5,303 research outputs found
Neuromodulatory effects on early visual signal processing
Understanding how the brain processes information and generates simple to complex behavior constitutes one of the core objectives in systems neuroscience. However, when studying different neural circuits, their dynamics and interactions researchers often assume fixed connectivity, overlooking a crucial factor - the effect of neuromodulators. Neuromodulators can modulate circuit activity depending on several aspects, such as different brain states or sensory contexts. Therefore, considering the modulatory effects of neuromodulators on the functionality of neural circuits is an indispensable step towards a more complete picture of the brain’s ability to process information. Generally, this issue affects all neural systems; hence this thesis tries to address this with an experimental and computational approach to resolve neuromodulatory effects on cell type-level in a well-define system, the mouse retina. In the first study, we established and applied a machine-learning-based classification algorithm to identify individual functional retinal ganglion cell types, which enabled detailed cell type-resolved analyses. We applied the classifier to newly acquired data of light-evoked retinal ganglion cell responses and successfully identified their functional types. Here, the cell type-resolved analysis revealed that a particular principle of efficient coding applies to all types in a similar way. In a second study, we focused on the issue of inter-experimental variability that can occur during the process of pooling datasets. As a result, further downstream analyses may be complicated by the subtle variations between the individual datasets. To tackle this, we proposed a theoretical framework based on an adversarial autoencoder with the objective to remove inter-experimental variability from the pooled dataset, while preserving the underlying biological signal of interest. In the last study of this thesis, we investigated the functional effects of the neuromodulator nitric oxide on the retinal output signal. To this end, we used our previously developed retinal ganglion cell type classifier to unravel type-specific effects and established a paired recording protocol to account for type-specific time-dependent effects. We found that certain
retinal ganglion cell types showed adaptational type-specific changes and that nitric oxide had a distinct modulation of a particular group of retinal ganglion cells.
In summary, I first present several experimental and computational methods that allow to
study functional neuromodulatory effects on the retinal output signal in a cell type-resolved manner and, second, use these tools to demonstrate their feasibility to study the neuromodulator nitric oxide
Meta-learning algorithms and applications
Meta-learning in the broader context concerns how an agent learns about their own learning, allowing them to improve their learning process. Learning how to learn is not only beneficial for humans, but it has also shown vast benefits for improving how machines learn. In the context of machine learning, meta-learning enables models to improve their learning process by selecting suitable meta-parameters that influence the learning. For deep learning specifically, the meta-parameters typically describe details of the training of the model but can also include description of the model itself - the architecture. Meta-learning is usually done with specific goals in mind, for example trying to improve ability to generalize or learn new concepts from only a few examples.
Meta-learning can be powerful, but it comes with a key downside: it is often computationally costly. If the costs would be alleviated, meta-learning could be more accessible to developers of new artificial intelligence models, allowing them to achieve greater goals or save resources. As a result, one key focus of our research is on significantly improving the efficiency of meta-learning. We develop two approaches: EvoGrad and PASHA, both of which significantly improve meta-learning efficiency in two common scenarios. EvoGrad allows us to efficiently optimize the value of a large number of differentiable meta-parameters, while PASHA enables us to efficiently optimize any type of meta-parameters but fewer in number.
Meta-learning is a tool that can be applied to solve various problems. Most commonly it is applied for learning new concepts from only a small number of examples (few-shot learning), but other applications exist too. To showcase the practical impact that meta-learning can make in the context of neural networks, we use meta-learning as a novel solution for two selected problems: more accurate uncertainty quantification (calibration) and general-purpose few-shot learning. Both are practically important problems and using meta-learning approaches we can obtain better solutions than the ones obtained using existing approaches. Calibration is important for safety-critical applications of neural networks, while general-purpose few-shot learning tests model's ability to generalize few-shot learning abilities across diverse tasks such as recognition, segmentation and keypoint estimation.
More efficient algorithms as well as novel applications enable the field of meta-learning to make more significant impact on the broader area of deep learning and potentially solve problems that were too challenging before. Ultimately both of them allow us to better utilize the opportunities that artificial intelligence presents
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
Differentially Private Stochastic Convex Optimization in (Non)-Euclidean Space Revisited
In this paper, we revisit the problem of Differentially Private Stochastic
Convex Optimization (DP-SCO) in Euclidean and general spaces.
Specifically, we focus on three settings that are still far from well
understood: (1) DP-SCO over a constrained and bounded (convex) set in Euclidean
space; (2) unconstrained DP-SCO in space; (3) DP-SCO with
heavy-tailed data over a constrained and bounded set in space. For
problem (1), for both convex and strongly convex loss functions, we propose
methods whose outputs could achieve (expected) excess population risks that are
only dependent on the Gaussian width of the constraint set rather than the
dimension of the space. Moreover, we also show the bound for strongly convex
functions is optimal up to a logarithmic factor. For problems (2) and (3), we
propose several novel algorithms and provide the first theoretical results for
both cases when and
Generative Modeling through the Semi-dual Formulation of Unbalanced Optimal Transport
Optimal Transport (OT) problem investigates a transport map that bridges two
distributions while minimizing a given cost function. In this regard, OT
between tractable prior distribution and data has been utilized for generative
modeling tasks. However, OT-based methods are susceptible to outliers and face
optimization challenges during training. In this paper, we propose a novel
generative model based on the semi-dual formulation of Unbalanced Optimal
Transport (UOT). Unlike OT, UOT relaxes the hard constraint on distribution
matching. This approach provides better robustness against outliers, stability
during training, and faster convergence. We validate these properties
empirically through experiments. Moreover, we study the theoretical upper-bound
of divergence between distributions in UOT. Our model outperforms existing
OT-based generative models, achieving FID scores of 2.97 on CIFAR-10 and 5.80
on CelebA-HQ-256.Comment: 23 pages, 15 figure
DeepMB: Deep neural network for real-time optoacoustic image reconstruction with adjustable speed of sound
Multispectral optoacoustic tomography (MSOT) is a high-resolution functional
imaging modality that can non-invasively access a broad range of
pathophysiological phenomena by quantifying the contrast of endogenous
chromophores in tissue. Real-time imaging is imperative to translate MSOT into
clinical imaging, visualize dynamic pathophysiological changes associated with
disease progression, and enable in situ diagnoses. Model-based reconstruction
affords state-of-the-art optoacoustic images; however, the image quality
provided by model-based reconstruction remains inaccessible during real-time
imaging because the algorithm is iterative and computationally demanding. Deep
learning affords faster reconstruction, but the lack of ground truth training
data can lead to reduced image quality for in vivo data. We introduce a
framework, termed DeepMB, that achieves accurate optoacoustic image
reconstruction for arbitrary input data in 31 ms per image by expressing
model-based reconstruction with a deep neural network. DeepMB facilitates
accurate generalization to experimental test data through training on signals
synthesized from real-world images and ground truth images generated by
model-based reconstruction. The framework affords in-focus images for a broad
range of anatomical locations because it supports dynamic adjustment of the
reconstruction speed of sound during imaging. Furthermore, DeepMB is compatible
with the data rates and image sizes of modern multispectral optoacoustic
tomography scanners. We evaluate DeepMB on a diverse dataset of in vivo images
and demonstrate that the framework reconstructs images 1000 times faster than
the iterative model-based reference method while affording near-identical image
qualities. Accurate and real-time image reconstructions with DeepMB can enable
full access to the high-resolution and multispectral contrast of handheld
optoacoustic tomography
Design of new algorithms for gene network reconstruction applied to in silico modeling of biomedical data
Programa de Doctorado en BiotecnologÃa, IngenierÃa y TecnologÃa QuÃmicaLÃnea de Investigación: IngenierÃa, Ciencia de Datos y BioinformáticaClave Programa: DBICódigo LÃnea: 111The root causes of disease are still poorly understood. The success of current therapies is limited because persistent diseases are frequently treated based on their symptoms rather than the underlying cause of the disease. Therefore, biomedical research is experiencing a technology-driven shift to data-driven holistic approaches to better characterize the molecular mechanisms causing disease. Using omics data as an input, emerging disciplines like network biology attempt to model the relationships between biomolecules. To this effect, gene co- expression networks arise as a promising tool for deciphering the relationships between genes in large transcriptomic datasets. However, because of their low specificity and high false positive rate, they demonstrate a limited capacity to retrieve the disrupted mechanisms that lead to disease onset, progression, and maintenance. Within the context of statistical modeling, we dove deeper into the reconstruction of gene co-expression networks with the specific goal of discovering disease-specific features directly from expression data. Using ensemble techniques, which combine the results of various metrics, we were able to more precisely capture biologically significant relationships between genes. We were able to find de novo potential disease-specific features with the help of prior biological knowledge and the development of new network inference techniques.
Through our different approaches, we analyzed large gene sets across multiple samples and used gene expression as a surrogate marker for the inherent biological processes, reconstructing robust gene co-expression networks that are simple to explore. By mining disease-specific gene co-expression networks we come up with a useful framework for identifying new omics-phenotype associations from conditional expression datasets.In this sense, understanding diseases from the perspective of biological network perturbations will improve personalized medicine, impacting rational biomarker discovery, patient stratification and drug design, and ultimately leading to more targeted therapies.Universidad Pablo de Olavide de Sevilla. Departamento de Deporte e Informátic
When Deep Learning Meets Polyhedral Theory: A Survey
In the past decade, deep learning became the prevalent methodology for
predictive modeling thanks to the remarkable accuracy of deep neural networks
in tasks such as computer vision and natural language processing. Meanwhile,
the structure of neural networks converged back to simpler representations
based on piecewise constant and piecewise linear functions such as the
Rectified Linear Unit (ReLU), which became the most commonly used type of
activation function in neural networks. That made certain types of network
structure \unicode{x2014}such as the typical fully-connected feedforward
neural network\unicode{x2014} amenable to analysis through polyhedral theory
and to the application of methodologies such as Linear Programming (LP) and
Mixed-Integer Linear Programming (MILP) for a variety of purposes. In this
paper, we survey the main topics emerging from this fast-paced area of work,
which bring a fresh perspective to understanding neural networks in more detail
as well as to applying linear optimization techniques to train, verify, and
reduce the size of such networks
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