Neural Decoding

Spike activity has been the dominant neural signal for behavior decoding because its high spatiotemporal resolution supports accurate decoding. However, as intracortical brain-computer interfaces (iBCIs) move toward higher channel counts and wireless operation, the high sampling rates required to record spikes create substantial power and bandwidth demands. Local field potentials (LFPs) offer complementary advantages, including greater long-term stability, lower energy consumption, and lower bandwidth requirements. However, LFP-based decoders often achieve lower accuracy and rely on non-causal architectures that cannot be used directly for real-time deployment. We propose REALM, a retrospective knowledge distillation (RKD) framework for causal LFP behavior decoding. Inspired by offline-to-online distillation in speech recognition, REALM transfers non-causal representational knowledge from a pretrained, multi-session bidirectional LFP teacher to a causal student model. We first pretrain a bidirectional Mamba-2 teacher across multiple recording sessions using continuous masked autoencoding (CMAE), and then distill its representation into a compact causal student using a combined objective of representation alignment and autoencoding. REALM achieves the highest mean accuracy among the compared decoders in both label-free and fine-tuned pipelines, with statistically significant improvements over each baseline, including the state-of-the-art CrossModalDistill. It does so using LFPs alone throughout pretraining, distillation, and decoding, with less than half the parameters of CrossModalDistill's published student and one-tenth of its pretraining time. These results show that a causal LFP-only model can achieve decoding accuracy competitive with a non-causal multi-modal model, offering a practical and scalable approach for next-generation wireless and implantable iBCIs.

Reconstructing dynamic visual experiences as videos from functional magnetic resonance imaging (fMRI) is pivotal for advancing the understanding of neural processes. However, current fMRI-to-video reconstruction methods are hindered by a semantic gap between noisy fMRI signals and the rich content of videos, stemming from a reliance on incomplete semantic embeddings that neither capture video-specific cues (e.g., actions) nor integrate prior knowledge. To this end, we draw inspiration from the dual-pathway processing mechanism in human brain and introduce CineNeuron, a novel hierarchical framework for semantically enhanced video reconstruction from fMRI signals with two synergistic stages. First, a bottom-up semantic enrichment stage maps fMRI signals to a rich embedding space that comprehensively captures textual semantics, image contents, action concepts, and object categories. Second, a top-down memory integration stage utilizes the proposed Mixture-of-Memories method to dynamically select relevant "memories" from previously seen data and fuse them with the fMRI embedding to refine the video reconstruction. Extensive experimental results on two fMRI-to-video benchmarks demonstrate that CineNeuron surpasses state-of-the-art methods across various metrics.

Decoding speech from non-invasive brain signals is challenging. For the LibriBrain 2025 Speech Detection task, we propose a novel two-step framework that bypasses direct reconstruction. First, a contrastive learning model retrieves the matching speech segment for the given test MEG from a large-scale audio library (LibriVox). Second, a speech detection model generates the binary silence/speech sequence directly from this retrieved audio. With this approach, our team Sherlock Holmes achieved first place in the extended track (F1-score: 0.962), demonstrating that leveraging external audio databases is a highly effective strategy.

Closed-loop brain-computer interfaces often require both a forecast of upcoming neural population activity and a readout of the animal's behavioral state. A single Mamba forecaster, trained only on next-step spike counts at Neuropixels scale, can deliver both in one forward pass. A lightweight per-session linear head reading the model's predicted rates decodes behavior better than the same linear classifier reading the raw spike counts, under matched temporal context. We test on the Steinmetz visual-discrimination benchmark, which spans 39 sessions, roughly 27,000 neurons, and 1,994 held-out trials. Across three training seeds, Mamba's predicted rates decode mouse choice at 75.7$\pm$0.2% trial vote, roughly 2.3 times chance level, and stimulus side at 66.1$\pm$0.6%, about twice chance. Compared to a matched 500 ms-context linear decoder on the raw spike counts, Mamba wins at trial vote by 4-6 pp on response and 4-6 pp on stimulus side. A session-start calibration block of about 100-150 trials brings the readout within 1-2 pp of asymptote, and the full pipeline fits inside the 50 ms bin budget on workstation-class GPUs typical of tethered chronic Neuropixels recordings.

Quantum error correction (QEC) is essential for enabling quantum advantages, with decoding as a central algorithmic primitive. Owing to its importance and intrinsic difficulty, substantial effort has been made to QEC decoder design, among which neural decoders have recently emerged as a promising data-driven paradigm. Despite this progress, practical deployment remains hindered by a fundamental accuracy-latency tradeoff, often on the microsecond timescale. To address this challenge, here we revisit neural decoders for surface-code decoding under explicit accuracy-latency constraints, considering code distances up to d=9 (161 physical qubits). We unify and redesign representative neural decoders into five architectural paradigms and develop an end-to-end compression pipeline to evaluate their deployability and performance on FPGA hardware. Through systematic experiments, we reveal several previously underexplored insights: (i) near-term decoding performance is driven more by data scale than architectural complexity; (ii) appropriate inductive bias is essential for achieving high decoding accuracy; and (iii) INT4 quantization is a prerequisite for meeting microsecond-scale latency requirements on FPGAs. Together, these findings provide concrete guidance toward scalable and real-time neural QEC decoding.

Forward error correction is essential for reliable communication over noisy channels. Attention-based model-free neural decoders have shown strong performance for short codes, but their scalability to longer codes is limited by the quadratic memory and computational cost of attention. In this paper, we introduce the Mamba message-passing decoder (MMPD), an attention-free syndrome-based neural decoder for binary linear codes. MMPD retains the Tanner-graph structure of a message-passing decoder by performing local pairwise aggregation along variable-check edges. To enable efficient long-range information propagation, these local updates are combined with bidirectional Mamba state-space blocks. By avoiding dense attention matrices, MMPD scales more favorably for long codes in both memory and computation. Experiments on the (1056, 880) LDPC code show that MMPD achieves a 0.45 dB gain over the state-of-the-art CrossMPT decoder at a specified target bit error rate, while reducing memory consumption by a factor of 1.5. This reduction factor increases substantially for longer codes, demonstrating the applicability of MMPD to scalable neural decoding of practical long codes.

Intracranial electrocorticography (ECoG) offers high signal-to-noise access to cortical activity for brain-computer interfaces, yet limited per-patient data has led most prior work to rely on small, subject-specific decoders that neglect information shared across patients. We investigate whether large pretrained scalp-EEG foundation models (EEG FMs) can be adapted to ECoG, enabling cross-patient learning and competitive decoding performance while calibrating to a held-out patient in 10-30 minutes on a single GPU. We introduce CORTEG, a cross-modality transfer framework that combines a pretrained EEG FM backbone, an electrode-aware KNNSoftFourier spatial adapter, a dual-stream tokenizer for low-frequency and high-gamma activity, and a leave-one-subject-out fine-tuning strategy. We evaluate CORTEG on two challenging regression tasks: public finger-trajectory regression ($n=9$) and private audio-envelope regression ($n=16$). CORTEG achieves state-of-the-art mean performance on both tasks, achieving the highest mean correlation among the compared methods on the public finger benchmark and larger, statistically significant gains on the audio task and in low-data-per-patient calibration. We further validate CORTEG on the public BrainTreebank stereo-EEG classification tasks, where it also performs strongly. Furthermore, CORTEG outperforms the compared intracranial-EEG foundation models across the continuous regression tasks. Feature analyses align with neurophysiology, and latent representations capture low-dimensional finger-movement structure. Together, these results provide systematic evidence that scalp-EEG pretraining can be repurposed across intracranial recording modalities and tasks, enabling data-efficient neural decoders that can adapt to new patients.

Decoding imagined speech from non-invasive brain recordings is challenging because imagined datasets are scarce and difficult to align temporally across subjects and sessions In this work, we propose a new approach to the decoding of imagined speech that leverages the richer and more reliably labeled recordings during listening to speech. We collected paired listened and imagined MEG recordings to rhythmic melodic and spoken stimuli from trained musicians. Using trained musicians helped improve temporal alignment across conditions. We then developed a three-stage decoding pipeline that revealed consistent and meaningful relationships between neural activity evoked by imagining and listening to the same stimuli. First, we trained six linear and neural models to map imagined MEG responses to listened responses. We evaluated these models against a null baseline from unseen subjects to validate that the predicted-listening responses preserve stimulus-specific information. In the second stage, we trained a contrastive word decoder exclusively on the listened MEG responses, and evaluated it using four embedding strategies including semantic, acoustic, and phonetic representations. In the third stage, we process the imagined MEG responses from held-out subjects through the mapping pipeline to compute the corresponding listening responses that are then decoded by the listened decoder. Using rank-based analysis, we show that the imagined words are decodable significantly above chance. We shall report here the results of a proof-of-concept implementation to decode imagined speech, where all evaluations are performed on held-out subjects. We also demonstrate that performance improves with training data size, suggesting that this approach is scalable and can directly be made applicable to realistic brain-computer interface scenarios.

Understanding the neural mechanisms underlying visual computation has long been a central challenge in neuroscience. Recent alignment based approaches have improved the accuracy of decoding visual stimuli from brain activity, yet they provide limited insight into the neural computations that give rise to these improvements. To address this gap, we propose Dual-Tower Image-Neural Alignment (DINA), an interpretable contrastive framework for analyzing population level visual computations in primary visual cortex (V1). DINA jointly trains a biologically motivated dual-tower architecture that aligns visual stimuli and corresponding V1 population responses in a shared latent space at the level of intermediate feature maps, enabling both accurate decoding and direct access to interpretable feature maps. Evaluated on large-scale two-photon calcium imaging data from mouse V1, DINA achieves accurate neural-based decoding while revealing that decoding performance is primarily supported by coarse, low-level visual structure, rather than semantic category information or fine-grained details. Further analysis reveals that alignable feature maps emerge from multiple spatially distributed image regions, capturing both shape and texture cues, and are predominantly reconstructed by sparse subsets of strongly responsive neurons and their functional interactions. Together, these results confirm that, beyond enabling accurate decoding, DINA provides a principled framework for probing the computational mechanisms underlying visual processing in V1.

Syndrome-based neural decoding (SBND) has emerged as a promising deep learning approach for soft-decision decoding of high-rate, short-length codes. However, this approach still has substantial room for improvement. In this paper, we show how to leverage code automorphisms to enhance the ability of existing SBND models to learn and generalize through data augmentation during training and inference. As a result, for the short high-rate codes considered, we obtain models that closely approach MLD performance using small datasets and proper training. Our findings also suggest that many prior results for SBND models in the literature underestimate their true correction capability due to undertraining. Code to reproduce all results is available at: https://github.com/lebidan/sbnd.

Activation-alignment measures such as Representational Similarity Analysis (RSA), Canonical Correlation Analysis (CCA), and Centered Kernel Alignment (CKA) are widely used to compare biological and artificial neural representations. Recent theoretical work interprets many of these methods as assessing agreement between optimal linear readouts over broad families of global tasks. However, agreement at the level of global readouts does not determine how a system uses local stimulus evidence. Specifically, representations may align in activation space yet differ in their sensitivity to small perturbations. To address this challenge, we introduce a complementary framework based on local decodable information, which focuses on a representation's ability, under noise, to discriminate small perturbations within a specified stimulus-coordinate subspace. Building on Fisher information and local representation geometry, we summarize each representation using the expected projected pullback/Fisher metric over that subspace. This formulation induces a second-moment family of local discrimination tasks, for which the resulting operator provides a minimal, complete dataset-level summary of expected discriminability. We compare these regularized signatures using a log-spectral distance on the manifold of symmetric positive definite (SPD) matrices, yielding the Spectral Riemannian Alignment Score (S-RAS) and a uniform multiplicative certificate over the corresponding family of lifted task values. Empirically, this framework enables the recovery of corresponding layers across independently trained artificial neural networks, supports transferable class-conditional probes, reveals controlled dissociations between standard and robust training, and uncovers stimulus-coordinate family effects across mouse visual cortex using the Allen Brain Observatory static gratings dataset.

Existing cross-subject fMRI decoding methods typically train a model on multiple scanned subjects and then adapt it to a new subject using substantial paired fMRI-image data. However, in realistic scenarios, new-subject fMRI data are often limited due to costly data acquisition, and raw data from previous subjects may be inaccessible, leading existing methods to suffer performance degradation during new-subject adaptation. In this paper, we identify that this degradation stems from two key issues: brain-side instability caused by large subject differences in fMRI responses, and image-side supervision unreliability caused by fine-grained visual details that are not reliably supported by limited fMRI signals. To address these challenges, we propose StableMind, a regularized adaptation framework designed to improve brain-side representation stability and image-side supervision reliability. (1) To stabilize brain representations, StableMind reuses ridge projections from the pretrained model as adaptation priors to constrain limited-data new-subject adaptation, and applies Fourier-based feature-level brain augmentation to improve robustness to individual variability. (2) To improve image supervision reliability, StableMind introduces difficulty-aware image blur for brain-image alignment, reducing the influence of fine-grained visual details that are weakly supported by limited fMRI signals while preserving stable visual structure. Experiments on the Natural Scenes Dataset under a unified 1-hour adaptation protocol demonstrate that StableMind achieves 84.02% image retrieval accuracy and 81.66% brain retrieval accuracy averaged over four subjects, surpassing the state-of-the-art method by 5.71% brain retrieval accuracy with fewer trainable adaptation parameters. Our code is available at https://github.com/lingeringlight/StableMind.

Modeling invasive neural spike data is fundamental to advancing high-performance brain-computer interfaces (BCIs). However, existing approaches face critical challenges, including limited-scale heterogeneous data, cross-domain distribution shift, and the intrinsic spatiotemporal complexity of invasive neural signals. In this work, we propose UniBCI, a unified pretrained model for invasive Brain-Computer Interfaces. The model integrates three key components: (1) a context-conditioned spatio-temporal tokenization (CST) scheme that embeds neural signals together with metadata into a shared representation space; (2) a hierarchical Interval-Area Attention (IAA) mechanism that captures patterns of spike dynamics in slots via linear attention and locality dependencies via sliding-window attention; and (3) a scalable self-supervised masked signals reconstruction objective for learning generalizable neural representations from large-scale unlabeled data. We construct a pretraining corpus spanning multiple species, subjects, brain regions, and behavioral experiment paradigms. These heterogeneous recordings are standardize via our proposed unified normalization and tokenization. Comprehensive experiments demonstrate that UniBCI achieves SOTA performance across diverse downstream tasks while improving generalization. Moreover, the model achieves a strong balance between accuracy and efficiency, with fewer trainable parameters and lower inference latency. These results suggest that UniBCI provides a practical step toward general-purpose neural foundation models, enabling robust, scalable, and transferable representation learning for invasive neural data. The code for this paper is available at: https://anonymous.4open.science/r/UniBCI-C805.

Foundation models of brain activity promise a new frontier for in silico neuroscience by emulating neural responses to complex stimuli across tasks and modalities. A natural next step is to ask whether these models can also be used in reverse. Can we recover a stimulus or its properties from synthetic brain activity? We study this question in a proof-of-concept setting using TRIBEv2. We pair the brain emulator with large language models (LLMs) that generate news headlines from linguistic parameters such as valence, arousal, and dominance. We then use simulation-based inference to learn a probabilistic mapping from brain maps to latent stimulus parameters. Our results show that these parameters can be recovered from predicted brain maps, validating the quality of neural encodings. They also show that LLMs can serve as controllable stimulus generators for simulated experiments. Together, these findings provide a step toward decoding and inverse design with foundation brain models.

The relationship between brain lateralization and cognitive functions is well-documented. The left hemisphere primarily handles tasks such as language and arithmetic, while the right hemisphere is involved in creative activities like drawing and music perception. Eye-tracking technology has shown the potential to reveal cognitive states by measuring ocular metrics such as pupil diameter and fixation duration. However, the ability to distinguish lateralized brain activity using these ocular metrics remains underexplored. Here, we demonstrate that pupil diameter and fixation duration can effectively classify left and right brain hemisphere activities. We obtained a considerably high classification performance, with an F1 score of 0.894. The results suggest that ocular metrics are robust indicators of lateralized brain activity and can be applied in cognitive monitoring and neurorehabilitation. Our future work expands on this by integrating these methods into real-time applications EyeBrain, potentially broadening their use across various cognitive and neurological domains.

State space models (SSMs) achieve linear-time complexity but struggle with multi-channel physiological signals due to three limitations: fixed kernels cannot capture multi-scale temporal dynamics (motor preparation over hundreds of milliseconds vs. execution transients in tens of milliseconds), Markovian state updates restrict global context for periodic oscillations, and channel-independent processing ignores spatial electrode topology. We introduce NAKUL, extending SSMs for medical signal analysis through three contributions: (1) Dynamic Kernel Generation-parallel SSM branches with varying kernel sizes (3, 5, 7, 11 timesteps) are weighted by a meta-network that analyzes input statistics, enabling adaptive temporal scale selection; (2) Spectral Context Modeling-FFT-based operations with learnable Gaussian frequency band filters capture global periodic patterns in $O(N \log N)$ complexity; (3) Graph-Guided Spatial Attention-fixed electrode topology provides spatial biases to multi-head attention for principled cross-channel interaction. On BCI Competition IV-2a motor imagery (our primary benchmark), NAKUL achieves 91.7$\pm$0.6% accuracy, matching EEG-Conformer (92.1$\pm$0.7%) while using 28% fewer parameters (2.5M vs 3.5M) and 2.0$\times$ faster inference (4.3ms vs 8.7ms). The model generalizes to EEG emotion recognition (83.6%), multimodal EEG-fMRI (91.4%), and medical imaging (92.8% on ultrasound), demonstrating architectural versatility. Ablations show dynamic kernels contribute +2.6% and exhibit interpretable scale selection patterns correlated with known neural dynamics.

Continuous estimation of high-dimensional finger kinematics from forearm surface electromyography (EMG) could enable natural control for hand prostheses, AR/XR interfaces, and teleoperation. However, the complexity of human hand gestures and the entanglement of forearm muscles make accurate recognition intrinsically challenging. Existing approaches typically reduce task complexity by relying on classification-based machine learning, limiting the controllable degrees of freedom and compromising on natural interaction. We present an end-to-end framework for continuous EMG-to-kinematics regression using only consumer-grade hardware. The framework combines an 8-channel EMG armband, a single webcam, and an automatic synchronization procedure, enabling the collection of the EMG Finger-Kinematics dataset (EMG-FK), a 10-h dataset of synchronized EMG and 15 finger joint angles from 20 participants performing rich, unconstrained right-hand motions. We also introduce the Temporal Riemannian Regressor (TRR), a lightweight GRU-based model that uses sequences of multi-band Riemannian covariance features to decode finger motion. Across EMG-FK and the public emg2pose benchmark, TRR outperforms state-of-the-art methods in both intra- and cross-subject evaluation. On EMG-FK, it reaches an average absolute error of $9.79 °\pm 1.48$ in intra-subject and $16.71 °\pm 3.97$ in cross-subject. Finally, we demonstrate real-time deployment on a Raspberry Pi 5 and intuitive control of a robotic hand; TRR runs at nearly 10 predictions/s and is roughly an order of magnitude faster than state-of-the-art approaches. Together, these contributions lower the barrier to reproducible, real-time EMG-based decoding of high-dimensional finger motion, and pave the way toward more natural and intuitive control of embedded EMG-based systems.

We tested whether auditory-evoked EEG supports subject-independent five-vowel perception decoding when trial identity, model identity, prediction provenance, and participant-level inference are controlled within a single benchmark. We reconstructed Study 2 event tables from OpenNeuro ds006104 version 1.0.1 and analysed the consonant-vowel pair task. One-to-one marker-stimulus pairing yielded 3,840 independent trials; control-condition selection and artifact rejection retained 1,094 epochs from 16 participants and 61 EEG channels. Thirteen unique implementations were evaluated using leave-one-subject-out testing, with participant metrics reconstructed from 36,102 trial predictions across 33 complete prediction replicas. Random Forest was numerically highest at 21.474% balanced accuracy (95% participant-bootstrap interval, 19.526-23.482%; chance, 20%), but neither its participant-level tests nor any implementation survived correction across the 13-model family. Deep-model performance was close to chance, and several architectures showed substantial seed-dependent variation and low trial-label agreement. An exploratory MDM analysis comprising 9,616 genuine refits across training cohorts of 3-15 participants showed no monotonic performance gain. Within this dataset and protocol, evidence for reliable cross-subject five-vowel decoding is limited. The benchmark provides a reproducible chain from source rows to retained epochs, predictions, participant-level metrics, multiplicity-adjusted inference, and bounded diagnostic analyses.

Speech neuroprosthesis systems decode intended speech from neural activity in the absence of audible output, offering a path to restoring communication for individuals with speech-impairing conditions. Current approaches decode predominantly from motor cortical areas, discarding others -- such as area 44, part of Broca's area -- that may encode complementary linguistic information. We introduce MoDAl (Modality Decorrelation and Alignment), a framework that discovers complementary neural modalities through the interplay of two objectives in a shared projection space. A contrastive loss aligns each of several parallel brain encoders with the text embeddings of a pretrained large language model (LLM), while a decorrelation loss prevents the encoders from coalescing to duplicative representations. We prove that these objectives are in productive tension: Contrastive alignment induces transitive modality coalescence, which decorrelation must counteract for the framework to discover diverse neurolinguistic modalities. On the Brain-to-Text Benchmark '24, MoDAl reduces word error rate (WER) from 26.3% to 21.6% compared to the previous best end-to-end method, with the gain from incorporating previously discarded area 44 signals arising entirely from the decorrelation mechanism. Analysis of the discovered modalities reveals functional specialization: Encoders receiving area 44 input capture structural and syntactic properties (sentence length, grammatical voice, wh-words), consistent with the neurolinguistic understanding of Broca's area.

Scaling data and artificial neural networks has transformed AI, driving breakthroughs in language and vision. Whether similar principles apply to modeling brain activity remains unclear. Here we leveraged a dataset of 3.1 million neurons from the visual cortex of 73 mice across 323 sessions, totaling more than 150 billion neural tokens recorded during natural movies, images and parametric stimuli, and behavior. We train multi-modal, multi-task models that support three regimes flexibly at test time: neural prediction, behavioral decoding, neural forecasting, or any combination of the three. OmniMouse achieves state-of-the-art performance, outperforming specialized baselines across nearly all evaluation regimes. We find that performance scales reliably with more data, but gains from increasing model size saturate. This inverts the standard AI scaling story: in language and computer vision, massive datasets make parameter scaling the primary driver of progress, whereas in brain modeling -- even in the mouse visual cortex, a relatively simple system -- models remain data-limited despite vast recordings. The observation of systematic scaling raises the possibility of phase transitions in neural modeling, where larger and richer datasets might unlock qualitatively new capabilities, paralleling the emergent properties seen in large language models. Code available at https://github.com/enigma-brain/omnimouse.

Recent progress in visual brain decoding from fMRI has been enabled by large-scale datasets such as the Natural Scenes Dataset (NSD) and powerful diffusion-based generative models. While current pipelines are primarily optimized for perception, their performance under mental-imagery remains less well understood. In this work, we study how a state-of-the-art (SOTA) perception decoder (DynaDiff) can be adapted to reconstruct imagined content from the NSD-Imagery benchmark. We propose a latent functional alignment (LFA) approach that maps imagery-evoked activity to the pretrained model's semantic content-enriched conditioning space, by adding a simple alignment module, while keeping the original remaining components frozen. To mitigate the limited amount of matched imagery-perception supervision, we further introduce a neural retrieval-based augmentation strategy that selects semantically related NSD perception trials from the same participants. Across four subjects, LFA consistently improves high-level semantic reconstruction metrics relative to the frozen pretrained baseline and a voxel-space ridge alignment baseline, and enables above-chance decoding from multiple cortical regions. These results suggest that semantic structure learned from perception can be leveraged to stabilize and improve visual imagery decoding under out-of-distribution conditions.

Recent progress in brain-guided image generation has improved the quality of fMRI-based reconstructions; however, fundamental challenges remain in preserving object-level structure and semantic fidelity. Many existing approaches overlook the spatial arrangement of salient objects, leading to conceptually inconsistent outputs. We propose a saliency-driven decoding framework that employs graph-informed saliency priors to translate structural cues from brain signals into spatial masks. These masks, together with semantic information extracted from embeddings, condition a diffusion model to guide image regeneration, helping preserve object conformity while maintaining natural scene composition. In contrast to pipelines that invoke multiple diffusion stages, our approach relies on a single frozen model, offering a more lightweight yet effective design. Experiments show that this strategy improves both conceptual alignment and structural similarity to the original stimuli, while also introducing a new direction for efficient, interpretable, and structurally grounded brain decoding.

Visual encoding and decoding models act as gateways to understanding the neural mechanisms underlying human visual perception. Typically, visual encoding models that predict brain activity from stimuli and decoding models that reproduce stimuli from brain activity are treated as distinct tasks, requiring separate models and training procedures. This separation is inefficient and fails to model the consistency between encoding and decoding processes. To address this limitation, we propose NeuroFlow, the first unified framework that jointly models visual encoding and decoding from neural activity within a single flow model. NeuroFlow introduces two key components: (1) NeuroVAE is designed as a variational backbone to model neural variability and establish a compact, semantically structured latent space for bidirectional modeling across visual and neural modalities. (2) Cross-modal Flow Matching (XFM) bypasses the typical paradigm of noise-to-data diffusion guided by a specific modality condition, instead learning a reversibly consistent flow model between visual and neural latent distributions. For the first time, visual encoding and decoding are reformulated as a time-dependent, reversible process within a shared latent space for unified modeling. Empirical results demonstrate that NeuroFlow achieves superior overall performance in visual encoding and decoding tasks with higher computational efficiency compared to any isolated methods. We further analyze principal factors that steer the model toward encoding-decoding consistency and, through brain functional analyses, demonstrate that NeuroFlow captures consistent activation patterns underlying neural variability. NeuroFlow marks a major step toward unified visual encoding and decoding from neural activity, providing mechanistic insights that inform future bidirectional visual brain-computer interfaces.

Visual decoding from brain signals is a key challenge at the intersection of computer vision and neuroscience, requiring methods that bridge neural representations and computational models of vision. A field-wide goal is to achieve generalizable, cross-subject models. A major obstacle towards this goal is the substantial variability in neural representations across individuals, which has so far required training bespoke models or fine-tuning separately for each subject. To address this challenge, we introduce a meta-optimized approach for semantic visual decoding from fMRI that generalizes to novel subjects without any fine-tuning. By simply conditioning on a small set of image-brain activation examples from the new individual, our model rapidly infers their unique neural encoding patterns to facilitate robust and efficient visual decoding. Our approach is explicitly optimized for in-context learning of the new subject's encoding model and performs decoding by hierarchical inference, inverting the encoder. First, for multiple brain regions, we estimate the per-voxel visual response encoder parameters by constructing a context over multiple stimuli and responses. Second, we construct a context consisting of encoder parameters and response values over multiple voxels to perform aggregated functional inversion. We demonstrate strong cross-subject and cross-scanner generalization across diverse visual backbones without retraining or fine-tuning. Moreover, our approach requires neither anatomical alignment nor stimulus overlap. This work is a critical step towards a generalizable foundation model for non-invasive brain decoding.

Quantum error correction (QEC) is essential for scalable quantum computing. However, it requires classical decoders that are fast and accurate enough to keep pace with quantum hardware. While quantum low-density parity-check codes have recently emerged as a promising route to efficient fault tolerance, current decoding algorithms do not allow one to realize the full potential of these codes in practical settings. Here, we introduce a convolutional neural network decoder that exploits the geometric structure of QEC codes, and use it to probe a novel "waterfall" regime of error suppression, demonstrating that the logical error rates required for large-scale fault-tolerant algorithms are attainable with modest code sizes at current physical error rates, and with latencies within the real-time budgets of several leading hardware platforms. For example, for the $[144, 12, 12]$ Gross code, the decoder achieves logical error rates up to $\sim 17$x below existing decoders - reaching logical error rates $\sim 10^{-10}$ at physical error $p=0.1\%$ - with 3-5 orders of magnitude higher throughput. This decoder also produces well-calibrated confidence estimates that can significantly reduce the time overhead of repeat-until-success protocols. Taken together, these results suggest that the space-time costs associated with fault-tolerant quantum computation may be significantly lower than previously anticipated.

This chapter presents a novel approach to brain-to-speech (BTS) synthesis from intracranial electroencephalography (iEEG) data, emphasizing prosody-aware feature engineering and advanced transformer-based models for high-fidelity speech reconstruction. Driven by the increasing interest in decoding speech directly from brain activity, this work integrates neuroscience, artificial intelligence, and signal processing to generate accurate and natural speech. We introduce a novel pipeline for extracting key prosodic features directly from complex brain iEEG signals, including intonation, pitch, and rhythm. To effectively utilize these crucial features for natural-sounding speech, we employ advanced deep learning models. Furthermore, this chapter introduces a novel transformer encoder architecture specifically designed for brain-to-speech tasks. Unlike conventional models, our architecture integrates the extracted prosodic features to significantly enhance speech reconstruction, resulting in generated speech with improved intelligibility and expressiveness. A detailed evaluation demonstrates superior performance over established baseline methods, such as traditional Griffin-Lim and CNN-based reconstruction, across both quantitative and perceptual metrics. By demonstrating these advancements in feature extraction and transformer-based learning, this chapter contributes to the growing field of AI-driven neuroprosthetics, paving the way for assistive technologies that restore communication for individuals with speech impairments. Finally, we discuss promising future research directions, including the integration of diffusion models and real-time inference systems.

Brain-computer interfaces (BCIs) for speech restoration hold transformative potential for the approximately 173,000--232,500 individuals worldwide with ALS-related dysarthria. Despite recent progress, high-performance speech BCIs have been demonstrated in only 22--31 patients globally, largely due to limitations in neural decoding accuracy and practical input interfaces. We present iPhoneme, a brain-to-text communication system that jointly addresses these challenges through integrated modeling and interaction design. The system combines a deep learning phoneme decoder based on a modified Conformer architecture (ConformerXL, 192.9M parameters) with a gaze-assisted phoneme input interface that mitigates the Midas touch problem in eye-tracking systems. The acoustic model incorporates a temporal prenet with multi-scale dilated convolutions and bidirectional GRU for neural jitter correction, temporal subsampling for CTC stability, and Pre-RMSNorm stabilization across 12 encoder blocks, trained with AdamW and cosine scheduling. On the interaction side, iPhoneme introduces a chorded gaze-plus-silent-speech paradigm that replaces dwell-time selection, enabling more efficient input. We evaluate the system on the T15 dataset (45 sessions, 8,071 trials) of 256-channel intracranial EEG from speech motor cortex regions. A 6-gram phoneme language model trained on 3.1M sequences, combined with WFST beam search (beam=128), achieves 92.14% phoneme accuracy (7.86% PER) and 73.39% word accuracy (26.61% WER), approximately 3% above prior state-of-the-art. The system operates on CPU with 180 ms latency, demonstrating real-time, high-accuracy brain-to-text communication for ALS.

This study investigates robust speech-related decoding from non-invasive MEG signals using the LibriBrain phoneme-classification benchmark from the 2025 PNPL competition. We compare residual convolutional neural networks (CNNs), an STFT-based CNN, and a CNN--Transformer hybrid, while also examining the effects of group averaging, label balancing, repeated grouping, normalization strategies, and data augmentation. Across our in-house implementations, preprocessing and data-configuration choices matter more than additional architectural complexity, among which instance normalization emerges as the most influential modification for generalization. The strongest of our own models, a CNN with group averaging, label balancing, repeated grouping, and instance normalization, achieves 60.95% F1-macro on the test split, compared with 39.53% for the plain CNN baseline. However, most of our models, without instance normalization, show substantial validation-to-test degradation, indicating that distribution shift induced by different normalization statistics is a major obstacle to generalization in our experiments. By contrast, MEGConformer maintains 64.09% F1-macro on both validation and test, and saliency-map analysis is qualitatively consistent with this contrast: weaker models exhibit more concentrated or repetitive phoneme-sensitive patterns across splits, whereas MEGConformer appears more distributed. Overall, the results suggest that improving the reliability of non-invasive phoneme decoding will likely require better handling of normalization-related distribution shift while also addressing the challenge of single-trial decoding.

Recent work suggests that large-scale, multi-animal modeling can significantly improve neural recording analysis. However, for functional calcium traces, existing approaches remain task-specific, limiting transfer across common neuroscience objectives. To address this challenge, we propose CalM, a self-supervised neural foundation model trained solely on neuronal calcium traces and adaptable to multiple downstream tasks, including forecasting and decoding. Our key contribution is a pretraining framework, composed of a high-performance tokenizer mapping single-neuron traces into a shared discrete vocabulary, and a dual-axis autoregressive transformer modeling dependencies along both the neural and the temporal axis. We evaluate CalM on a large-scale, multi-animal, multi-session dataset. On the neural population dynamics forecasting task, CalM achieves competitive performance against strong specialized baselines after pretraining. With a task-specific head, CalM further adapts to the behavior decoding task and achieves superior results compared with supervised decoding models. Moreover, linear analyses of CalM representations reveal interpretable functional structures beyond predictive accuracy. Taken together, we propose a novel and effective self-supervised pretraining paradigm for foundation models based on calcium traces, paving the way for scalable pretraining and broad applications in functional neural analysis. Code is released at https://github.com/TSuXinH/CalM.

Electroencephalography (EEG) provides a non-invasive window into brain activity, offering high temporal resolution crucial for understanding and interacting with neural processes through brain-computer interfaces (BCIs). Current dual-stream neural networks for EEG often process temporal and spatial features independently through parallel branches, delaying their integration until a final, late-stage fusion. This design inherently leads to an "information silo" problem, precluding intermediate cross-stream refinement and hindering spatial-temporal decompositions essential for full feature utilization. We propose LI-DSN, a layer-wise interactive dual-stream network that facilitates progressive, cross-stream communication at each layer, thereby overcoming the limitations of late-fusion paradigms. LI-DSN introduces a novel Temporal-Spatial Integration Attention (TSIA) mechanism, which constructs a Spatial Affinity Correlation Matrix (SACM) to capture inter-electrode spatial structural relationships and a Temporal Channel Aggregation Matrix (TCAM) to integrate cosine-gated temporal dynamics under spatial guidance. Furthermore, we employ an adaptive fusion strategy with learnable channel weights to optimize the integration of dual-stream features. Extensive experiments across eight diverse EEG datasets, encompassing motor imagery (MI) classification, emotion recognition, and steady-state visual evoked potentials (SSVEP), consistently demonstrate that LI-DSN significantly outperforms 13 state-of-the-art (SOTA) baseline models, showcasing its superior robustness and decoding performance. The code will be publicized after acceptance.