q-bio.NC

33 posts

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.

\'Abel S\'agodi, Guillermo Mart\'in-S\'anchez, Piotr Sok\'o\l, Il Memming Park1/22/2025

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.

Lisa Hemforth, Baptiste Couvy-Duchesne, Kevin De Matos, Camille Brianceau, Matthieu Joulot, Tobias Banaschewski, Arun L. W. Bokde, Sylvane Desrivi\`eres, Herta Flor, Antoine Grigis, Hugh Garavan, Penny Gowland, Andreas Heinz, R\"udiger Br\"uhl, Jean-Luc Martinot, Marie-Laure Paill\`ere Martinot, Eric Artiges, Dimitri Papadopoulos, Herve Lemaitre, Tomas Paus, Luise Poustka, Sarah Hohmann, Nathalie Holz, Juliane H. Fr\"ohner, Michael N. Smolka, Nilakshi Vaidya, Henrik Walter, Robert Whelan, Gunter Schumann, Christian B\"uchel, JB Poline, Bernd Itterman, Vincent Frouin, Alexandre Martin, IMAGEN study group, Claire Cury, Olivier Colliot1/22/2025

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.

Gabriel A. Silva1/22/2025

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.

Taiki Yamada, Yuichi Katori, Kantaro Fujiwara1/22/2025

arXiv:2501.06762v1 Announce Type: cross Abstract: Continuous, adaptive learning-the ability to adapt to the environment and improve performance-is a hallmark of both natural and artificial intelligence. Biological organisms excel in acquiring, transferring, and retaining knowledge while adapting to dynamic environments, making them a rich source of inspiration for artificial neural networks (ANNs). This study explores how neuromodulation, a fundamental feature of biological learning systems, can help address challenges such as catastrophic forgetting and enhance the robustness of ANNs in continuous learning scenarios. Driven by neuromodulators including dopamine (DA), acetylcholine (ACh), serotonin (5-HT) and noradrenaline (NA), neuromodulatory processes in the brain operate at multiple scales, facilitating dynamic responses to environmental changes through mechanisms ranging from local synaptic plasticity to global network-wide adaptability. Importantly, the relationship between neuromodulators, and their interplay in the modulation of sensory and cognitive processes are more complex than expected, demonstrating a "many-to-one" neuromodulator-to-task mapping. To inspire the design of novel neuromodulation-aware learning rules, we highlight (i) how multi-neuromodulatory interactions enrich single-neuromodulator-driven learning, (ii) the impact of neuromodulators at multiple spatial and temporal scales, and correspondingly, (iii) strategies to integrate neuromodulated learning into or approximate it in ANNs. To illustrate these principles, we present a case study to demonstrate how neuromodulation-inspired mechanisms, such as DA-driven reward processing and NA-based cognitive flexibility, can enhance ANN performance in a Go/No-Go task. By integrating multi-scale neuromodulation, we aim to bridge the gap between biological learning and artificial systems, paving the way for ANNs with greater flexibility, robustness, and adaptability.

Jie Mei, Alejandro Rodriguez-Garcia, Daigo Takeuchi, Gabriel Wainstein, Nina Hubig, Yalda Mohsenzadeh, Srikanth Ramaswamy1/14/2025

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.

Tangyao Li, Qiyuan Zhan, Yitong Zhu, Bojing Hou, Yuyang Wang1/14/2025

arXiv:2501.06196v1 Announce Type: cross Abstract: How do the synthetic neurons in language models create "thought categories" to segment and analyze their informational environment? What are the cognitive characteristics, at the very level of formal neurons, of this artificial categorical thought? Based on the mathematical nature of algebraic operations inherent to neuronal aggregation functions, we attempt to identify mathematico-cognitive factors that genetically shape the categorical reconstruction of the informational world faced by artificial cognition. This study explores these concepts through the notions of priming, attention, and categorical phasing.

Michael Pichat, William Pogrund, Armanush Gasparian, Paloma Pichat, Samuel Demarchi, Michael Veillet-Guillem1/14/2025

arXiv:2501.06192v1 Announce Type: new Abstract: In the fields of computation and neuroscience, much is still unknown about the underlying computations that enable key cognitive functions including learning, memory, abstraction and behavior. This paper proposes a mathematical and computational model of learning and memory based on a small set of bio-plausible functions that include coincidence detection, signal modulation, and reward/penalty mechanisms. Our theoretical approach proposes that these basic functions are sufficient to establish and modulate an information space over which computation can be carried out, generating signal gradients usable for inference and behavior. The computational method used to test this is a structurally dynamic cellular automaton with continuous-valued cell states and a series of recursive steps propagating over an undirected graph with the memory function embedded entirely in the creation and modulation of graph edges. The experimental results show: that the toy model can make near-optimal choices to re-discover a reward state after a single training run; that it can avoid complex penalty configurations; that signal modulation and network plasticity can generate exploratory behaviors in sparse reward environments; that the model generates context-dependent memory representations; and that it exhibits high computational efficiency because of its minimal, single-pass training requirements combined with flexible and contextual memory representation.

Jeet Singh1/14/2025

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.

Lokesh Boominathan, Yizhou Chen, Matthew McGinley, Xaq Pitkow1/14/2025

arXiv:2404.14325v3 Announce Type: replace Abstract: Brains have evolved diverse neurons with varying morphologies and dynamics that impact temporal information processing. In contrast, most neural network models use homogeneous units that vary only in spatial parameters (weights and biases). To explore the importance of temporal parameters, we trained spiking neural networks on tasks with varying temporal complexity, holding different parameter subsets constant. We found that adapting conduction delays is crucial for solving all test conditions under tight resource constraints. Remarkably, these tasks can be solved using only temporal parameters (delays and time constants) with constant weights. In more complex spatio-temporal tasks, an adaptable bursting parameter was essential. Overall, allowing adaptation of both temporal and spatial parameters enhances network robustness to noise, a vital feature for biological brains and neuromorphic computing systems. Our findings suggest that rich and adaptable dynamics may be the key for solving temporally structured tasks efficiently in evolving organisms, which would help explain the diverse physiological properties of biological neurons.

Karim G. Habashy, Benjamin D. Evans, Dan F. M. Goodman, Jeffrey S. Bowers1/14/2025

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.

Amber Hu, David Zoltowski, Aditya Nair, David Anderson, Lea Duncker, Scott Linderman1/14/2025

arXiv:2409.08303v2 Announce Type: replace-cross Abstract: Motor dysfunction is a common sign of neurodegenerative diseases (NDs) such as Parkinson's disease (PD) and Alzheimer's disease (AD), but may be difficult to detect, especially in the early stages. In this work, we examine the behavior of a wide array of explainable metrics extracted from the handwriting signals of 113 subjects performing multiple tasks on a digital tablet, as part of the Neurological Signals dataset. The aim is to measure their effectiveness in characterizing NDs, including AD and PD. To this end, task-agnostic and task-specific metrics are extracted from 14 distinct tasks. Subsequently, through statistical analysis and a series of classification experiments, we investigate which metrics provide greater discriminative power between NDs and healthy controls and amongst different NDs. Preliminary results indicate that the tasks at hand can all be effectively leveraged to distinguish between the considered set of NDs, specifically by measuring the stability, the speed of writing, the time spent not writing, and the pressure variations between groups from our handcrafted explainable metrics, which shows p-values lower than 0.0001 for multiple tasks. Using various binary classification algorithms on the computed metrics, we obtain up to 87 % accuracy for the discrimination between AD and healthy controls (CTL), and up to 69 % for the discrimination between PD and CTL.

Thomas Thebaud, Anna Favaro, Casey Chen, Gabrielle Chavez, Laureano Moro-Velazquez, Ankur Butala, Najim Dehak1/14/2025

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.

Patrick Styll, Dowon Kim, Jiook Cha1/14/2025

arXiv:2501.03246v1 Announce Type: cross Abstract: Understanding the neural mechanisms behind auditory and linguistic processing is key to advancing cognitive neuroscience. In this study, we use Magnetoencephalography (MEG) data to analyze brain responses to spoken language stimuli. We develop two distinct encoding models: an audio-to-MEG encoder, which uses time-frequency decompositions (TFD) and wav2vec2 latent space representations, and a text-to-MEG encoder, which leverages CLIP and GPT-2 embeddings. Both models successfully predict neural activity, demonstrating significant correlations between estimated and observed MEG signals. However, the text-to-MEG model outperforms the audio-based model, achieving higher Pearson Correlation (PC) score. Spatially, we identify that auditory-based embeddings (TFD and wav2vec2) predominantly activate lateral temporal regions, which are responsible for primary auditory processing and the integration of auditory signals. In contrast, textual embeddings (CLIP and GPT-2) primarily engage the frontal cortex, particularly Broca's area, which is associated with higher-order language processing, including semantic integration and language production, especially in the 8-30 Hz frequency range. The strong involvement of these regions suggests that auditory stimuli are processed through more direct sensory pathways, while linguistic information is encoded via networks that integrate meaning and cognitive control. Our results reveal distinct neural pathways for auditory and linguistic information processing, with higher encoding accuracy for text representations in the frontal regions. These insights refine our understanding of the brain's functional architecture in processing auditory and textual information, offering quantitative advancements in the modelling of neural responses to complex language stimuli.

Matteo Ciferri, Matteo Ferrante, Nicola Toschi1/8/2025

arXiv:2501.03571v1 Announce Type: new Abstract: Auditory attention decoding from electroencephalogram (EEG) could infer to which source the user is attending in noisy environments. Decoding algorithms and experimental paradigm designs are crucial for the development of technology in practical applications. To simulate real-world scenarios, this study proposed a cue-masked auditory attention paradigm to avoid information leakage before the experiment. To obtain high decoding accuracy with low latency, an end-to-end deep learning model, AADNet, was proposed to exploit the spatiotemporal information from the short time window of EEG signals. The results showed that with a 0.5-second EEG window, AADNet achieved an average accuracy of 93.46% and 91.09% in decoding auditory orientation attention (OA) and timbre attention (TA), respectively. It significantly outperformed five previous methods and did not need the knowledge of the original audio source. This work demonstrated that it was possible to detect the orientation and timbre of auditory attention from EEG signals fast and accurately. The results are promising for the real-time multi-property auditory attention decoding, facilitating the application of the neuro-steered hearing aids and other assistive listening devices.

Keren Shi, Xu Liu, Xue Yuan, Haijie Shang, Ruiting Dai, Hanbin Wang, Yunfa Fu, Ning Jiang, Jiayuan He1/8/2025

arXiv:2403.20177v3 Announce Type: replace Abstract: The pursuit of artificial consciousness requires conceptual clarity to navigate its theoretical and empirical challenges. This paper introduces a composite, multilevel, and multidimensional model of consciousness as a heuristic framework to guide research in this field. Consciousness is treated as a complex phenomenon, with distinct constituents and dimensions that can be operationalized for study and for evaluating their replication. We argue that this model provides a balanced approach to artificial consciousness research by avoiding binary thinking (e.g., conscious vs. non-conscious) and offering a structured basis for testable hypotheses. To illustrate its utility, we focus on "awareness" as a case study, demonstrating how specific dimensions of consciousness can be pragmatically analyzed and targeted for potential artificial instantiation. By breaking down the conceptual intricacies of consciousness and aligning them with practical research goals, this paper lays the groundwork for a robust strategy to advance the scientific and technical understanding of artificial consciousness.

K. Evers, M. Farisco, R. Chatila, B. D. Earp, I. T. Freire, F. Hamker, E. Nemeth, P. F. M. J. Verschure, M. Khamassi1/3/2025

arXiv:2501.01022v1 Announce Type: new Abstract: Reconstructing the intricate local morphology of neurons and their long-range projecting axons can address many connectivity related questions in neuroscience. The main bottleneck in connectomics pipelines is correcting topological errors, as multiple entangled neuronal arbors is a challenging instance segmentation problem. More broadly, segmentation of curvilinear, filamentous structures continues to pose significant challenges. To address this problem, we extend the notion of simple points from digital topology to connected sets of voxels (i.e. supervoxels) and propose a topology-aware neural network segmentation method with minimal computational overhead. We demonstrate its effectiveness on a new public dataset of 3-d light microscopy images of mouse brains, along with the benchmark datasets DRIVE, ISBI12, and CrackTree.

Anna Grim, Jayaram Chandrashekar, Uygar Sumbul1/3/2025

arXiv:2412.18445v1 Announce Type: new Abstract: Vection, the visual illusion of self-motion, provides a strong marker of the VR user experience and plays an important role in both presence and cybersickness. Traditional measurements have been conducted using questionnaires, which exhibit inherent limitations due to their subjective nature and preventing real-time adjustments. Detecting vection in real time would allow VR systems to adapt to users' needs, improving comfort and minimizing negative effects like motion sickness. This paper investigates the presence of vection markers in electroencephalogram (EEG) brain signals using evoked potentials (brain responses to external stimulations). We designed a VR experiment that induces vection using two conditions: (1) forward acceleration or (2) backward acceleration. We recorded both electroencephalographic (EEG) signals and gathered subjective reports on thirty (30) participants. We found an evoked potential of vection characterized by a positive peak around 600 ms (P600) after stimulus onset in the parietal region and a simultaneous negative peak in the frontal region. Our results also found participant variability in sensitivity to vection and cybersickness and EEG markers of acceleration across subjects. This result is promising for potential detection of vection using EEG and paves the way for future studies towards a better understanding of vection. It also provides insights into the functional role of the visual system and its integration with the vestibular system during motion-perception. It has the potential to help enhance VR user experience by qualifying users' perceived vection and adapting the VR environments accordingly.

Ga\"el Van der Lee, Anatole L\'ecuyer, Maxence Naud, Reinhold Scherer, Fran\c{c}ois Cabestaing, Hakim Si-Mohammed12/25/2024

arXiv:2412.18354v1 Announce Type: new Abstract: Artificial intelligence has advanced rapidly in the last decade, driven primarily by progress in the scale of deep-learning systems. Despite these advances, the creation of intelligent systems that can operate effectively in diverse, real-world environments remains a significant challenge. In this white paper, we outline the Thousand Brains Project, an ongoing research effort to develop an alternative, complementary form of AI, derived from the operating principles of the neocortex. We present an early version of a thousand-brains system, a sensorimotor agent that is uniquely suited to quickly learn a wide range of tasks and eventually implement any capabilities the human neocortex has. Core to its design is the use of a repeating computational unit, the learning module, modeled on the cortical columns found in mammalian brains. Each learning module operates as a semi-independent unit that can model entire objects, represents information through spatially structured reference frames, and both estimates and is able to effect movement in the world. Learning is a quick, associative process, similar to Hebbian learning in the brain, and leverages inductive biases around the spatial structure of the world to enable rapid and continual learning. Multiple learning modules can interact with one another both hierarchically and non-hierarchically via a "cortical messaging protocol" (CMP), creating more abstract representations and supporting multimodal integration. We outline the key principles motivating the design of thousand-brains systems and provide details about the implementation of Monty, our first instantiation of such a system. Code can be found at https://github.com/thousandbrainsproject/tbp.monty, along with more detailed documentation at https://thousandbrainsproject.readme.io/.

Viviane Clay, Niels Leadholm, Jeff Hawkins12/25/2024

arXiv:2412.16231v1 Announce Type: new Abstract: Cognition and emotion must be partnered in any complete model of a humanlike mind. This article proposes an extension to the Common Model of Cognition -- a developing consensus concerning what is required in such a mind -- for emotion that includes a linked pair of modules for emotion and metacognitive assessment, plus pervasive connections between these two new modules and the Common Model's existing modules and links.

Paul S. Rosenbloom, John E. Laird, Christian Lebiere, Andrea Stocco, Richard H. Granger, Christian Huyck12/24/2024