q-bio.NC

arXiv:2503.21796v1 Announce Type: new Abstract: Self-supervised learning has become an increasingly important paradigm in the domain of machine intelligence. Furthermore, evidence for self-supervised adaptation, such as contrastive formulations, has emerged in recent computational neuroscience and brain-inspired research. Nevertheless, current work on self-supervised learning relies on biologically implausible credit assignment -- in the form of backpropagation of errors -- and feedforward inference, typically a forward-locked pass. Predictive coding, in its mechanistic form, offers a biologically plausible means to sidestep these backprop-specific limitations. However, unsupervised predictive coding rests on learning a generative model of raw pixel input (akin to ``generative AI'' approaches), which entails predicting a potentially high dimensional input; on the other hand, supervised predictive coding, which learns a mapping between inputs to target labels, requires human annotation, and thus incurs the drawbacks of supervised learning. In this work, we present a scheme for self-supervised learning within a neurobiologically plausible framework that appeals to the free energy principle, constructing a new form of predictive coding that we call meta-representational predictive coding (MPC). MPC sidesteps the need for learning a generative model of sensory input (e.g., pixel-level features) by learning to predict representations of sensory input across parallel streams, resulting in an encoder-only learning and inference scheme. This formulation rests on active inference (in the form of sensory glimpsing) to drive the learning of representations, i.e., the representational dynamics are driven by sequences of decisions made by the model to sample informative portions of its sensorium.

arXiv:2503.21964v1 Announce Type: new Abstract: Integrating functional magnetic resonance imaging (fMRI) connectivity data with phenotypic textual descriptors (e.g., disease label, demographic data) holds significant potential to advance our understanding of neurological conditions. However, existing cross-modal alignment methods often lack interpretability and risk introducing biases by encoding sensitive attributes together with diagnostic-related features. In this work, we propose NeuroLIP, a novel cross-modal contrastive learning framework. We introduce text token-conditioned attention (TTCA) and cross-modal alignment via localized tokens (CALT) to the brain region-level embeddings with each disease-related phenotypic token. It improves interpretability via token-level attention maps, revealing brain region-disease associations. To mitigate bias, we propose a loss for sensitive attribute disentanglement that maximizes the attention distance between disease tokens and sensitive attribute tokens, reducing unintended correlations in downstream predictions. Additionally, we incorporate a negative gradient technique that reverses the sign of CALT loss on sensitive attributes, further discouraging the alignment of these features. Experiments on neuroimaging datasets (ABIDE and ADHD-200) demonstrate NeuroLIP's superiority in terms of fairness metrics while maintaining the overall best standard metric performance. Qualitative visualization of attention maps highlights neuroanatomical patterns aligned with diagnostic characteristics, validated by the neuroscientific literature. Our work advances the development of transparent and equitable neuroimaging AI.

arXiv:2406.03044v4 Announce Type: replace Abstract: We present a self-supervised framework that learns population-level codes for arbitrary ensembles of neural recordings at scale. We address key challenges in scaling models with neural time-series data, namely, sparse and variable electrode distribution across subjects and datasets. The Population Transformer (PopT) stacks on top of pretrained temporal embeddings and enhances downstream decoding by enabling learned aggregation of multiple spatially-sparse data channels. The pretrained PopT lowers the amount of data required for downstream decoding experiments, while increasing accuracy, even on held-out subjects and tasks. Compared to end-to-end methods, this approach is computationally lightweight, while achieving similar or better decoding performance. We further show how our framework is generalizable to multiple time-series embeddings and neural data modalities. Beyond decoding, we interpret the pretrained and fine-tuned PopT models to show how they can be used to extract neuroscience insights from large amounts of data. We release our code as well as a pretrained PopT to enable off-the-shelf improvements in multi-channel intracranial data decoding and interpretability. Code is available at https://github.com/czlwang/PopulationTransformer.

arXiv:2503.10518v1 Announce Type: cross Abstract: This paper presents a novel information-theoretic proof demonstrating that the human brain as currently understood cannot function as a classical digital computer. Through systematic quantification of distinguishable conscious states and their historical dependencies, we establish that the minimum information required to specify a conscious state exceeds the physical information capacity of the human brain by a significant factor. Our analysis calculates the bit-length requirements for representing consciously distinguishable sensory "stimulus frames" and demonstrates that consciousness exhibits mandatory temporal-historical dependencies that multiply these requirements beyond the brain's storage capabilities. This mathematical approach offers new insights into the fundamental limitations of computational models of consciousness and suggests that non-classical information processing mechanisms may be necessary to account for conscious experience.

arXiv:2503.10195v1 Announce Type: new Abstract: Spiking Neural Networks (SNNs) have emerged as a promising tool for event-based optical flow estimation tasks due to their ability to leverage spatio-temporal information and low-power capabilities. However, the performance of SNN models is often constrained, limiting their application in real-world scenarios. In this work, we address this gap by proposing a novel neural network architecture, ST-FlowNet, specifically tailored for optical flow estimation from event-based data. The ST-FlowNet architecture integrates ConvGRU modules to facilitate cross-modal feature augmentation and temporal alignment of the predicted optical flow, improving the network's ability to capture complex motion dynamics. Additionally, to overcome the challenges associated with training SNNs, we introduce a novel approach to derive SNN models from pre-trained artificial neural networks (ANNs) through ANN-to-SNN conversion or our proposed BISNN method. Notably, the BISNN method alleviates the complexities involved in biological parameter selection, further enhancing the robustness of SNNs in optical flow estimation tasks. Extensive evaluations on three benchmark event-based datasets demonstrate that the SNN-based ST-FlowNet model outperforms state-of-the-art methods, delivering superior performance in accurate optical flow estimation across a diverse range of dynamic visual scenes. Furthermore, the inherent energy efficiency of SNN models is highlighted, establishing a compelling advantage for their practical deployment. Overall, our work presents a novel framework for optical flow estimation using SNNs and event-based data, contributing to the advancement of neuromorphic vision applications.

arXiv:2502.18485v3 Announce Type: replace-cross Abstract: The burgeoning growth of open-sourced vision-language models (VLMs) has catalyzed a plethora of applications across diverse domains. Ensuring the transparency and interpretability of these models is critical for fostering trustworthy and responsible AI systems. In this study, our objective is to delve into the internals of VLMs to interpret the functions of individual neurons. We observe the activations of neurons with respects to the input visual tokens and text tokens, and reveal some interesting findings. Particularly, we found that there are neurons responsible for only visual or text information, or both, respectively, which we refer to them as visual neurons, text neurons, and multi-modal neurons, respectively. We build a framework that automates the explanation of neurons with the assistant of GPT-4o. Meanwhile, for visual neurons, we propose an activation simulator to assess the reliability of the explanations for visual neurons. System statistical analyses on top of one representative VLM of LLaVA, uncover the behaviors/characteristics of different categories of neurons.

arXiv:2503.09980v1 Announce Type: cross Abstract: The fundamental thermodynamic bound is derived for the energy cost of inference in Deep Neural Networks (DNNs). By applying Landauer's principle, we demonstrate that the linear operations in DNNs can, in principle, be performed reversibly, whereas the non-linear activation functions impose an unavoidable energy cost. The resulting theoretical lower bound on the inference energy is determined by the average number of neurons undergoing state transition for each inference. We also restate the thermodynamic bound in terms of negentropy, a metric which is more universal than energy for assessing thermodynamic cost of information processing. Concept of negentropy is further elaborated in the context of information processing in biological and engineered system as well as human intelligence. Our analysis provides insight into the physical limits of DNN efficiency and suggests potential directions for developing energy-efficient AI architectures that leverage reversible analog computing.

arXiv:2503.10362v1 Announce Type: cross Abstract: Electroencephalography (EEG) serves as an essential diagnostic tool in neurology; however, its accurate manual interpretation is a time-intensive process that demands highly specialized expertise, which remains relatively scarce and not consistently accessible. To address these limitations, the implementation of automated pre-screening and analysis systems for EEG data holds considerable promise. Advances in self-supervised learning made it possible to pre-train complex deep learning architectures on large volumes of unlabeled EEG data to learn generalizable representations, that can later be used to enhance performance on multiple tasks while needing less downstream data. In the present paper, we introduce BioSerenity-E1, the first of a family of self-supervised foundation models for clinical EEG applications that combines spectral tokenization with masked prediction to achieve state-of-the-art performance across relevant diagnostic tasks. The two-phase self-supervised pretraining framework initially acquires compressed EEG representations via a transformer-based VQ-VAE architecture designed to reconstruct log-multitaper spectral projections, then implements extensive (70% block) masked token prediction to force the model to learn complex spatiotemporal dependencies in EEG signals. BioSerenity-E1 achieves strong performance across three clinical tasks, either in line or above state-of-the-art methods: seizure detection (AUROC = 0.926, Sensitivity = 0.909), normal/abnormal classification (AUPRC = 0.970 on proprietary data; 0.910 on TUH-Abnormal), and multiclass pathology differentiation on unbalanced data (Weighted F1 = 0.730). The utility of BioSerenity-E1 is further confirmed in low-data regimes scenarios, showing clear improvements in AUPRC (from +2% to 17%) when trained on less than 10% of the available data.

arXiv:2503.10556v1 Announce Type: new Abstract: In this study, we examined whether a short-form AI literacy intervention could reduce the adoption of incorrect recommendations from large language models. High school seniors were randomly assigned to either a control or an intervention group, which received an educational text explaining ChatGPT's working mechanism, limitations, and proper use. Participants solved math puzzles with the help of ChatGPT's recommendations, which were incorrect in half of the cases. Results showed that students adopted incorrect suggestions 52.1% of the time, indicating widespread over-reliance. The educational intervention did not significantly reduce over-reliance. Instead, it led to an increase in ignoring ChatGPT's correct recommendations. We conclude that the usage of ChatGPT is associated with over-reliance and it is not trivial to increase AI literacy to counter over-reliance.

arXiv:2503.01906v2 Announce Type: replace Abstract: We present a model inspired by the Global Workspace Theory that integrates specialized modules to perform a sequential reasoning task. A controller selectively routes information between modules through the workspace using a gating mechanism. This approach allows the model to chain operations by iteratively broadcasting information between specialized domains, mimicking System-2 reasoning. We evaluate the model's performance on a simple addition task, where two addends must be summed. The task can be solved by routing information sequentially through an Input module, an Increment module (multiple times), and finally an Output module. We consider two implementations of this system with increasing complexity. First, using hand-designed modules operating on one-hot digit representations, the controller (a LSTM recurrent network) learns to select the appropriate modules (input, increment, output) in the appropriate sequence. Second, we replace the hand-designed modules with learned representation modules for MNIST images and an increment module trained on the task objectives; here again, the controller learns the appropriate sequential module selection to solve the task. Finally, we show that the Global Workspace model, while having fewer parameters, outperforms LSTMs and Transformers when tested on unseen addition operations (both interpolations and extrapolations of addition operations seen during training). Our results highlight the potential of architectures inspired by the Global Workspace Theory to enhance deep learning's reasoning capabilities.

arXiv:2503.05031v1 Announce Type: cross Abstract: Alzheimer's disease (AD) is a major neurodegenerative condition that affects millions around the world. As one of the main biomarkers in the AD diagnosis procedure, brain amyloid positivity is typically identified by positron emission tomography (PET), which is costly and invasive. Brain structural magnetic resonance imaging (sMRI) may provide a safer and more convenient solution for the AD diagnosis. Recent advances in geometric deep learning have facilitated sMRI analysis and early diagnosis of AD. However, determining AD pathology, such as brain amyloid deposition, in preclinical stage remains challenging, as less significant morphological changes can be observed. As a result, few AD classification models are generalizable to the brain amyloid positivity classification task. Blood-based biomarkers (BBBMs), on the other hand, have recently achieved remarkable success in predicting brain amyloid positivity and identifying individuals with high risk of being brain amyloid positive. However, individuals in medium risk group still require gold standard tests such as Amyloid PET for further evaluation. Inspired by the recent success of transformer architectures, we propose a geometric deep learning model based on transformer that is both scalable and robust to variations in input volumetric mesh size. Our work introduced a novel tokenization scheme for tetrahedral meshes, incorporating anatomical landmarks generated by a pre-trained Gaussian process model. Our model achieved superior classification performance in AD classification task. In addition, we showed that the model was also generalizable to the brain amyloid positivity prediction with individuals in the medium risk class, where BM alone cannot achieve a clear classification. Our work may enrich geometric deep learning research and improve AD diagnosis accuracy without using expensive and invasive PET scans.

arXiv:2503.04848v1 Announce Type: new Abstract: Specific empirical phenomena spanning human natural language, and mathematical and logical abilities, are rigorously situated in the well-studied grammar-automata (G-A) hierarchy. We identify three tiers and corresponding two transitions within the hierarchy and show their correspondence to the emergence of particular abilities in humans and in transformer-based language models (LMs). These emergent abilities have often been described in terms of "scaling"; we show that it is the transition between tiers, rather than size itself, that determines a system's capabilities. Specifically, humans effortlessly process language yet require specific training to perform arithmetic or logical reasoning tasks; and LMs possess language abilities absent from predecessor systems yet still struggle with logical processing. The resulting principled analyses provide underlying explanatory accounts of both the abilities and shortfalls of these systems, and suggest actionable insights into the expansion of logic abilities in AI systems.

arXiv:2501.11409v1 Announce Type: new Abstract: Conventional echo state networks (ESNs) require supervised learning to train the readout layer, using the desired outputs as training data. In this study, we focus on input reconstruction (IR), which refers to training the readout layer to reproduce the input time series in its output. We reformulate the learning algorithm of the ESN readout layer to perform IR using unsupervised learning (UL). By conducting theoretical analysis and numerical experiments, we demonstrate that IR in ESNs can be effectively implemented under realistic conditions without explicitly using the desired outputs as training data; in this way, UL is enabled. Furthermore, we demonstrate that applications relying on IR, such as dynamical system replication and noise filtering, can be reformulated within the UL framework. Our findings establish a theoretically sound and universally applicable IR formulation, along with its related tasks in ESNs. This work paves the way for novel predictions and highlights unresolved theoretical challenges in ESNs, particularly in the context of time-series processing methods and computational models of the brain.

arXiv:2408.02496v2 Announce Type: replace-cross Abstract: Incomplete Hippocampal Inversion (IHI), sometimes called hippocampal malrotation, is an atypical anatomical pattern of the hippocampus found in about 20% of the general population. IHI can be visually assessed on coronal slices of T1 weighted MR images, using a composite score that combines four anatomical criteria. IHI has been associated with several brain disorders (epilepsy, schizophrenia). However, these studies were based on small samples. Furthermore, the factors (genetic or environmental) that contribute to the genesis of IHI are largely unknown. Large-scale studies are thus needed to further understand IHI and their potential relationships to neurological and psychiatric disorders. However, visual evaluation is long and tedious, justifying the need for an automatic method. In this paper, we propose, for the first time, to automatically rate IHI. We proceed by predicting four anatomical criteria, which are then summed up to form the IHI score, providing the advantage of an interpretable score. We provided an extensive experimental investigation of different machine learning methods and training strategies. We performed automatic rating using a variety of deep learning models (conv5-FC3, ResNet and SECNN) as well as a ridge regression. We studied the generalization of our models using different cohorts and performed multi-cohort learning. We relied on a large population of 2,008 participants from the IMAGEN study, 993 and 403 participants from the QTIM/QTAB studies as well as 985 subjects from the UKBiobank. We showed that deep learning models outperformed a ridge regression. We demonstrated that the performances of the conv5-FC3 network were at least as good as more complex networks while maintaining a low complexity and computation time. We showed that training on a single cohort may lack in variability while training on several cohorts improves generalization.

arXiv:2408.00109v3 Announce Type: replace-cross Abstract: Continuous attractors offer a unique class of solutions for storing continuous-valued variables in recurrent system states for indefinitely long time intervals. Unfortunately, continuous attractors suffer from severe structural instability in general--they are destroyed by most infinitesimal changes of the dynamical law that defines them. This fragility limits their utility especially in biological systems as their recurrent dynamics are subject to constant perturbations. We observe that the bifurcations from continuous attractors in theoretical neuroscience models display various structurally stable forms. Although their asymptotic behaviors to maintain memory are categorically distinct, their finite-time behaviors are similar. We build on the persistent manifold theory to explain the commonalities between bifurcations from and approximations of continuous attractors. Fast-slow decomposition analysis uncovers the persistent manifold that survives the seemingly destructive bifurcation. Moreover, recurrent neural networks trained on analog memory tasks display approximate continuous attractors with predicted slow manifold structures. Therefore, continuous attractors are functionally robust and remain useful as a universal analogy for understanding analog memory.

arXiv:2403.18963v3 Announce Type: replace-cross Abstract: The exploration of new problem classes for quantum computation is an active area of research. In this paper, we introduce and solve a novel problem class related to dynamics on large-scale networks relevant to neurobiology and machine learning. Specifically, we ask if a network can sustain inherent dynamic activity beyond some arbitrary observation time or if the activity ceases through quiescence or saturation via an epileptic-like state. We show that this class of problems can be formulated and structured to take advantage of quantum superposition and solved efficiently using the Deutsch-Jozsa and Grover quantum algorithms. To do so, we extend their functionality to address the unique requirements of how input (sub)sets into the algorithms must be mathematically structured while simultaneously constructing the inputs so that measurement outputs can be interpreted as meaningful properties of the network dynamics. This, in turn, allows us to answer the question we pose.

arXiv:2501.06698v1 Announce Type: new Abstract: In virtual reality applications, users often navigate through virtual environments, but the issue of physiological responses, such as cybersickness, fatigue, and cognitive workload, can disrupt or even halt these activities. Despite its impact, the underlying mechanisms of how the sensory system encodes information in VR remain unclear. In this study, we compare three sensory encoding models, Bayesian Efficient Coding, Fitness Maximizing Coding, and the Linear Nonlinear Poisson model, regarding their ability to simulate human navigation behavior in VR. By incorporating the factor of physiological responses into the models, we find that the Bayesian Efficient Coding model generally outperforms the others. Furthermore, the Fitness Maximizing Code framework provides more accurate estimates when the error penalty is small. Our results suggest that the Bayesian Efficient Coding framework offers superior predictions in most scenarios, providing a better understanding of human navigation behavior in VR environments.

arXiv:2412.07783v2 Announce Type: replace-cross Abstract: Brain development in the first few months of human life is a critical phase characterized by rapid structural growth and functional organization. Accurately predicting developmental outcomes during this time is crucial for identifying delays and enabling timely interventions. This study introduces the SwiFT (Swin 4D fMRI Transformer) model, designed to predict Bayley-III composite scores using neonatal fMRI data from the Developing Human Connectome Project (dHCP). To enhance predictive accuracy, we apply dimensionality reduction via group independent component analysis (ICA) and pretrain SwiFT on large adult fMRI datasets to address the challenges of limited neonatal data. Our analysis shows that SwiFT significantly outperforms baseline models in predicting cognitive, motor, and language outcomes, leveraging both single-label and multi-label prediction strategies. The model's attention-based architecture processes spatiotemporal data end-to-end, delivering superior predictive performance. Additionally, we use Integrated Gradients with Smoothgrad sQuare (IG-SQ) to interpret predictions, identifying neural spatial representations linked to early cognitive and behavioral development. These findings underscore the potential of Transformer models to advance neurodevelopmental research and clinical practice.

arXiv:2408.03330v3 Announce Type: replace-cross Abstract: Understanding how the collective activity of neural populations relates to computation and ultimately behavior is a key goal in neuroscience. To this end, statistical methods which describe high-dimensional neural time series in terms of low-dimensional latent dynamics have played a fundamental role in characterizing neural systems. Yet, what constitutes a successful method involves two opposing criteria: (1) methods should be expressive enough to capture complex nonlinear dynamics, and (2) they should maintain a notion of interpretability often only warranted by simpler linear models. In this paper, we develop an approach that balances these two objectives: the Gaussian Process Switching Linear Dynamical System (gpSLDS). Our method builds on previous work modeling the latent state evolution via a stochastic differential equation whose nonlinear dynamics are described by a Gaussian process (GP-SDEs). We propose a novel kernel function which enforces smoothly interpolated locally linear dynamics, and therefore expresses flexible -- yet interpretable -- dynamics akin to those of recurrent switching linear dynamical systems (rSLDS). Our approach resolves key limitations of the rSLDS such as artifactual oscillations in dynamics near discrete state boundaries, while also providing posterior uncertainty estimates of the dynamics. To fit our models, we leverage a modified learning objective which improves the estimation accuracy of kernel hyperparameters compared to previous GP-SDE fitting approaches. We apply our method to synthetic data and data recorded in two neuroscience experiments and demonstrate favorable performance in comparison to the rSLDS.

arXiv:2501.07440v1 Announce Type: cross Abstract: Being attentive to task-relevant features can improve task performance, but paying attention comes with its own metabolic cost. Therefore, strategic allocation of attention is crucial in performing the task efficiently. This work aims to understand this strategy. Recently, de Gee et al. conducted experiments involving mice performing an auditory sustained attention-value task. This task required the mice to exert attention to identify whether a high-order acoustic feature was present amid the noise. By varying the trial duration and reward magnitude, the task allows us to investigate how an agent should strategically deploy their attention to maximize their benefits and minimize their costs. In our work, we develop a reinforcement learning-based normative model of the mice to understand how it balances attention cost against its benefits. The model is such that at each moment the mice can choose between two levels of attention and decide when to take costly actions that could obtain rewards. Our model suggests that efficient use of attentional resources involves alternating blocks of high attention with blocks of low attention. In the extreme case where the agent disregards sensory input during low attention states, we see that high attention is used rhythmically. Our model provides evidence about how one should deploy attention as a function of task utility, signal statistics, and how attention affects sensory evidence.