arXiv subjects

Konstantin Anokhin

Publications and source records attributed to Konstantin Anokhin.

4 recordsLinked to original sources

arXiv2026

DRIADA: A Python Toolkit for Cross-Scale Analysis of Single-Neuron Selectivity and Population Dynamics

Brain activity spans single-neuron, population, and network levels, and core questions in neural coding require moving between them. Yet current tools target a single paradigm and incompatible data formats, leaving cross-level questions hard to address. We present DRIADA, an open-source Python framework that unifies neural signals and time-aligned behavior in a shared data model, so selectivity testing, dimensionality reduction, and network analysis operate within a unified workflow. We evaluate it on synthetic data with known ground truth, hippocampal calcium imaging from 13~mice in an open field, and a simulated toroidal attractor network. In the hippocampal data, selectivity-based filtering restored a two-dimensional spatial embedding from a collapsed all-neuron embedding, while reverse analysis showed that ${\sim}57\%$ of neurons informative about leading manifold dimensions were not selective to any of the 11 measured behavioral features. On the toroidal benchmark, four independent modules recovered the expected topology. DRIADA makes cross-scale analysis routine across calcium imaging, spike trains, and simulated networks.

q-bio.NC↗

arXiv2026

INTENSE: Detecting and disentangling neuronal selectivity in calcium imaging data

Neurons encode information about the environment through their activity. As animals explore the environment, neurons rapidly acquire selectivity for distinct features of the external world; characterizing how these selectivity patterns emerge, reorganize, and overlap is key to linking neural activity to behavior and cognition. Calcium imaging in freely behaving animals can record large neuronal populations, but quantifying neuron-behavior selectivity directly from continuous fluorescence is challenging because both signals are temporally autocorrelated and calcium kinetics introduce time lags. Here we present INTENSE (INformation-Theoretic Evaluation of Neuronal SElectivity), an open-source framework that uses mutual information to detect neuron-behavior associations from raw calcium fluorescence data. INTENSE controls false discoveries using circular-shift permutation testing that preserves temporal structure and optimizes temporal delays to account for indicator kinetics and prospective/retrospective encoding. To separate genuine mixed selectivity from associations driven by behavioral covariance, INTENSE applies conditional mutual information-based disentanglement. We validated INTENSE on synthetic datasets, demonstrating robust detection across diverse signal-to-noise ratios and reliability conditions, whereas methods lacking temporal controls show poor performance. Applied to CA1 miniscope recordings in mice freely exploring an open field, INTENSE reveals robust selectivity to multiple variables (place, head direction, object interaction, locomotion) and refines mixed-selectivity estimates by distinguishing redundant from genuinely multi-variable encoding. Together, INTENSE enables high-throughput, information-theoretic selectivity mapping with principled control of temporal structure and behavioral covariance, bridging large-scale recordings to circuit-level hypotheses.

q-bio.NC↗

arXiv2024

Fast gradient-free activation maximization for neurons in spiking neural networks

Elements of neural networks, both biological and artificial, can be described by their selectivity for specific cognitive features. Understanding these features is important for understanding the inner workings of neural networks. For a living system, such as a neuron, whose response to a stimulus is unknown and not differentiable, the only way to reveal these features is through a feedback loop that exposes it to a large set of different stimuli. The properties of these stimuli should be varied iteratively in order to maximize the neuronal response. To utilize this feedback loop for a biological neural network, it is important to run it quickly and efficiently in order to reach the stimuli that maximizes certain neurons' activation with the least number of iterations possible. Here we present a framework with an efficient design for such a loop. We successfully tested it on an artificial spiking neural network (SNN), which is a model that simulates the asynchronous spiking activity of neurons in living brains. Our optimization method for activation maximization is based on the low-rank Tensor Train decomposition of the discrete activation function. The optimization space is the latent parameter space of images generated by SN-GAN or VQ-VAE generative models. To our knowledge, this is the first time that effective AM has been applied to SNNs. We track changes in the optimal stimuli for artificial neurons during training and show that highly selective neurons can form already in the early epochs of training and in the early layers of a convolutional spiking network. This formation of refined optimal stimuli is associated with an increase in classification accuracy. Some neurons, especially in the deeper layers, may gradually change the concepts they are selective for during learning, potentially explaining their importance for model performance.

cs.NE↗

arXiv2022

Topology of cognitive maps

In present paper we discuss several approaches to reconstructing the topology of the physical space from neural activity data of CA1 fields in mice hippocampus, in particular, having Cognitome theory of brain function in mind. In our experiments, animals were placed in different new environments and discovered these moving freely while their physical and neural activity was recorded. We test possible approaches to identifying place cell groups out of the observed CA1 neurons. We also test and discuss various methods of dimension reduction and topology reconstruction. In particular, two main strategies we focus on are the Nerve theorem and point cloud-based methods. Conclusions on the results of reconstruction are supported with illustrations and mathematical background which is also briefly discussed.

q-bio.NC↗