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Andreas Tolias

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10 papers

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NeurIPS Conference 2025 Conference Paper

Learning to cluster neuronal function

Nina Nellen
Polina Turishcheva
Michaela Vystrčilová
Shashwat Sridhar
Tim Gollisch
Andreas Tolias
Alexander Ecker

Deep neural networks trained to predict neural activity from visual input and behaviour have shown great potential to serve as digital twins of the visual cortex. Per-neuron embeddings derived from these models could potentially be used to map the functional landscape or identify cell types. However, state-of-the-art predictive models of mouse V1 do not generate functional embeddings that exhibit clear clustering patterns which would correspond to cell types. This raises the question whether the lack of clustered structure is due to limitations of current models or a true feature of the functional organization of mouse V1. In this work, we introduce DECEMber -- Deep Embedding Clustering via Expectation Maximization-based refinement -- an explicit inductive bias into predictive models that enhances clustering by adding an auxiliary $t$-distribution-inspired loss function that enforces structured organization among per-neuron embeddings. We jointly optimize both neuronal feature embeddings and clustering parameters, updating cluster centers and scale matrices using the EM-algorithm. We demonstrate that these modifications improve cluster consistency while preserving high predictive performance and surpassing standard clustering methods in terms of stability. Moreover, DECEMber generalizes well across species (mice, primates) and visual areas (retina, V1, V4). The code is available at https: //github. com/Nisone2000/DECEMber, https: //github. com/ecker-lab/cnn-training.

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NeurIPS Conference 2025 Conference Paper

TRACE: Contrastive learning for multi-trial time series data in neuroscience

Lisa Schmors
Dominic Gonschorek
Jan Niklas Böhm
Yongrong Qiu
Na Zhou
Dmitry Kobak
Andreas Tolias
Fabian Sinz

Modern neural recording techniques such as two-photon imaging or Neuropixel probes allow to acquire vast time-series datasets with responses of hundreds or thousands of neurons. Contrastive learning is a powerful self-supervised framework for learning representations of complex datasets. Existing applications for neural time series rely on generic data augmentations and do not exploit the multi-trial data structure inherent in many neural datasets. Here we present TRACE, a new contrastive learning framework that averages across different subsets of trials to generate positive pairs. TRACE allows to directly learn a two-dimensional embedding, combining ideas from contrastive learning and neighbor embeddings. We show that TRACE outperforms other methods, resolving fine response differences in simulated data. Further, using in vivo recordings, we show that the representations learned by TRACE capture both biologically relevant continuous variation, cell-type-related cluster structure, and can assist data quality control.

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NeurIPS Conference 2023 Conference Paper

Energy Guided Diffusion for Generating Neurally Exciting Images

Pawel Pierzchlewicz
Konstantin Willeke
Arne Nix
Pavithra Elumalai
Kelli Restivo
Tori Shinn
Cate Nealley
Gabrielle Rodriguez

In recent years, most exciting inputs (MEIs) synthesized from encoding models of neuronal activity have become an established method for studying tuning properties of biological and artificial visual systems. However, as we move up the visual hierarchy, the complexity of neuronal computations increases. Consequently, it becomes more challenging to model neuronal activity, requiring more complex models. In this study, we introduce a novel readout architecture inspired by the mechanism of visual attention. This new architecture, which we call attention readout, together with a data-driven convolutional core outperforms previous task-driven models in predicting the activity of neurons in macaque area V4. However, as our predictive network becomes deeper and more complex, synthesizing MEIs via straightforward gradient ascent (GA) can struggle to produce qualitatively good results and overfit to idiosyncrasies of a more complex model, potentially decreasing the MEI's model-to-brain transferability. To solve this problem, we propose a diffusion-based method for generating MEIs via Energy Guidance (EGG). We show that for models of macaque V4, EGG generates single neuron MEIs that generalize better across varying model architectures than the state-of-the-art GA, while at the same time reducing computational costs by a factor of 4. 7x, facilitating experimentally challenging closed-loop experiments. Furthermore, EGG diffusion can be used to generate other neurally exciting images, like most exciting naturalistic images that are on par with a selection of highly activating natural images, or image reconstructions that generalize better across architectures. Finally, EGG is simple to implement, requires no retraining of the diffusion model, and can easily be generalized to provide other characterizations of the visual system, such as invariances. Thus, EGG provides a general and flexible framework to study the coding properties of the visual system in the context of natural images.

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NeurIPS Conference 2023 Conference Paper

Taking the neural sampling code very seriously: A data-driven approach for evaluating generative models of the visual system

Suhas Shrinivasan
Konstantin-Klemens Lurz
Kelli Restivo
George Denfield
Andreas Tolias
Edgar Walker
Fabian Sinz

Prevailing theories of perception hypothesize that the brain implements perception via Bayesian inference in a generative model of the world. One prominent theory, the Neural Sampling Code (NSC), posits that neuronal responses to a stimulus represent samples from the posterior distribution over latent world state variables that cause the stimulus. Although theoretically elegant, NSC does not specify the exact form of the generative model or prescribe how to link the theory to recorded neuronal activity. Previous works assume simple generative models and test their qualitative agreement with neurophysiological data. Currently, there is no precise alignment of the normative theory with neuronal recordings, especially in response to natural stimuli, and a quantitative, experimental evaluation of models under NSC has been lacking. Here, we propose a novel formalization of NSC, that (a) allows us to directly fit NSC generative models to recorded neuronal activity in response to natural images, (b) formulate richer and more flexible generative models, and (c) employ standard metrics to quantitatively evaluate different generative models under NSC. Furthermore, we derive a stimulus-conditioned predictive model of neuronal responses from the trained generative model using our formalization that we compare to neural system identification models. We demonstrate our approach by fitting and comparing classical- and flexible deep learning-based generative models on population recordings from the macaque primary visual cortex (V1) to natural images, and show that the flexible models outperform classical models in both their generative- and predictive-model performance. Overall, our work is an important step towards a quantitative evaluation of NSC. It provides a framework that lets us \textit{learn} the generative model directly from neuronal population recordings, paving the way for an experimentally-informed understanding of probabilistic computational principles underlying perception and behavior.

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NeurIPS Conference 2021 Conference Paper

A flow-based latent state generative model of neural population responses to natural images

Mohammad Bashiri
Edgar Walker
Konstantin-Klemens Lurz
Akshay Jagadish
Taliah Muhammad
Zhiwei Ding
Zhuokun Ding
Andreas Tolias

We present a joint deep neural system identification model for two major sources of neural variability: stimulus-driven and stimulus-conditioned fluctuations. To this end, we combine (1) state-of-the-art deep networks for stimulus-driven activity and (2) a flexible, normalizing flow-based generative model to capture the stimulus-conditioned variability including noise correlations. This allows us to train the model end-to-end without the need for sophisticated probabilistic approximations associated with many latent state models for stimulus-conditioned fluctuations. We train the model on the responses of thousands of neurons from multiple areas of the mouse visual cortex to natural images. We show that our model outperforms previous state-of-the-art models in predicting the distribution of neural population responses to novel stimuli, including shared stimulus-conditioned variability. Furthermore, it successfully learns known latent factors of the population responses that are related to behavioral variables such as pupil dilation, and other factors that vary systematically with brain area or retinotopic location. Overall, our model accurately accounts for two critical sources of neural variability while avoiding several complexities associated with many existing latent state models. It thus provides a useful tool for uncovering the interplay between different factors that contribute to variability in neural activity.

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NeurIPS Conference 2021 Conference Paper

Towards robust vision by multi-task learning on monkey visual cortex

Shahd Safarani
Arne Nix
Konstantin Willeke
Santiago Cadena
Kelli Restivo
George Denfield
Andreas Tolias
Fabian Sinz

Deep neural networks set the state-of-the-art across many tasks in computer vision, but their generalization ability to simple image distortions is surprisingly fragile. In contrast, the mammalian visual system is robust to a wide range of perturbations. Recent work suggests that this generalization ability can be explained by useful inductive biases encoded in the representations of visual stimuli throughout the visual cortex. Here, we successfully leveraged these inductive biases with a multi-task learning approach: we jointly trained a deep network to perform image classification and to predict neural activity in macaque primary visual cortex (V1) in response to the same natural stimuli. We measured the out-of-distribution generalization abilities of our resulting network by testing its robustness to common image distortions. We found that co-training on monkey V1 data indeed leads to increased robustness despite the absence of those distortions during training. Additionally, we showed that our network's robustness is often very close to that of an Oracle network where parts of the architecture are directly trained on noisy images. Our results also demonstrated that the network's representations become more brain-like as their robustness improves. Using a novel constrained reconstruction analysis, we investigated what makes our brain-regularized network more robust. We found that our monkey co-trained network is more sensitive to content than noise when compared to a Baseline network that we trained for image classification alone. Using DeepGaze-predicted saliency maps for ImageNet images, we found that the monkey co-trained network tends to be more sensitive to salient regions in a scene, reminiscent of existing theories on the role of V1 in the detection of object borders and bottom-up saliency. Overall, our work expands the promising research avenue of transferring inductive biases from biological to artificial neural networks on the representational level, and provides a novel analysis of the effects of our transfer.

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NeurIPS Conference 2020 Conference Paper

Factorized Neural Processes for Neural Processes: K-Shot Prediction of Neural Responses

Ronald (James) Cotton
Fabian Sinz
Andreas Tolias

In recent years, artificial neural networks have achieved state-of-the-art performance for predicting the responses of neurons in the visual cortex to natural stimuli. However, they require a time consuming parameter optimization process for accurately modeling the tuning function of newly observed neurons, which prohibits many applications including real-time, closed-loop experiments. We overcome this limitation by formulating the problem as $K$-shot prediction to directly infer a neuron's tuning function from a small set of stimulus-response pairs using a Neural Process. This required us to developed a Factorized Neural Process, which embeds the observed set into a latent space partitioned into the receptive field location and the tuning function properties. We show on simulated responses that the predictions and reconstructed receptive fields from the Factorized Neural Process approach ground truth with increasing number of trials. Critically, the latent representation that summarizes the tuning function of a neuron is inferred in a quick, single forward pass through the network. Finally, we validate this approach on real neural data from visual cortex and find that the predictive accuracy is comparable to --- and for small $K$ even greater than --- optimization based approaches, while being substantially faster. We believe this novel deep learning systems identification framework will facilitate better real-time integration of artificial neural network modeling into neuroscience experiments.

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NeurIPS Conference 2019 Conference Paper

Learning from brains how to regularize machines

Zhe Li
Wieland Brendel
Edgar Walker
Erick Cobos
Taliah Muhammad
Jacob Reimer
Matthias Bethge
Fabian Sinz

Despite impressive performance on numerous visual tasks, Convolutional Neural Networks (CNNs) --- unlike brains --- are often highly sensitive to small perturbations of their input, e. g. adversarial noise leading to erroneous decisions. We propose to regularize CNNs using large-scale neuroscience data to learn more robust neural features in terms of representational similarity. We presented natural images to mice and measured the responses of thousands of neurons from cortical visual areas. Next, we denoised the notoriously variable neural activity using strong predictive models trained on this large corpus of responses from the mouse visual system, and calculated the representational similarity for millions of pairs of images from the model's predictions. We then used the neural representation similarity to regularize CNNs trained on image classification by penalizing intermediate representations that deviated from neural ones. This preserved performance of baseline models when classifying images under standard benchmarks, while maintaining substantially higher performance compared to baseline or control models when classifying noisy images. Moreover, the models regularized with cortical representations also improved model robustness in terms of adversarial attacks. This demonstrates that regularizing with neural data can be an effective tool to create an inductive bias towards more robust inference.

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NeurIPS Conference 2018 Conference Paper

Stimulus domain transfer in recurrent models for large scale cortical population prediction on video

Fabian Sinz
Alexander Ecker
Paul Fahey
Edgar Walker
Erick Cobos
Emmanouil Froudarakis
Dimitri Yatsenko
Zachary Pitkow

To better understand the representations in visual cortex, we need to generate better predictions of neural activity in awake animals presented with their ecological input: natural video. Despite recent advances in models for static images, models for predicting responses to natural video are scarce and standard linear-nonlinear models perform poorly. We developed a new deep recurrent network architecture that predicts inferred spiking activity of thousands of mouse V1 neurons simultaneously recorded with two-photon microscopy, while accounting for confounding factors such as the animal's gaze position and brain state changes related to running state and pupil dilation. Powerful system identification models provide an opportunity to gain insight into cortical functions through in silico experiments that can subsequently be tested in the brain. However, in many cases this approach requires that the model is able to generalize to stimulus statistics that it was not trained on, such as band-limited noise and other parameterized stimuli. We investigated these domain transfer properties in our model and find that our model trained on natural images is able to correctly predict the orientation tuning of neurons in responses to artificial noise stimuli. Finally, we show that we can fully generalize from movies to noise and maintain high predictive performance on both stimulus domains by fine-tuning only the final layer's weights on a network otherwise trained on natural movies. The converse, however, is not true.

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NeurIPS Conference 2003 Conference Paper

Prediction on Spike Data Using Kernel Algorithms

Jan Eichhorn
Andreas Tolias
Alexander Zien
Malte Kuss
Jason Weston
Nikos Logothetis
Bernhard Schölkopf
Carl Rasmussen

We report and compare the performance of different learning algorithms based on data from cortical recordings. The task is to predict the orienta- tion of visual stimuli from the activity of a population of simultaneously recorded neurons. We compare several ways of improving the coding of the input (i. e. , the spike data) as well as of the output (i. e. , the orienta- tion), and report the results obtained using different kernel algorithms.

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