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1. System identification of neural systems: If we got it right, would we know?

   Han, Yena; Poggio, Tomaso; Cheung, Brian (July 2022, Center for Brains, Minds and Machines (CBMM))

   Various artificial neural networks developed by engineers have been evaluated as models of the brain, such as the ventral stream in the primate visual cortex. After being trained on large datasets, the network outputs are compared to recordings of biological neurons. Good performance in reproducing neural responses is taken as validation for the model. This system identification approach is different from the traditional ways to test theories and associated models in the natural sciences. Furthermore, it lacks a clear foundation in terms of theory and empirical validation. Here we begin characterizing some of these emerging approaches: what do they tell us? To address this question, we benchmark their ability to correctly identify a model by replacing the brain recordings with recordings from a known ground truth model. We evaluate commonly used identification techniques such as neural regression (linear regression on a population of model units) and centered kernel alignment (CKA). Even in the setting where the correct model is among the candidates, we find that the performance of these approaches at system identification is quite variable; it also depends significantly on factors independent of the ground truth architecture, such as scoring function and dataset. 

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2. Mapping epileptic directional brain networks using intracranial EEG data

   https://doi.org/10.1093/biostatistics/kxz056  

   Li, Huazhang; Wang, Yaotian; Tanabe, Seiji; Sun, Yinge; Yan, Guofen; Quigg, Mark S.; Zhang, Tingting (December 2019, Biostatistics)

   Summary The human brain is a directional network system, in which brain regions are network nodes and the influence exerted by one region on another is a network edge. We refer to this directional information flow from one region to another as directional connectivity. Seizures arise from an epileptic directional network; abnormal neuronal activities start from a seizure onset zone and propagate via a network to otherwise healthy brain regions. As such, effective epilepsy diagnosis and treatment require accurate identification of directional connections among regions, i.e., mapping of epileptic patients’ brain networks. This article aims to understand the epileptic brain network using intracranial electroencephalographic data—recordings of epileptic patients’ brain activities in many regions. The most popular models for directional connectivity use ordinary differential equations (ODE). However, ODE models are sensitive to data noise and computationally costly. To address these issues, we propose a high-dimensional state-space multivariate autoregression (SSMAR) model for the brain’s directional connectivity. Different from standard multivariate autoregression and SSMAR models, the proposed SSMAR features a cluster structure, where the brain network consists of several clusters of densely connected brain regions. We develop an expectation–maximization algorithm to estimate the proposed model and use it to map the interregional networks of epileptic patients in different seizure stages. Our method reveals the evolution of brain networks during seizure development. 

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3. Benefits of Synthetically Pre-trained Depth-Prediction Networks for Indoor/Outdoor Image Classification

   https://doi.org/10.1109/WACVW58289.2023.00040  

   Lin, Kelly X.; Cho, Irene; Walimbe, Amey; Zamora, Bryan A.; Rich, Alex; Zhang, Sirius Z.; Höllerer, Tobias (January 2023, 2023 IEEE/CVF Winter Conference on Applications of Computer Vision Workshops (WACVW))

   Ground truth depth information is necessary for many computer vision tasks. Collecting this information is chal-lenging, especially for outdoor scenes. In this work, we propose utilizing single-view depth prediction neural networks pre-trained on synthetic scenes to generate relative depth, which we call pseudo-depth. This approach is a less expen-sive option as the pre-trained neural network obtains ac-curate depth information from synthetic scenes, which does not require any expensive sensor equipment and takes less time. We measure the usefulness of pseudo-depth from pre-trained neural networks by training indoor/outdoor binary classifiers with and without it. We also compare the difference in accuracy between using pseudo-depth and ground truth depth. We experimentally show that adding pseudo-depth to training achieves a 4.4% performance boost over the non-depth baseline model on DIODE, a large stan-dard test dataset, retaining 63.8% of the performance boost achieved from training a classifier on RGB and ground truth depth. It also boosts performance by 1.3% on another dataset, SUN397, for which ground truth depth is not avail-able. Our result shows that it is possible to take information obtained from a model pre-trained on synthetic scenes and successfully apply it beyond the synthetic domain to real-world data. 

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4. Hierarchical VAEs provide a normative account of motion processing in the primate brain

   Vafaii, H; Yates, Jacob L; Butts, Daniel A (December 2023, Advances in Neural Information Processing Systems (Curran Associates, Inc.))

   Oh, A; Naumann, T; Globerson, A; Saenko, K; Hardt, M; Levine, S (Ed.)

   The relationship between perception and inference, as postulated by Helmholtz in the 19th century, is paralleled in modern machine learning by generative models like Variational Autoencoders (VAEs) and their hierarchical variants. Here, we evaluate the role of hierarchical inference and its alignment with brain function in the domain of motion perception. We first introduce a novel synthetic data framework, Retinal Optic Flow Learning (ROFL), which enables control over motion statistics and their causes. We then present a new hierarchical VAE and test it against alternative models on two downstream tasks: (i) predicting ground truth causes of retinal optic flow (e.g., self-motion); and (ii) predicting the responses of neurons in the motion processing pathway of primates. We manipulate the model architectures (hierarchical versus non-hierarchical), loss functions, and the causal structure of the motion stimuli. We find that hierarchical latent structure in the model leads to several improvements. First, it improves the linear decodability of ground truth factors and does so in a sparse and disentangled manner. Second, our hierarchical VAE outperforms previous state-of-the-art models in predicting neuronal responses and exhibits sparse latent-to-neuron relationships. These results depend on the causal structure of the world, indicating that alignment between brains and artificial neural networks depends not only on architecture but also on matching ecologically relevant stimulus statistics. Taken together, our results suggest that hierarchical Bayesian inference underlines the brain’s understanding of the world, and hierarchical VAEs can effectively model this understanding. 

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5. CREIMBO: Cross-Regional Ensemble Interactions in Multi-view Brain Observations

   Mudrik, Noga; Ly, Ryan; Ruebel, Oliver; Charles, Adam S (January 2025, The International Conference on Learning Representations)

   Modern recordings of neural activity provide diverse observations of neurons across brain areas, behavioral conditions, and subjects; presenting an exciting opportunity to reveal the fundamentals of brain-wide dynamics. Current analysis methods, however, often fail to fully harness the richness of such data, as they provide either uninterpretable representations (e.g., via deep networks) or oversimplify models (e.g., by assuming stationary dynamics or analyzing each session independently). Here, instead of regarding asynchronous neural recordings that lack alignment in neural identity or brain areas as a limitation, we leverage these diverse views into the brain to learn a unified model of neural dynamics. Specifically, we assume that brain activity is driven by multiple hidden global sub-circuits. These sub-circuits represent global basis interactions between neural ensembles—functional groups of neurons—such that the time-varying decomposition of these sub-circuits defines how the ensembles’ interactions evolve over time non-stationarily and non-linearly. We discover the neural ensembles underlying non-simultaneous observations, along with their non-stationary evolving interactions, with our new model, CREIMBO (Cross-Regional Ensemble Interactions in Multi-view Brain Observations). CREIMBO identifies the hidden composition of per-session neural ensembles through novel graph-driven dictionary learning and models the ensemble dynamics on a low-dimensional manifold spanned by a sparse time-varying composition of the global sub-circuits. Thus, CREIMBO disentangles overlapping temporal neural processes while preserving interpretability due to the use of a shared underlying sub-circuit basis. Moreover, CREIMBO distinguishes session-specific computations from global (session-invariant) ones by identifying session covariates and variations in sub-circuit activations. We demonstrate CREIMBO’s ability to recover true components in synthetic data, and uncover meaningful brain dynamics in human high-density electrode recordings, including cross-subject neural mechanisms as well as inter- vs. intra-region dynamical motifs. Furthermore, using mouse whole-brain recordings, we show CREIMBO’s ability to discover dynamical interactions that capture task and behavioral variables and meaningfully align with the biological importance of the brain areas they represent 

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