arXiv subjects

Michael Eickenberg

Publications and source records attributed to Michael Eickenberg.

46 records · Page 3Linked to original sources

arXiv2021

Phase Retrieval with Holography and Untrained Priors: Tackling the Challenges of Low-Photon Nanoscale Imaging

Phase retrieval is the inverse problem of recovering a signal from magnitude-only Fourier measurements, and underlies numerous imaging modalities, such as Coherent Diffraction Imaging (CDI). A variant of this setup, known as holography, includes a reference object that is placed adjacent to the specimen of interest before measurements are collected. The resulting inverse problem, known as holographic phase retrieval, is well-known to have improved problem conditioning relative to the original. This innovation, i.e. Holographic CDI, becomes crucial at the nanoscale, where imaging specimens such as viruses, proteins, and crystals require low-photon measurements. This data is highly corrupted by Poisson shot noise, and often lacks low-frequency content as well. In this work, we introduce a dataset-free deep learning framework for holographic phase retrieval adapted to these challenges. The key ingredients of our approach are the explicit and flexible incorporation of the physical forward model into an automatic differentiation procedure, the Poisson log-likelihood objective function, and an optional untrained deep image prior. We perform extensive evaluation under realistic conditions. Compared to competing classical methods, our method recovers signal from higher noise levels and is more resilient to suboptimal reference design, as well as to large missing regions of low frequencies in the observations. Finally, we show that these properties carry over to experimental data acquired on optical wavelengths. To the best of our knowledge, this is the first work to consider a dataset-free machine learning approach for holographic phase retrieval.

cs.LG↗

arXiv2020

Decoupled Greedy Learning of CNNs

A commonly cited inefficiency of neural network training by back-propagation is the update locking problem: each layer must wait for the signal to propagate through the full network before updating. Several alternatives that can alleviate this issue have been proposed. In this context, we consider a simpler, but more effective, substitute that uses minimal feedback, which we call Decoupled Greedy Learning (DGL). It is based on a greedy relaxation of the joint training objective, recently shown to be effective in the context of Convolutional Neural Networks (CNNs) on large-scale image classification. We consider an optimization of this objective that permits us to decouple the layer training, allowing for layers or modules in networks to be trained with a potentially linear parallelization in layers. With the use of a replay buffer we show this approach can be extended to asynchronous settings, where modules can operate with possibly large communication delays. We show theoretically and empirically that this approach converges. Then, we empirically find that it can lead to better generalization than sequential greedy optimization. We demonstrate the effectiveness of DGL against alternative approaches on the CIFAR-10 dataset and on the large-scale ImageNet dataset.

cs.LG↗

arXiv2019

Greedy Layerwise Learning Can Scale to ImageNet

Shallow supervised 1-hidden layer neural networks have a number of favorable properties that make them easier to interpret, analyze, and optimize than their deep counterparts, but lack their representational power. Here we use 1-hidden layer learning problems to sequentially build deep networks layer by layer, which can inherit properties from shallow networks. Contrary to previous approaches using shallow networks, we focus on problems where deep learning is reported as critical for success. We thus study CNNs on image classification tasks using the large-scale ImageNet dataset and the CIFAR-10 dataset. Using a simple set of ideas for architecture and training we find that solving sequential 1-hidden-layer auxiliary problems lead to a CNN that exceeds AlexNet performance on ImageNet. Extending this training methodology to construct individual layers by solving 2-and-3-hidden layer auxiliary problems, we obtain an 11-layer network that exceeds several members of the VGG model family on ImageNet, and can train a VGG-11 model to the same accuracy as end-to-end learning. To our knowledge, this is the first competitive alternative to end-to-end training of CNNs that can scale to ImageNet. We illustrate several interesting properties of these models theoretically and conduct a range of experiments to study the properties this training induces on the intermediate layers.

cs.LG↗

arXiv2018

Solid Harmonic Wavelet Scattering for Predictions of Molecule Properties

We present a machine learning algorithm for the prediction of molecule properties inspired by ideas from density functional theory. Using Gaussian-type orbital functions, we create surrogate electronic densities of the molecule from which we compute invariant "solid harmonic scattering coefficients" that account for different types of interactions at different scales. Multi-linear regressions of various physical properties of molecules are computed from these invariant coefficients. Numerical experiments show that these regressions have near state of the art performance, even with relatively few training examples. Predictions over small sets of scattering coefficients can reach a DFT precision while being interpretable.

physics.chem-ph↗

arXiv2017

Gaussian Processes for HRF estimation for BOLD fMRI

We present a non-parametric joint estimation method for fMRI task activation values and the hemodynamic response function (HRF). The HRF is modeled as a Gaussian process, making continuous evaluation possible for jittered paradigms and providing a variance estimate at each point.

stat.AP↗

arXiv2015

FAASTA: A fast solver for total-variation regularization of ill-conditioned problems with application to brain imaging

The total variation (TV) penalty, as many other analysis-sparsity problems, does not lead to separable factors or a proximal operatorwith a closed-form expression, such as soft thresholding for the $\ell\_1$ penalty. As a result, in a variational formulation of an inverse problem or statisticallearning estimation, it leads to challenging non-smooth optimization problemsthat are often solved with elaborate single-step first-order methods. When thedata-fit term arises from empirical measurements, as in brain imaging, it isoften very ill-conditioned and without simple structure. In this situation, in proximal splitting methods, the computation cost of thegradient step can easily dominate each iteration. Thus it is beneficialto minimize the number of gradient steps.We present fAASTA, a variant of FISTA, that relies on an internal solver forthe TV proximal operator, and refines its tolerance to balance computationalcost of the gradient and the proximal steps. We give benchmarks andillustrations on "brain decoding": recovering brain maps from noisymeasurements to predict observed behavior. The algorithm as well as theempirical study of convergence speed are valuable for any non-exact proximaloperator, in particular analysis-sparsity problems.

q-bio.NC↗

arXiv2014

Machine Learning for Neuroimaging with Scikit-Learn

Statistical machine learning methods are increasingly used for neuroimaging data analysis. Their main virtue is their ability to model high-dimensional datasets, e.g. multivariate analysis of activation images or resting-state time series. Supervised learning is typically used in decoding or encoding settings to relate brain images to behavioral or clinical observations, while unsupervised learning can uncover hidden structures in sets of images (e.g. resting state functional MRI) or find sub-populations in large cohorts. By considering different functional neuroimaging applications, we illustrate how scikit-learn, a Python machine learning library, can be used to perform some key analysis steps. Scikit-learn contains a very large set of statistical learning algorithms, both supervised and unsupervised, and its application to neuroimaging data provides a versatile tool to study the brain.

cs.LG↗

arXiv2014

Data-driven HRF estimation for encoding and decoding models

Despite the common usage of a canonical, data-independent, hemodynamic response function (HRF), it is known that the shape of the HRF varies across brain regions and subjects. This suggests that a data-driven estimation of this function could lead to more statistical power when modeling BOLD fMRI data. However, unconstrained estimation of the HRF can yield highly unstable results when the number of free parameters is large. We develop a method for the joint estimation of activation and HRF using a rank constraint causing the estimated HRF to be equal across events/conditions, yet permitting it to be different across voxels. Model estimation leads to an optimization problem that we propose to solve with an efficient quasi-Newton method exploiting fast gradient computations. This model, called GLM with Rank-1 constraint (R1-GLM), can be extended to the setting of GLM with separate designs which has been shown to improve decoding accuracy in brain activity decoding experiments. We compare 10 different HRF modeling methods in terms of encoding and decoding score in two different datasets. Our results show that the R1-GLM model significantly outperforms competing methods in both encoding and decoding settings, positioning it as an attractive method both from the points of view of accuracy and computational efficiency.

cs.CE↗

arXiv2013

Second order scattering descriptors predict fMRI activity due to visual textures

Second layer scattering descriptors are known to provide good classification performance on natural quasi-stationary processes such as visual textures due to their sensitivity to higher order moments and continuity with respect to small deformations. In a functional Magnetic Resonance Imaging (fMRI) experiment we present visual textures to subjects and evaluate the predictive power of these descriptors with respect to the predictive power of simple contour energy - the first scattering layer. We are able to conclude not only that invariant second layer scattering coefficients better encode voxel activity, but also that well predicted voxels need not necessarily lie in known retinotopic regions.

cs.CV↗

arXiv2013

HRF estimation improves sensitivity of fMRI encoding and decoding models

Extracting activation patterns from functional Magnetic Resonance Images (fMRI) datasets remains challenging in rapid-event designs due to the inherent delay of blood oxygen level-dependent (BOLD) signal. The general linear model (GLM) allows to estimate the activation from a design matrix and a fixed hemodynamic response function (HRF). However, the HRF is known to vary substantially between subjects and brain regions. In this paper, we propose a model for jointly estimating the hemodynamic response function (HRF) and the activation patterns via a low-rank representation of task effects.This model is based on the linearity assumption behind the GLM and can be computed using standard gradient-based solvers. We use the activation patterns computed by our model as input data for encoding and decoding studies and report performance improvement in both settings.

cs.LG↗