Ulisse Ferrari

dblp:140/4792 · DBLP profile ↗
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6ranked-venue papers
2as first author
3since 2021 · last 2025
0000-0002-3131-5537ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 4 · 1 first-author · 2 since 2021Applied, interdisciplinary, general and emerging computing · 2 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
2 papers
Bioinformatics and computational biology · 100%
Theoretical computer science
1 paper
Information theory · 100%
Artificial intelligence
1 paper
Probabilistic and Bayesian machine learning · 77% Deep learning architectures and training · 23%

Topics — the 6 heaviest of 6, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
computational neuroscience
1.322025
Decomposing stimulus-specific sensory neural information via diffusion models · NeurIPS 2025
A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons · NeurIPS 2020
Bioinformatics and computational biology › computational neuroscience › neural coding
brain encoding
0.912025
Decomposing stimulus-specific sensory neural information via diffusion models · NeurIPS 2025
Information theory › information measures
information decomposition
0.912025
Decomposing stimulus-specific sensory neural information via diffusion models · NeurIPS 2025
Information theory › information measures
mutual information
0.912025
Decomposing stimulus-specific sensory neural information via diffusion models · NeurIPS 2025
Machine learning › Probabilistic and Bayesian machine learning › statistical inference › regression
generalized linear model
0.412020
A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons · NeurIPS 2020
Machine learning › Deep learning architectures and training
convolutional neural network
0.112020
A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons · NeurIPS 2020

Methods — techniques the papers use, named apart from their topics

fisher information · 1.7diffusion model · 1.7axiomatic decomposition · 1.7two-step inference · 0.9maximum likelihood estimation · 0.9generalized linear model · 0.9
YearPublicationVenuePosition
2025 Convolution Goes Higher-Order: A Biologically Inspired Mechanism Empowers Image Classification
abstract
We propose a novel enhancement to Convolutional Neural Networks (CNNs) by incorporating learnable higher-order convolutions inspired by nonlinear biological visual processing. Our model extends the classical convolution operator using a Volterra-like expansion to capture multiplicative interactions observed in biological vision. Through extensive evaluation on standard benchmarks and synthetic datasets, we demonstrate that our architecture consistently outperforms traditional CNN baselines, achieving optimal performance with 3rd/4th order expansions. Systematic perturbation analysis and Representational Similarity Analysis reveal that different orders of convolution process distinct aspects of visual information, aligning with the statistical properties of natural images. This biologically-inspired approach offers both improved performance and deeper insights into visual information processing.
Simone Azeglio, Olivier Marre, Peter Neri, Ulisse Ferrari
NeurIPS4
2025 Decomposing stimulus-specific sensory neural information via diffusion models
abstract
A central question in sensory neuroscience is how much, but also what information neurons transmit about the world. While Shannon’s information theory provides a principled framework to quantify the amount of information neurons encode about all stimuli, it does not reveal which stimuli contribute most, or what stimulus features are encoded. As a concrete example, it is known that neurons in the early visual cortex are 'sensitive' to stimuli in a small region of space (their receptive field). However, it is not clear how such simple intuitions carry to more complex scenarios, e.g. with large, noisy & non-linear population of neurons and high-dimensional stimuli. Several previous measures of neural sensitivity have been proposed. For example, the Fisher information quantifies the sensitivity of neural responses to infinitesimal stimulus perturbations. However, as the Fisher is not a valid decomposition of the mutual information it cannot say how different stimuli contribute to the total encoded information. On the other hand, previous works have proposed stimulus dependent decompositions of mutual information, which define a function $ I(x) $ such that $ I(R; X) = \mathbb{E}[I(x)] $. However, this decomposition is inherently ill-posed: infinitely many functions $I(x)$ satisfy the constraint, with no principled way to select among them. Further, different decompositions behave in qualitatively different ways, making it hard to interpret what are they are telling us. Finally, most proposed decompositions are computationally intractable for the high-dimensional stimuli and non-linear encoding models relevant for neuroscience. To resolve these limitations, we propose a set of axioms that any stimulus specific and feature-specific information decomposition should satisfy in order to serve as a meaningful and interpretable measure of neural sensitivity. These axioms formalize intuitive desiderata: that the information assigned to each stimulus, and stimulus feature, should be non-negative, and additive with respect to repeated measurements. We also require the decomposition to respect a form of locality: changes in how a neuron responds to a stimulus $ x $ should not affect the information attributed to a distant stimulus $ x' $. Finally, the attribution must be insensitive to irrelevant features, which do not contribute to the total information. Together, these constraints ensure that the decomposition is both interpretable and theoretically grounded. We show that existing decompositions violate one or more of these axioms, limiting their interpretability and use as information theoretic measures of neural sensitivity. We then introduce a novel decomposition that satisfies all of our axioms. It generalizes Fisher information by capturing neural sensitivity to both infinitesimal and finite stimulus perturbations. Moreover, it supports further decomposition across individual stimulus features (e.g., image pixels), enabling fine-grained analysis of neural representations. Beyond satisfying our theoretical axioms, our decomposition is computationally tractable for large neural populations and high-dimensional naturalistic stimuli, through the use of diffusion models. We demonstrate the power of our method by quantifying the information encoded by a model of visual neurons about individual images and pixels. Our approach uncovers aspects of the neural code that are not picked up by standard methods, such as the Fisher information, and opens the door to similar analyses in higher-order sensory areas, and artificial neural networks.
Steeve Laquitaine, Simone Azeglio, Carlo Paris, Ulisse Ferrari, Matthew Chalk
NeurIPS4
2021 Predicting synchronous firing of large neural populations from sequential recordings
abstract
A major goal in neuroscience is to understand how populations of neurons code for stimuli or actions. While the number of neurons that can be recorded simultaneously is increasing at a fast pace, in most cases these recordings cannot access a complete population: some neurons that carry relevant information remain unrecorded. In particular, it is hard to simultaneously record all the neurons of the same type in a given area. Recent progress have made possible to profile each recorded neuron in a given area thanks to genetic and physiological tools, and to pool together recordings from neurons of the same type across different experimental sessions. However, it is unclear how to infer the activity of a full population of neurons of the same type from these sequential recordings. Neural networks exhibit collective behaviour, e.g. noise correlations and synchronous activity, that are not directly captured by a conditionally-independent model that would just put together the spike trains from sequential recordings. Here we show that we can infer the activity of a full population of retina ganglion cells from sequential recordings, using a novel method based on copula distributions and maximum entropy modeling. From just the spiking response of each ganglion cell to a repeated stimulus, and a few pairwise recordings, we could predict the noise correlations using copulas, and then the full activity of a large population of ganglion cells of the same type using maximum entropy modeling. Remarkably, we could generalize to predict the population responses to different stimuli with similar light conditions and even to different experiments. We could therefore use our method to construct a very large population merging cells' responses from different experiments. We predicted that synchronous activity in ganglion cell populations saturates only for patches larger than 1.5mm in radius, beyond what is today experimentally accessible.
Oleksandr Sorochynskyi, Stéphane Deny, Olivier Marre, Ulisse Ferrari
PLoS Comput. Biol.4
2020 A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons
abstract
Generalized linear models are one of the most efficient paradigms for predicting the correlated stochastic activity of neuronal networks in response to external stimuli, with applications in many brain areas. However, when dealing with complex stimuli, the inferred coupling parameters often do not generalise across different stimulus statistics, leading to degraded performance and blowup instabilities. Here, we develop a two-step inference strategy that allows us to train robust generalised linear models of interacting neurons, by explicitly separating the effects of correlations in the stimulus from network interactions in each training step. Applying this approach to the responses of retinal ganglion cells to complex visual stimuli, we show that, compared to classical methods, the models trained in this way exhibit improved performance, are more stable, yield robust interaction networks, and generalise well across complex visual statistics. The method can be extended to deep convolutional neural networks, leading to models with high predictive accuracy for both the neuron firing rates and their correlations.
Gabriel Mahuas, Giulio Isacchini, Olivier Marre, Ulisse Ferrari, Thierry Mora
NeurIPS4
2020 Towards optogenetic vision restoration with high resolution
abstract
In many cases of inherited retinal degenerations, ganglion cells are spared despite photoreceptor cell death, making it possible to stimulate them to restore visual function. Several studies have shown that it is possible to express an optogenetic protein in ganglion cells and make them light sensitive, a promising strategy to restore vision. However the spatial resolution of optogenetically-reactivated retinas has rarely been measured, especially in the primate. Since the optogenetic protein is also expressed in axons, it is unclear if these neurons will only be sensitive to the stimulation of a small region covering their somas and dendrites, or if they will also respond to any stimulation overlapping with their axon, dramatically impairing spatial resolution. Here we recorded responses of mouse and macaque retinas to random checkerboard patterns following an in vivo optogenetic therapy. We show that optogenetically activated ganglion cells are each sensitive to a small region of visual space. A simple model based on this small receptive field predicted accurately their responses to complex stimuli. From this model, we simulated how the entire population of light sensitive ganglion cells would respond to letters of different sizes. We then estimated the maximal acuity expected by a patient, assuming it could make an optimal use of the information delivered by this reactivated retina. The obtained acuity is above the limit of legal blindness. Our model also makes interesting predictions on how acuity might vary upon changing the therapeutic strategy, assuming an optimal use of the information present in the retinal activity. Optogenetic therapy could thus potentially lead to high resolution vision, under conditions that our model helps to determinine.
Ulisse Ferrari, Stéphane Deny, Abhishek Sengupta, Romain Caplette, Francesco Trapani, José-Alain Sahel, Deniz Dalkara, Serge Picaud, Jens Duebel, Olivier Marre
PLoS Comput. Biol.1
2018 A Simple Model for Low Variability in Neural Spike Trains
abstract
Neural noise sets a limit to information transmission in sensory systems. In several areas, the spiking response (to a repeated stimulus) has shown a higher degree of regularity than predicted by a Poisson process. However, a simple model to explain this low variability is still lacking. Here we introduce a new model, with a correction to Poisson statistics, that can accurately predict the regularity of neural spike trains in response to a repeated stimulus. The model has only two parameters but can reproduce the observed variability in retinal recordings in various conditions. We show analytically why this approximation can work. In a model of the spike-emitting process where a refractory period is assumed, we derive that our simple correction can well approximate the spike train statistics over a broad range of firing rates. Our model can be easily plugged to stimulus processing models, like a linear-nonlinear model or its generalizations, to replace the Poisson spike train hypothesis that is commonly assumed. It estimates the amount of information transmitted much more accurately than Poisson models in retinal recordings. Thanks to its simplicity, this model has the potential to explain low variability in other areas.
Ulisse Ferrari, Stéphane Deny, Olivier Marre, Thierry Mora
Neural Comput.1