-to-end Vision-Language-Action model, we propose a VLM-Planner interface that uses a VLM to select a candidate index from the planner's proposal set and then fuse it with the planner's initial output. However, VLMs take 1--3s per query and so cannot directly drive a 5--20Hz control loop. We contribute a training-free, latency-resilient trajectory-level fusion layer that turns a stale VLM selection into real-time planner scoring via geometric similarity with exponential decay. On $\sim$2,000 challenging real-world scenarios (e.g., junctions, pedestrian encounters), VLM selection achieves 30% ADE reduction versus the planner's best selection, while the planner remains competitive in routine situations. In simulation, Score Fusion maintains >80% success rate with delays up to 5s. We demonstrate the full system on a mobile robot navigating challenging campus sidewalks with varied network latency.

Three-dimensional (3D) brain MRI is central to clinical neurology and neuro-oncology, where generative models could augment under-represented cohorts, simulate disease trajectories, and support privacy-preserving data sharing. Latent diffusion has been the go-to solution for modeling imaging data, but it places two competing demands on the tokenizer: encoder embeddings must retain the clinical information that downstream tasks act on, and the decoder must reconstruct anatomically faithful volumes. Existing reconstruction-driven tokenizers achieve the second at the expense of the first. To address this, we introduce a fully volumetric masked-autoencoder (MAE) based tokenizer for 3D brain MRI latent diffusion, decoupling encoder and decoder: a frozen 3D MAE encoder produces clinically informative embeddings, while a dedicated CNN decoder reconstructs voxels from a linear projection of those embeddings. We pretrain the encoder on 35,309 volumes from 18 public cohorts spanning four modalities, ten disease categories, and 200+ acquisition sites, and demonstrate its dual utility in two settings. First, on a 23-task linear-probing benchmark, the encoder outperforms or matches SOTA models (i.e., BrainIAC, BrainSegFounder, and MedicalNet) on 21 of 23 tasks. Second, a conditional diffusion transformer (DiT) trained on these clinically informative embeddings supports both conditional generation across six variables and patient-specific longitudinal forecasting. Together these results establish a single 3D brain-MRI embedding space capable of both downstream clinical tasks and controllable generation.

Glioma segmentation in multiparametric MRI is a critical component of treatment planning. A segmentation model that fails silently on treatment-critical sub-regions represents a patient safety risk that overlap-based metrics such as Dice scores cannot expose. We ask whether voxel-level uncertainty estimation via Monte Carlo (MC) Dropout can reliably identify segmentation errors in clinically critical sub-regions, and whether calibration failure modes are detectable from standard reporting metrics alone. In an empirical two-model case study on 126 BraTS21 patients, we evaluate a high-performance pretrained SegResNet and a locally trained UNet with residual units (UNet-Res). MC dropout preserved segmentation accuracy ($|Δ\text{Dice}|$ $<0.01$) while achieving strong uncertainty-error alignment (AUROC for entropy (H) $\approx$0.97), indicating uncertainty correctly ranks erroneous voxels above correct ones. Entropy-based patient stratification identified a high-uncertainty subgroup with substantially lower segmentation performance (median whole-tumour Dice $0.835$ vs. $0.925$), supporting uncertainty as a practical triage signal. However, global alignment can mask important region-specific differences. Despite similar AUROC, UNet-Res exhibited near-zero enhancing tumour entropy ($0.054$) and Expected Calibration Error (ECE) of $0.915$, with a Dice of only $0.714$, indicating severely miscalibrated confidence on the most clinically critical sub-region, a failure mode invisible to standard Dice and AUROC reporting. These findings demonstrate that strong uncertainty-error alignment is necessary but insufficient for clinical safety: sub-region-specific calibration assessment must accompany AUROC evaluation when selecting models for clinical deployment.

This paper proposes an unsupervised workflow to pseudo-label extracellular spikes from human brain slice MEA recordings into two putative cell types: pyramidal cells and interneurons. Here, the raw data from the data acquisition system is used and processed. The pipeline for pre-processing includes bandpass filtering, threshold--based spike detection, frame alignment and normalization. In the ML workflow, dimensionality reduction (PCA, t-SNE, UMAP), clustering (GMM, k-means). To achieve an online system, template matching and OSort under varying curation strictness is also considered. All pipelines are evaluated by different cluster quality with within-cluster Pearson correlation, Silhouette score, and Calinski-Harabasz index. Applying stricter curation improves separation at some cost to inclusivity.

Multimodal large language models (MLLMs) hold great potential for medicine, as they inherit knowledge from LLM and allow multiple data modalities to be integrated, analysed and interpreted in natural language. However, the field of medical MLLMs is constrained by non-trivial challenges, notably the scarcity of high-quality training data and the frequent occurrence of missing data in the real-world clinical setting. Here, we propose a novel unified multimodal model, UniBrain, for brain magnetic resonance image (MRI) analysis. To address potential missing brain MRI modalities, we employ a unified training strategy to perform joint imaging modality imputation and brain image understanding. During training, an interleaved and description-enriched data flow is constructed to train the model in an autoregressive manner, enabling medical reasoning with generated multimodal data. A self-alignment strategy is introduced to leverage dense image embeddings to learn fine-grained anatomical features without requiring detailed image captions. Furthermore, we propose a dynamic hidden state mechanism to alleviate the exposure bias during long-context multimodal inference. Extensive experiments on multi-disease brain MRI dataset demonstrate that UniBrain achieves high performance for brain image imputation, understanding, and disease diagnosis under various extents of modality incompleteness.

A common objection to artificial or simulated consciousness is that a simulated brain is no more conscious than simulated water is wet. We address this from the perspective of Intrinsic Computational Functionalism (ICF): if consciousness is computationally constituted, it depends not on externally imposed descriptions but on the computational structures a system physically realizes in virtue of its own causal-dynamical organization. In previous work we developed Canonical Functionalism as a mathematically precise special case of this anti-interpretivist program, identifying functional states by their complete future input-output roles under a fixed interface. Here we argue that this input-output construction, though important, is incomplete: as a behavioral boundary case of ICF, it makes lookup tables and unfolded systems that preserve the same boundary behavior canonically equivalent. A consciousness-relevant canonical representation must instead include internal mechanisms, interventions, and joint readouts belonging to the relevant intrinsic organization. We therefore define a mechanism-enriched canonical structure and use it to formulate Intrinsic Causal-Computational Realization (ICCR), a realization relation preserving physical implementation, intrinsic state individuation, transition structure, intervention profiles, and the relevant agent-body-world boundary. The central result is conditional: if conscious properties are invariants of intrinsic causal-computational organization, then any system satisfying ICCR realizes the same consciousness-relevant properties, whether biological, artificial, or simulated. We discuss objections including biological naturalism and integrated information theory. We conclude that to deny consciousness to a simulation, one must identify a consciousness-relevant intrinsic causal-computational structure that the simulation fails to realize.

The success of large-scale deep learning models in neuroscience is fundamentally constrained by severe data heterogeneity. Native fMRI data aggregated from diverse sources exhibit substantial variation in both spatial and temporal resolutions. Consequently, most existing frameworks rely on lengthy, rigid preprocessing pipelines that enforce uniformity across datasets. This practice introduces two critical limitations: (1) potential degradation of subject-specific anatomical information; (2) significant computational overhead, often requiring hours of processing per subject. Here, we propose FlexiBrain, a resolution-agnostic voxel-level encoding framework for native fMRI based on Mamba-JEPA. FlexiBrain defines patch sizes in real-world physical units and employs a dynamic patch resizing, thereby bypassing destructive spatial standardization while enabling direct ingestion of data in native space. We instantiate the framework using an efficient Mamba-JEPA backbone to model high-dimensional 4D fMRI signals. Across five diverse downstream neuroscience tasks, FlexiBrain consistently outperforms recent state-of-the-art methods, achieving gains of up to 12 percentage points without external data augmentation. Importantly, FlexiBrain functions as a seamless plug-in module, substantially reducing preprocessing costs and accelerating the development of robust voxel-level fMRI foundation models. Code is available at https://github.com/OneMore1/FlexiBrain.

The state-of-the-art generative models, such as CycleGAN, Pix2Pix, and diffusion models have demonstrated remarkable performance in the face generation task. However, they fail to effectively capture cross-modality semantic information in craniofacial reconstruction when translating from the skull (x-ray) to the face (optical) domain, due to a mismatch in the alignment of structural identity across modalities. To address this issue, we propose Cranio-Diff, a diffusion-based framework for cross-domain cranio-facial reconstruction from 2D X-ray skull images. The proposed approach integrates skull-conditioned structural guidance through ControlNet with biometric text conditioning to generate a face which is more semantically and structurally aligned with the given skull. The proposed Cranio-diff method is evaluated on skull-face dataset obtained from X-ray scans of 120 subjects in lateral and frontal views. To enable controlled evaluation, each face image is synthesised across three age groups (25, 45, 65) and three BMI variations of -10%, baseline and +10%, yielding 4320 paired samples. To the best of our knowledge, this is the only X-ray-face dataset with this magnitude. Extensive experiments showed that the proposed method outperforms recent existing approaches in both generated image quality and retrieval task. Finally, to evaluate the performance of our proposed method, we have evaluated the quality of the generated image using FID, IS, SSIM, LPIPS, PSNR and ArcFace score. Additionally, retrieval performance is evaluated using recall@k, mAP@k and MRR@k. Obtained experimental results demonstrate that the proposed method can be used as an alternate tool in providing aid in forensic investigations.

Decoding emotional states from neural signals has been typically framed as a discrete, single-label classification task based on emotionally stable stimuli, a formulation that oversimplifies the continuous, fluid, and co-occurring nature of human affect. This study reconceptualizes emotion decoding by adopting a multi-target regression framework to track multiple overlapping emotional dimensions as continuous trajectories over time. Leveraging the robust generalization capabilities of Large Language Models (LLMs), we extracted fine-grained, continuous sentiment profiles from a naturalistic auditory narrative, Alice in Wonderland, to serve as scalable proxies for subjective affect from human fMRI dataset. Departing from standard classification paradigms or mass-univariate subtractive contrasts that filter out network dynamics, we leverage regularized and kernel-based machine learning algorithms as continuous estimators to track the magnitude of macroscale neural state variations. We demonstrate that models trained on temporal snapshots of Dynamic Functional Connectivity (DFC) significantly outperform static region-of-interest (ROI) amplitude representations, effectively capturing continuous emotional trajectories under rapidly fluctuating narrative input. Furthermore, by implementing graph-theoretical Explainable AI (XAI) techniques, we deconstruct the underlying predictive features to reveal highly interpretable, emotion-specific topological configurations. Collectively, these results highlight the utility of LLM-automated annotation in affective neuroscience and provide compelling empirical evidence for psychological constructionist frameworks, demonstrating that dynamic, distributed network interactions offer superior explanatory power over strictly locationist accounts of emotion.

Diffusion MRI (dMRI) tractography is the only noninvasive approach for mapping white-matter pathways in the living human brain. It represents each brain as a tractogram: a large, unordered set of three-dimensional streamlines that includes information about both local streamline geometry and whole-brain anatomical organization. This structure makes tractograms a natural but challenging target for representation learning. Existing methods treat streamline classification and subject-level prediction as separate problems: streamline classifiers focus on geometric patterns, whereas subject-level prediction often depends on hand-crafted features. As a result, current methods do not learn reusable representations that connect streamline anatomy with whole-brain inter-subject variation. Here we introduce TractFM, a tractogram foundation model that learns reusable representations directly from whole-brain streamline sets. TractFM combines a local streamline encoder with a permutation-equivariant tractogram encoder, allowing all streamlines from a subject to be contextualized jointly in a single forward pass. Pretraining on dense anatomical tract parcellation, i.e., assigning anatomical labels to individual streamlines, yields two complementary representations: contextualized streamline-level embeddings for tract parcellation and compact subject-level descriptors for downstream prediction of subject phenotypes. Across three tractography algorithms and five dMRI datasets, TractFM transfers to both streamline-level and subject-level tasks. Its frozen representations achieve accurate tract parcellation and predict age and sex across independent datasets. These results show that whole-brain geometric context, learned once, can generalize across tractography pipelines, datasets, and prediction tasks.

Understanding the relationship between deep visual representations and the human visual system is a fundamental challenge in computational neuroscience. While modern vision models achieve strong performance in image recognition, their correspondence with the hierarchical organization of the human visual cortex remains an open question. In this study, we propose CHASMBrain, a novel hierarchical two-stage framework for image-to-fMRI encoding. Our architecture leverages a dual-stream Mamba design to explicitly separate and process global semantic tokens and local spatial patches, motivated by the functional organization of the visual cortex. A coarse-to-fine strategy is employed: Stage 1 predicts denoised ROI-level activations, while Stage 2 refines these coarse responses into full voxel-level predictions using a Mamba-VAE. Experiments on the Natural Scenes Dataset (NSD) demonstrate that our method achieves a Pearson correlation of 0.429 and an MSE of 0.261, outperforming all evaluated baselines including ridge regression and DINOv2 linear probes. Beyond predictive performance, causal branch-ablation experiments reveal an asymmetric specialization: the patch stream is specifically locked to early visual cortex (retinotopic regions), while the CLS stream contributes broader semantic context to higher-order areas -- a correspondence that holds causally, not merely correlationally. Cross-subject transfer experiments further show that the learned backbone generalizes across individuals with minimal per-subject adaptation, suggesting the model captures a shared, subject-agnostic visual representation.

Maximal safe resection is the primary objective in glioma surgery. Neuronavigation guidance is progressively degraded by brain shift after dural opening. Intraoperative MRI can compensate but needs dedicated infrastructure and is rarely available, whereas intraoperative ultrasound (ioUS) is inexpensive, repeatable, and compatible with routine workflows. Navigation systems combining ioUS with preoperative MRI usually rely on rigid registration; even deformable multimodal registration is limited by ultrasound speckle contrast, a narrow field of view, and the inability to represent structures absent from the preoperative scan, most critically the resection cavity and residual tumor. We propose an end-to-end pipeline that generates a new whole-brain MRI volume in the preoperative imaging space by merging the preoperative MRI, a synthetic MRI generated from the ioUS, and a deformable registration anchored on that synthetic image. It integrates a 2.5D residual-transformer synthesis backbone (ResViT-2.5D) and a two-stage registration coupling NiftyReg with a synthesis-anchored SynthMorph stage, operating directly on raw scanner inputs. On a post-resection ReMIND cohort, ResViT-2.5D produced synthetic images closely matching the intraoperative T2 across structural, intensity, and perceptual metrics. In 14 subjects with 215 expert landmarks, the synthesis-anchored registration reduced the mean target registration error from 6.27 to 5.86 mm, matching a strong classical NiftyReg baseline (5.85 mm) while yielding a diffeomorphic deformation field in every subject. The contribution is not a gain in registration accuracy but the integrated volume itself, which inside the ultrasound field of view it reflects the intraoperative post-resection state. This provides the surgeon with an MRI-like update of the operative field with potential for integration into surgical-navigation workflows.

Computational models of epilepsy promise patient-specific treatment design, but most optimization workflows still search for parameters that perform well on average. In neuromodulation, this is a weak target: a protocol that improves the mean response can still fail in the patient whose network is least tolerant to stimulation. We present a literature-guided minimax pipeline that couples PubMed-scale hypothesis extraction, The Virtual Brain (TVB) Epileptor simulations, and large-language-model-guided black-box optimization. The optimizer proposes either intrinsic model-control parameters or clinically interpretable external-stimulation protocols; TVB evaluates each proposal across sampled virtual patients; and the objective maximizes worst-case reward, defined as the negative variance of simulated seizure activity. In the intrinsic model-control experiment, the best archived parameter set improved worst-case reward from -0.5285 to -0.3182, a 39.8% gain over baseline. The clinical-style external-stimulation search produced a much smaller worst-case improvement (1.7%), and a 20-patient virtual cohort showed no aggregate benefit (p=0.9019), despite a 55% responder rate and a positive temporal-lobe subgroup signal. The study should be read as an in silico proof of concept for robust, literature-aware neurostimulation design, not as clinical evidence.

Understanding complex interactions between brain regions is critical for early neurodegenerative disease classification such as Alzheimer's Disease (AD) and Parkinson's Disease (PD). While graph-based models are widely used to analyze brain networks, most existing approaches primarily focus on pairwise interactions between directly connected nodes, limiting their ability to capture higher-order dependencies across multiple regions. Although hypergraph-based methods have been proposed to model higher-order relations, many rely on predefined hyperedges or restrict learning to hyperedge weights, reducing flexibility and limiting their capacity to capture multi-resolution structural patterns. In this regard, we introduce an adaptive multi-scale hyperedge learning framework, i.e., MuHL, which constructs hierarchical node features and dynamically learns high-order interactions through continuous hyperedge construction over multi-resolution graph signals. Extensive experiments on multiple brain network benchmarks demonstrate that MuHL consistently improves disease classification performance across different stages, and further identifies key regions of interest (ROIs) and their group-wise interactions from the learned hyperedges that are associated with disease progression, highlighting its potential as a powerful tool for brain network analysis in neurodegenerative disorders.

Electroencephalography (EEG) is the cornerstone of non-invasive brain-computer interfaces (BCIs), yet conventional decoding relies on fragmented, task-specific architectures that severely limit cross-task scalability. While EEG foundation models pre-trained on massive corpora promise universal brain decoding, current post-training depends on task-isolated fine-tuning. This static paradigm restricts knowledge transfer across heterogeneous tasks, hinders model scalability, and incurs computational and storage overheads that scale linearly with task count. To overcome these bottlenecks, we formulate downstream adaptation as a cross-task continual learning problem and propose EvoBrain, a dynamic, task-aware continual learning framework for unified EEG decoding. EvoBrain addresses the plasticity-stability trade-off via two complementary components: (1) Neuro-Spectral Task Normalization (NSN) aligns incoming tasks with historical statistics while recalibrating spectral responses to handle distributional and neuro-spectral shifts; and (2) Response-Affinity Distillation (RAD), combined with time-dependent replay, preserves old-task response geometry and promotes selective knowledge transfer between spectrally compatible tasks, effectively mitigating forgetting. Extensive evaluations across six distinct BCI tasks demonstrate that EvoBrain consistently surpasses state-of-the-art methods across diverse foundation backbones, optimally balancing plasticity and stability. To our knowledge, this work pioneers cross-task continual learning in the EEG domain, advancing the realization of a unified, one-for-all brain decoding system.

Multimodal neuroimaging fusion of functional MRI (fMRI) and diffusion tensor imaging (DTI) provides complementary information for cognitive impairment analysis, but remains challenged by heterogeneous feature spaces and misaligned representations. We propose \textit{NeuroAlign}, a hierarchical framework for structured multimodal fusion. It introduces (1) \textit{Dual-Modal Hierarchical Alignment} (DMHA), which models multi-scale dynamic connectivity and aligns dynamic-static and functional-structural embeddings; and (2) \textit{Dual-Domain Hierarchical Interaction} (DDHI), which enables fine-grained modulation and global interaction between connectivity- and region-level features. To support feature-level inspection, we design \textit{Synergistic Activation Mapping} (SAM), a gradient-free, marker-oriented attribution method for DFC, SFC, ALFF, and FA. Evaluated on GUTCM, ADNI, and OASIS under five-fold validation, NeuroAlign achieves competitive MCI/SCD detection and preliminary cross-dataset transferability. Attribution analyses reveal modality-specific and partially consistent brain patterns, providing model-derived evidence for multimodal representation analysis.

Intraoperative ultrasound (ioUS) is a versatile, cost-effective modality in brain tumour surgery, but its interpretation is difficult: acquisition planes are non-standard, artefacts are modality-specific, and its appearance differs markedly from the preoperative MRI on which surgical-planning tools, segmentation models and the surgeon's experience rely. Synthesising MRI-like images from ioUS could let this MRI-based infrastructure be reused intraoperatively without an extra scan. Most prior work evaluates a single architecture in isolation; to our knowledge, no benchmark has spanned architectural paradigms, inference regimes and downstream-task endpoints under a common protocol. We address this gap on the public ReMIND data set (76 patients; 153 paired ioUS/T2w and 104 paired ioUS/FLAIR studies; 60/16 patient-level train/held-out split). Six generators (four GAN baselines: Pix2Pix, SwinPix2Pix, CycleGAN, CUT; the transformer-augmented ResViT; and the few-step diffusion model SynDiff) were each trained under four inference regimes (2D, 2.5D, 2D + 3D-refinement, full-3D) and two targets (T2w only; T2w + FLAIR multi-task), yielding 48 experiments. Image-fidelity metrics (SSIM, PSNR, MAE, LPIPS) were complemented by an nnU-Net v2 downstream segmentation evaluation (tumour and resection cavity) and by subgroup analyses by histological grade and reoperation. No architecture dominated every axis, and, critically, perceptual quality tracked downstream utility most closely (LPIPS, r=-0.66, p<0.001), whereas higher SSIM was associated with worse utility (r=-0.64, p<0.001); SynDiff-2.5D best preserved downstream segmentation (U_Dice=0.55). Perceptual and downstream-task metrics should therefore be reported alongside or in preference to global SSIM, and architecture choice conditioned on surgical phase, patient history and clinical objective.

Forecasting the progression of neurodegenerative diseases, such as Parkinson's disease, is essential for effective long-term planning and personalized therapeutic intervention. Existing systems typically produce scalar clinical scores that ignore the rich structure of longitudinal neuroimaging, while traditional generative approaches suffer from a loss of anatomical details and blurring subtle progression patterns. To address this, we introduce a novel treatment-conditioned diffusion framework that predicts high-fidelity future brain states by conditioning the generative process on patients' screening DaTscan images and levodopa equivalent daily dose over one year. The pipeline uses a Transformer-based encoder to represent non-linear, time-dependent pharmacological dynamics and optimizes generation through a multi-weight region-of-interest mask that focuses on biologically critical areas. Experimental evaluation shows that our framework maintains sharp anatomical boundaries and significantly improves clinical fidelity relative to the baseline, achieving 14.0% lower MSE, 7.2% lower MAE, and 4.9% higher SSIM.

Decoding visual content from fMRI signals recorded while a person views images, and specifically answering questions about the seen images, is a long-standing challenge. While significant progress has been made in recent years in visual question answering (VQA) from fMRI, performance remains limited. Moreover, although recent models can make increasingly accurate predictions, they have rarely been used as tools for understanding the structure of visual representations in the brain. We present Brain-IT-VQA, a framework for visual question answering from fMRI. Building on the Brain Interaction Transformer (Brain-IT), our method decodes language tokens from brain activity and integrates them with a language model to answer visual questions. Our model substantially outperforms previous fMRI-based captioning and VQA approaches. We further introduce NSD-VQA, a new dataset and benchmark for visual question answering from fMRI. Unlike existing image-fMRI VQA datasets, which typically provide only a few broad and weakly controlled questions per image, NSD-VQA provides on average 20 question-answer pairs per image across 20 controlled question categories that disentangle multiple levels of visual understanding. This enables more reliable and interpretable evaluation despite limited fMRI test data. Together, Brain-IT-VQA and NSD-VQA provide both a strong predictive framework and a tool for studying brain representations. Using this benchmark, we quantify which forms of visual and semantic information can be reliably decoded from fMRI responses to natural images. We further analyze the contributions of different brain regions across question types.

Functional magnetic resonance imaging (fMRI) is a powerful tool for investigating human brain function. However, the high cost of data acquisition and the inherent subjectivity of psychiatric rating scales often lead to datasets with small sample sizes and variable label quality, especially when targeting a specific neurological condition. Combined with the inherently high dimensionality of fMRI data, these limitations substantially increase the risk of model overfitting. Recent years have seen growing interest in developing fMRI foundation models by combining multiple datasets; however, the computational resources needed for pretraining and fine-tuning are often prohibitive. We show that a lightweight self-supervised framework yields representations that generalize across diverse downstream tasks, outperforming fully supervised baselines and approaching the performance of large-scale models. We introduce BrainSimSiam, a data-efficient self-supervised representation learning framework that leverages positive-only data pairs to learn robust and generalizable features. We demonstrate that the learned representations achieve strong performance across multiple downstream classification and regression tasks, highlighting the potential of BrainSimSiam for data-limited neuroimaging applications.

Electroencephalography (EEG) is a critical, non-invasive method to monitor electrical brain activity. EEGs can span anywhere from a couple seconds to multiple hours, posing a major hurdle for existing deep learning methods due to two major factors: (1) existing EEG models are predominantly built upon the attention mechanism, incurring quadratic scaling as the sequence length increases, and (2) raw EEG signals must be processed in a sliding-window fashion due to fixed-length input requirements, preventing global understanding of the entire signal. To this extent, we propose CaMBRAIN - the first Causal, Mamba-based state space model (SSM) capable of real-time inference of EEG signals, arguing that bidirectional approaches are needlessly expensive given the causal, unidirectional nature of EEG. However, training such a model is non-trivial, as crucial EEG events can be extremely brief - within fractions of a second - yet separated by long intervals spanning minutes. Current EEG methods use self-supervised objectives that optimize for signal reconstruction, but these are not well suited for streaming SSMs; they fail to explicitly train the hidden state to retain the salient long-range context needed for streaming inference. We therefore introduce a multi-stage self-supervised training pipeline specifically tailored to encourage long-range memory retention and strong performance on EEG signals, while preserving the linear-time complexity of state space models. CaMBRAIN achieves state-of-the-art (SOTA) results across 3 different EEG datasets with >10x higher throughput than existing models, enabling the first model capable of long-range, continuous inference of variable-length EEG signals.

Large language models (LLMs) display strong comprehensive abilities, yet the internal mechanisms that support these behaviors remain insufficiently understood. In this work, we show that across a wide range of open-weight Transformers, a subset of neurons remains consistently highly activated during inference across tasks of multiple capability dimensions. By probing along the cross-task activation strength, an extremely sparse subset is isolated, whose removal causes a collapse in model behavior, which we term keystone neurons. Our analysis reveals that keystone neurons are a stable and intrinsic neuron subset of the model that is largely established during pretraining. The parameters associated with these neurons are tightly calibrated during the training process, and their precise values are critical for the capabilities of the model. Building on these insights, we propose a supervised fine-tuning approach that updates only keystone neurons, achieving task gains comparable to or even better than full-parameter fine-tuning while better preserving performance in other capability dimensions, despite modifying a much smaller number of parameters.

Brain-LLM alignment is well established in English, yet the brain's language network is neuroanatomically universal across languages. Does alignment also generalize cross-linguistically, and what governs the variation? We test this using fMRI data from 112 participants across English, Chinese, and French (the Le Petit Prince corpus) and seven LLMs spanning English-dominant, Chinese-dominant, and multilingual architectures. Our central finding is that training-language dominance, not an inherent property of English, drives the alignment pattern: a Chinese-dominant model (Baichuan2-7B), architecture-matched to LLaMA-2-7B, reverses the gradient entirely, aligning best with Chinese brains and worst with English. Beyond training dominance, formal typological distance independently covaries with alignment degradation, syntax-associated brain regions (IFG) show $2.3\times$ steeper typological gradients than lexico-semantic regions (PTL), and tokenization fertility accounts for $\sim$60% of a cross-linguistic shift in optimal encoding layer. These results reveal that the apparent "English advantage" in brain-LLM alignment is an artifact of training data composition, while the remaining variation reflects genuine typological structure concentrated in syntactic processing.

The Thousand Brains Theory (TBT) and its open-source Monty framework model object recognition through sensorimotor inference -- identifying objects by actively moving a sensor across their surface and building evidence contact by contact. The current implementation encodes each contact as a dense floating-point vector. While Monty tracks inter-step displacement and accumulates evidence across contacts, it treats the feature activation pattern at each contact as an unordered set - the directional sequence in which features are encountered carries no representational weight. In TBT, the sequence of contacts carries spatial meaning: knowing that feature A was felt before feature B during a left-to-right sweep tells you something about where A and B sit on the object. Dense vectors discard this ordering. We propose replacing dense vectors with rank-order spike packets: each contact produces a brief burst of neural events where the most strongly activated neuron fires first. The time gap between successive bursts implicitly encodes sensor displacement without explicit coordinate calculations. A biologically motivated learning rule (STDP) encodes traversal direction into synaptic weights. A learnable parameter lambda adjusts reliance on earlier versus recent contacts, adapting to each object's geometry. We derive three testable predictions and specify an implementation of four components in approximately 450 lines of NumPy. Three synthetic experiments confirm the core claims: temporal coding achieves perfect discrimination accuracy on objects with identical features in different spatial arrangements, where dense accumulation performs at chance; temporal coding maintains a 30-50 percentage point advantage across all tested noise levels; the adaptive lambda converges to distinct values, reflecting object geometric complexity. End-to-end evaluation on Monty's YCB benchmark is left for future work.

Decoding visual experience from brain activity has advanced substantially, but current brain-to-text systems largely recover semantic content while discarding affect. Additionally, language models can generate emotional text when prompted with categorical labels, but such labels collapse rich inter-subject variability into coarse discrete bins. We present EmoMind, the first end-to-end pipeline for decoding affective captions directly from fMRI signals. EmoMind first retrieves a semantically grounded neutral scene description from brain-decoded visual features, then rewrites it using a continuous 34-dimensional emotion vector decoded from the same fMRI recording. To control the balance between content preservation and affective expression, we train the rewriter with classifier-free guidance against an identity-preserving null branch, enabling smooth interpolation between semantic fidelity and affective expressivity. We evaluate affective caption generation with a three-axis validation framework spanning subject-specificity, structural geometry, and causal control. We further augment this framework with a synthetic-brain substitution test that probes robustness to the measurement apparatus, and we benchmark each axis against GPT-4 prompted with brain-decoded top-5 emotion labels as a strong discrete baseline. Across two independent emotion fMRI datasets, EmoMind significantly outperforms label-prompted GPT-4 on all three axes, with the largest gains on metrics that require person-specific affective structure rather than population-level emotion aggregation. These results establish continuous brain-decoded affect as a viable control signal for individualized affective caption generation and open new directions for studying individual affective brain organisation.