q-bio.NC

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.

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.

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/.

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.

arXiv:2412.01110v3 Announce Type: replace-cross Abstract: Statistical physics provides tools for analyzing high-dimensional problems in machine learning and theoretical neuroscience. These calculations, particularly those using the replica method, often involve lengthy derivations that can obscure physical interpretation. We give concise, non-replica derivations of several key results and highlight their underlying similarities. Specifically, we introduce a cavity approach to analyzing high-dimensional learning problems and apply it to three cases: perceptron classification of points, perceptron classification of manifolds, and kernel ridge regression. These problems share a common structure -- a bipartite system of interacting feature and datum variables -- enabling a unified analysis. For perceptron-capacity problems, we identify a symmetry that allows derivation of correct capacities through a na\"ive method. These results match those obtained through the replica method.

arXiv:2412.17227v1 Announce Type: new Abstract: Speech brain-computer interfaces aim to decipher what a person is trying to say from neural activity alone, restoring communication to people with paralysis who have lost the ability to speak intelligibly. The Brain-to-Text Benchmark '24 and associated competition was created to foster the advancement of decoding algorithms that convert neural activity to text. Here, we summarize the lessons learned from the competition ending on June 1, 2024 (the top 4 entrants also presented their experiences in a recorded webinar). The largest improvements in accuracy were achieved using an ensembling approach, where the output of multiple independent decoders was merged using a fine-tuned large language model (an approach used by all 3 top entrants). Performance gains were also found by improving how the baseline recurrent neural network (RNN) model was trained, including by optimizing learning rate scheduling and by using a diphone training objective. Improving upon the model architecture itself proved more difficult, however, with attempts to use deep state space models or transformers not yet appearing to offer a benefit over the RNN baseline. The benchmark will remain open indefinitely to support further work towards increasing the accuracy of brain-to-text algorithms.

arXiv:2412.16773v1 Announce Type: cross Abstract: Gaussian processes are now commonly used in dimensionality reduction approaches tailored to neuroscience, especially to describe changes in high-dimensional neural activity over time. As recording capabilities expand to include neuronal populations across multiple brain areas, cortical layers, and cell types, interest in extending Gaussian process factor models to characterize multi-population interactions has grown. However, the cubic runtime scaling of current methods with the length of experimental trials and the number of recorded populations (groups) precludes their application to large-scale multi-population recordings. Here, we improve this scaling from cubic to linear in both trial length and group number. We present two approximate approaches to fitting multi-group Gaussian process factor models based on (1) inducing variables and (2) the frequency domain. Empirically, both methods achieved orders of magnitude speed-up with minimal impact on statistical performance, in simulation and on neural recordings of hundreds of neurons across three brain areas. The frequency domain approach, in particular, consistently provided the greatest runtime benefits with the fewest trade-offs in statistical performance. We further characterize the estimation biases introduced by the frequency domain approach and demonstrate effective strategies to mitigate them. This work enables a powerful class of analysis techniques to keep pace with the growing scale of multi-population recordings, opening new avenues for exploring brain function.

arXiv:2410.00332v3 Announce Type: replace Abstract: Conservation is a critical milestone of cognitive development considered to be supported by both the understanding of quantitative concepts and the reversibility of mental operations. To assess whether this critical component of human intelligence has emerged in Vision Language Models, we have curated the ConserveBench, a battery of 365 cognitive experiments across four dimensions of physical quantities: volume, solid quantity, length, and number. The former two involve only transformational tasks, whereas the latter two involve non-transformational tasks assessing the understanding of quantitative concepts alone. Surprisingly, we find that while Vision Language Models are generally capable of conserving, they tend to fail at non-transformational tasks whose successes are typically considered to be evidence of the ability to conserve. This implies that the law of conservation, at least in concrete domains, may exist without corresponding conceptual understanding of quantity. $\href{https://growing-ai-like-a-child.github.io/pages/Conservation/}{Website}$

arXiv:2410.24070v4 Announce Type: replace Abstract: Methods for analyzing representations in neural systems have become a popular tool in both neuroscience and mechanistic interpretability. Having measures to compare how similar activations of neurons are across conditions, architectures, and species, gives us a scalable way of learning how information is transformed within different neural networks. In contrast to this trend, recent investigations have revealed how some metrics can respond to spurious signals and hence give misleading results. To identify the most reliable metric and understand how measures could be improved, it is going to be important to identify specific test cases which can serve as benchmarks. Here we propose that the phenomena of compositional learning in recurrent neural networks (RNNs) allows us to build a test case for dynamical representation alignment metrics. By implementing this case, we show it enables us to test whether metrics can identify representations which gradually develop throughout learning and probe whether representations identified by metrics are relevant to computations executed by networks. By building both an attractor- and RNN-based test case, we show that the new Dynamical Similarity Analysis (DSA) is more noise robust and identifies behaviorally relevant representations more reliably than prior metrics (Procrustes, CKA). We also show how test cases can be used beyond evaluating metrics to study new architectures. Specifically, results from applying DSA to modern (Mamba) state space models, suggest that, in contrast to RNNs, these models may not exhibit changes to their recurrent dynamics due to their expressiveness. Overall, by developing test cases, we show DSA's exceptional ability to detect compositional dynamical motifs, thereby enhancing our understanding of how computations unfold in RNNs.

arXiv:2412.02078v2 Announce Type: replace Abstract: In the application of brain-computer interface (BCI), while pursuing accurate decoding of brain signals, we also need consider the computational efficiency of BCI devices. ECoG signals are multi-channel temporal signals which is collected using a high-density electrode array at a high sampling frequency. The data between channels has a high similarity or redundancy in the temporal domain. The redundancy of data not only reduces the computational efficiency of the model, but also overwhelms the extraction of effective features, resulting in a decrease in performance. How to efficiently utilize ECoG multi-channel signals is one of the research topics. Effective channel screening or compression can greatly reduce the model size, thereby improving computational efficiency, this would be a good direction to solve the problem. Based on previous work [1], this paper proposes a very simple channel compression method, which uses a learnable matrix to perform matrix multiplication on the original channels, that is, assigning weights to the channels and then linearly add them up. This effectively reduces the number of final channels. In the experiment, we used the vision-based ECoG multi-classification dataset owned by our laboratory to test the proposed channel selection (compression) method. We found that the new method can compress the original 128-channel ECoG signal to 32 channels (of which subject MonJ is compressed to 8 channels), greatly reducing the size of the model. The demand for GPU memory resources during model training is reduced by about 68.57%, 84.33% for each subject respectively; the model training speed also increased up around 3.82, 4.65 times of the original speed for each subject respectively. More importantly, the performance of the model has improved by about 1.10% compared with our previous work, reached the SOTA level of our unique visual based ECoG dataset

arXiv:2304.13796v2 Announce Type: replace-cross Abstract: It has been proposed that information sharing, which is a ubiquitous and consequential behavior, plays a critical role in cultivating and maintaining a sense of shared reality. Across three studies, we tested this theory by investigating whether or not people are especially likely to share information that they believe will be interpreted similarly by others in their social circles. Using neuroimaging while members of the same community viewed brief film clips, we found that more similar neural responding of participants was associated with a greater likelihood to share content. We then tested this relationship using two behavioral studies and found (1) that people were particularly likely to share content that they believed others in their social circles would interpret similarly and (2) that perceived similarity with others leads to increased sharing likelihood. In concert, our findings support the idea that people are driven to share information to create and reinforce shared understanding, which is critical to social connection.

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.

arXiv:2412.15560v1 Announce Type: cross Abstract: Recent studies have demonstrated that the representations of artificial neural networks (ANNs) can exhibit notable similarities to cortical representations when subjected to identical auditory sensory inputs. In these studies, the ability to predict cortical representations is probed by regressing from ANN representations to cortical representations. Building upon this concept, our approach reverses the direction of prediction: we utilize ANN representations as a supervisory signal to train recognition models using noisy brain recordings obtained through non-invasive measurements. Specifically, we focus on constructing a recognition model for music identification, where electroencephalography (EEG) brain recordings collected during music listening serve as input. By training an EEG recognition model to predict ANN representations-representations associated with music identification-we observed a substantial improvement in classification accuracy. This study introduces a novel approach to developing recognition models for brain recordings in response to external auditory stimuli. It holds promise for advancing brain-computer interfaces (BCI), neural decoding techniques, and our understanding of music cognition. Furthermore, it provides new insights into the relationship between auditory brain activity and ANN representations.

arXiv:2412.15620v1 Announce Type: cross Abstract: The current study investigates possible neural mechanisms underling autonomous shifts between focus state and mind-wandering by conducting model simulation experiments. On this purpose, we modeled perception processes of continuous sensory sequences using our previous proposed variational RNN model which was developed based on the free energy principle. The current study extended this model by introducing an adaptation mechanism of a meta-level parameter, referred to as the meta-prior $\mathbf{w}$, which regulates the complexity term in the free energy. Our simulation experiments demonstrated that autonomous shifts between focused perception and mind-wandering take place when $\mathbf{w}$ switches between low and high values associated with decrease and increase of the average reconstruction error over the past window. In particular, high $\mathbf{w}$ prioritized top-down predictions while low $\mathbf{w}$ emphasized bottom-up sensations. This paper explores how our experiment results align with existing studies and highlights their potential for future research.

arXiv:2412.15818v1 Announce Type: cross Abstract: Although advances in brain surgery techniques have led to fewer postoperative complications requiring Intensive Care Unit (ICU) monitoring, the routine transfer of patients to the ICU remains the clinical standard, despite its high cost. Predictive Gradient Boosted Trees based on clinical data have attempted to optimize ICU admission by identifying key risk factors pre-operatively; however, these approaches overlook valuable imaging data that could enhance prediction accuracy. In this work, we show that multimodal approaches that combine clinical data with imaging data outperform the current clinical data only baseline from 0.29 [F1] to 0.30 [F1], when only pre-operative clinical data is used and from 0.37 [F1] to 0.41 [F1], for pre- and post-operative data. This study demonstrates that effective ICU admission prediction benefits from multimodal data fusion, especially in contexts of severe class imbalance.

arXiv:2402.07242v2 Announce Type: replace Abstract: There is a growing consensus among neuroscientists that many neural circuits critical for survival result from a process of genomic decompression, hence are constructed based on the information contained within the genome. Aligning with this perspective, we introduce SynaptoGen, a novel computational framework designed to bring the advent of synthetic biological intelligence closer, facilitating the development of neural biological agents through the precise control of genetic factors governing synaptogenesis. SynaptoGen represents the first model in the well-established family of Connectome Models (CMs) to offer a possible mechanistic explanation of synaptic multiplicity based on genetic expression and protein interaction probabilities, modeling connectivity with unprecedented granularity. Furthermore, SynaptoGen connects these genetic factors through a differentiable function, effectively working as a neural network in which each synaptic weight is computed as the average number of synapses between neurons, multiplied by its corresponding conductance, and derived from a specific genetic profile. Differentiability is a critical feature of the framework, enabling its integration with gradient-based optimization techniques. This allows SynaptoGen to generate patterns of genetic expression and/or genetic rules capable of producing pre-wired biological agents tailored to specific tasks. The framework is validated in simulated synaptogenesis scenarios with varying degrees of biological plausibility. It successfully produces biological agents capable of solving tasks in four different reinforcement learning benchmarks, consistently outperforming the state-of-the-art and a control baseline designed to represent populations of neurons where synapses form freely, i.e., without guided manipulations.

arXiv:2410.14697v2 Announce Type: replace-cross Abstract: The cortico-spinal neural pathway is fundamental for motor control and movement execution, and in humans it is typically studied using concurrent electroencephalography (EEG) and electromyography (EMG) recordings. However, current approaches for capturing high-level and contextual connectivity between these recordings have important limitations. Here, we present a novel application of statistical dependence estimators based on orthonormal decomposition of density ratios to model the relationship between cortical and muscle oscillations. Our method extends from traditional scalar-valued measures by learning eigenvalues, eigenfunctions, and projection spaces of density ratios from realizations of the signal, addressing the interpretability, scalability, and local temporal dependence of cortico-muscular connectivity. We experimentally demonstrate that eigenfunctions learned from cortico-muscular connectivity can accurately classify movements and subjects. Moreover, they reveal channel and temporal dependencies that confirm the activation of specific EEG channels during movement. Our code is available at https://github.com/bohu615/corticomuscular-eigen-encoder.

arXiv:2412.15279v1 Announce Type: new Abstract: The human brain is a complex system, and understanding its mechanisms has been a long-standing challenge in neuroscience. The study of the functional connectome, which maps the functional connections between different brain regions, has provided valuable insights through various advanced analysis techniques developed over the years. Similarly, neural networks, inspired by the brain's architecture, have achieved notable success in diverse applications but are often noted for their lack of interpretability. In this paper, we propose a novel approach that bridges neural networks and human brain functions by leveraging brain-inspired techniques. Our approach, grounded in the insights from the functional connectome, offers scalable ways to characterize topology of large neural networks using stable statistical and machine learning techniques. Our empirical analysis demonstrates its capability to enhance the interpretability of neural networks, providing a deeper understanding of their underlying mechanisms.