arXiv subjects

Carlos Fernandez-Granda

Publications and source records attributed to Carlos Fernandez-Granda.

At least 55 records · Page 3Linked to original sources

arXiv2021

Unsupervised Deep Video Denoising

Deep convolutional neural networks (CNNs) for video denoising are typically trained with supervision, assuming the availability of clean videos. However, in many applications, such as microscopy, noiseless videos are not available. To address this, we propose an Unsupervised Deep Video Denoiser (UDVD), a CNN architecture designed to be trained exclusively with noisy data. The performance of UDVD is comparable to the supervised state-of-the-art, even when trained only on a single short noisy video. We demonstrate the promise of our approach in real-world imaging applications by denoising raw video, fluorescence-microscopy and electron-microscopy data. In contrast to many current approaches to video denoising, UDVD does not require explicit motion compensation. This is advantageous because motion compensation is computationally expensive, and can be unreliable when the input data are noisy. A gradient-based analysis reveals that UDVD automatically adapts to local motion in the input noisy videos. Thus, the network learns to perform implicit motion compensation, even though it is only trained for denoising.

eess.IV↗

arXiv2021

Adaptive Denoising via GainTuning

Deep convolutional neural networks (CNNs) for image denoising are usually trained on large datasets. These models achieve the current state of the art, but they have difficulties generalizing when applied to data that deviate from the training distribution. Recent work has shown that it is possible to train denoisers on a single noisy image. These models adapt to the features of the test image, but their performance is limited by the small amount of information used to train them. Here we propose "GainTuning", in which CNN models pre-trained on large datasets are adaptively and selectively adjusted for individual test images. To avoid overfitting, GainTuning optimizes a single multiplicative scaling parameter (the "Gain") of each channel in the convolutional layers of the CNN. We show that GainTuning improves state-of-the-art CNNs on standard image-denoising benchmarks, boosting their denoising performance on nearly every image in a held-out test set. These adaptive improvements are even more substantial for test images differing systematically from the training data, either in noise level or image type. We illustrate the potential of adaptive denoising in a scientific application, in which a CNN is trained on synthetic data, and tested on real transmission-electron-microscope images. In contrast to the existing methodology, GainTuning is able to faithfully reconstruct the structure of catalytic nanoparticles from these data at extremely low signal-to-noise ratios.

cs.CV↗

arXiv2021

Deep Denoising For Scientific Discovery: A Case Study In Electron Microscopy

Denoising is a fundamental challenge in scientific imaging. Deep convolutional neural networks (CNNs) provide the current state of the art in denoising natural images, where they produce impressive results. However, their potential has barely been explored in the context of scientific imaging. Denoising CNNs are typically trained on real natural images artificially corrupted with simulated noise. In contrast, in scientific applications, noiseless ground-truth images are usually not available. To address this issue, we propose a simulation-based denoising (SBD) framework, in which CNNs are trained on simulated images. We test the framework on data obtained from transmission electron microscopy (TEM), an imaging technique with widespread applications in material science, biology, and medicine. SBD outperforms existing techniques by a wide margin on a simulated benchmark dataset, as well as on real data. Apart from the denoised images, SBD generates likelihood maps to visualize the agreement between the structure of the denoised image and the observed data. Our results reveal shortcomings of state-of-the-art denoising architectures, such as their small field-of-view: substantially increasing the field-of-view of the CNNs allows them to exploit non-local periodic patterns in the data, which is crucial at high noise levels. In addition, we analyze the generalization capability of SBD, demonstrating that the trained networks are robust to variations of imaging parameters and of the underlying signal structure. Finally, we release the first publicly available benchmark dataset of TEM images, containing 18,000 examples.

cs.CV↗

arXiv2021

Weakly-supervised High-resolution Segmentation of Mammography Images for Breast Cancer Diagnosis

In the last few years, deep learning classifiers have shown promising results in image-based medical diagnosis. However, interpreting the outputs of these models remains a challenge. In cancer diagnosis, interpretability can be achieved by localizing the region of the input image responsible for the output, i.e. the location of a lesion. Alternatively, segmentation or detection models can be trained with pixel-wise annotations indicating the locations of malignant lesions. Unfortunately, acquiring such labels is labor-intensive and requires medical expertise. To overcome this difficulty, weakly-supervised localization can be utilized. These methods allow neural network classifiers to output saliency maps highlighting the regions of the input most relevant to the classification task (e.g. malignant lesions in mammograms) using only image-level labels (e.g. whether the patient has cancer or not) during training. When applied to high-resolution images, existing methods produce low-resolution saliency maps. This is problematic in applications in which suspicious lesions are small in relation to the image size. In this work, we introduce a novel neural network architecture to perform weakly-supervised segmentation of high-resolution images. The proposed model selects regions of interest via coarse-level localization, and then performs fine-grained segmentation of those regions. We apply this model to breast cancer diagnosis with screening mammography, and validate it on a large clinically-realistic dataset. Measured by Dice similarity score, our approach outperforms existing methods by a large margin in terms of localization performance of benign and malignant lesions, relatively improving the performance by 39.6% and 20.0%, respectively. Code and the weights of some of the models are available at https://github.com/nyukat/GLAM

cs.CV↗

arXiv2021

Developing and Evaluating Deep Neural Network-based Denoising for Nanoparticle TEM Images with Ultra-low Signal-to-Noise

A deep convolutional neural network has been developed to denoise atomic-resolution TEM image datasets of nanoparticles acquired using direct electron counting detectors, for applications where the image signal is severely limited by shot noise. The network was applied to a model system of CeO2-supported Pt nanoparticles. We leverage multislice image simulations to generate a large and flexible dataset for training and testing the network. The proposed network outperforms state-of-the-art denoising methods by a significant margin both on simulated and experimental test data. Factors contributing to the performance are identified, including most importantly (a) the geometry of the images used during training and (b) the size of the network's receptive field. Through a gradient-based analysis, we investigate the mechanisms learned by the network to denoise experimental images. This shows that the network exploits global and local information in the noisy measurements, for example, by adapting its filtering approach when it encounters atomic-level defects at the nanoparticle surface. Extensive analysis has been done to characterize the network's ability to correctly predict the exact atomic structure at the nanoparticle surface. Finally, we develop an approach based on the log-likelihood ratio test that provides a quantitative measure of the agreement between the noisy observation and the atomic-level structure in the network-denoised image.

cond-mat.mtrl-sci↗

arXiv2021

Data-driven Estimation of Sinusoid Frequencies

Frequency estimation is a fundamental problem in signal processing, with applications in radar imaging, underwater acoustics, seismic imaging, and spectroscopy. The goal is to estimate the frequency of each component in a multisinusoidal signal from a finite number of noisy samples. A recent machine-learning approach uses a neural network to output a learned representation with local maxima at the position of the frequency estimates. In this work, we propose a novel neural-network architecture that produces a significantly more accurate representation, and combine it with an additional neural-network module trained to detect the number of frequencies. This yields a fast, fully-automatic method for frequency estimation that achieves state-of-the-art results. In particular, it outperforms existing techniques by a substantial margin at medium-to-high noise levels.

cs.LG↗

arXiv2020

An artificial intelligence system for predicting the deterioration of COVID-19 patients in the emergency department

During the coronavirus disease 2019 (COVID-19) pandemic, rapid and accurate triage of patients at the emergency department is critical to inform decision-making. We propose a data-driven approach for automatic prediction of deterioration risk using a deep neural network that learns from chest X-ray images and a gradient boosting model that learns from routine clinical variables. Our AI prognosis system, trained using data from 3,661 patients, achieves an area under the receiver operating characteristic curve (AUC) of 0.786 (95% CI: 0.745-0.830) when predicting deterioration within 96 hours. The deep neural network extracts informative areas of chest X-ray images to assist clinicians in interpreting the predictions and performs comparably to two radiologists in a reader study. In order to verify performance in a real clinical setting, we silently deployed a preliminary version of the deep neural network at New York University Langone Health during the first wave of the pandemic, which produced accurate predictions in real-time. In summary, our findings demonstrate the potential of the proposed system for assisting front-line physicians in the triage of COVID-19 patients.

cs.LG↗

arXiv2020

Adaptive Test Allocation for Outbreak Detection and Tracking in Social Contact Networks

We present a general framework for adaptive allocation of viral tests in social contact networks. We pose and solve several complementary problems. First, we consider the design of a social sensing system whose objective is the early detection of a novel epidemic outbreak. In particular, we propose an algorithm to select a subset of individuals to be tested in order to detect the onset of an epidemic outbreak as fast as possible. We pose this problem as a hitting time probability maximization problem and use submodularity optimization techniques to derive explicit quality guarantees for the proposed solution. Second, once an epidemic outbreak has been detected, we consider the problem of adaptively distributing viral tests over time in order to maximize the information gained about the current state of the epidemic. We formalize this problem in terms of information entropy and mutual information and propose an adaptive allocation strategy with quality guarantees. For these problems, we derive analytical solutions for any stochastic compartmental epidemic model with Markovian dynamics, as well as efficient Monte-Carlo-based algorithms for non-Markovian dynamics. Finally, we illustrate the performance of the proposed framework in numerical experiments involving a model of Covid-19 applied to a real human contact network.

cs.SI↗

arXiv2020

Early-Learning Regularization Prevents Memorization of Noisy Labels

We propose a novel framework to perform classification via deep learning in the presence of noisy annotations. When trained on noisy labels, deep neural networks have been observed to first fit the training data with clean labels during an "early learning" phase, before eventually memorizing the examples with false labels. We prove that early learning and memorization are fundamental phenomena in high-dimensional classification tasks, even in simple linear models, and give a theoretical explanation in this setting. Motivated by these findings, we develop a new technique for noisy classification tasks, which exploits the progress of the early learning phase. In contrast with existing approaches, which use the model output during early learning to detect the examples with clean labels, and either ignore or attempt to correct the false labels, we take a different route and instead capitalize on early learning via regularization. There are two key elements to our approach. First, we leverage semi-supervised learning techniques to produce target probabilities based on the model outputs. Second, we design a regularization term that steers the model towards these targets, implicitly preventing memorization of the false labels. The resulting framework is shown to provide robustness to noisy annotations on several standard benchmarks and real-world datasets, where it achieves results comparable to the state of the art.

cs.LG↗

arXiv2020

A Sampling Theorem for Deconvolution in Two Dimensions

This work studies the problem of estimating a two-dimensional superposition of point sources or spikes from samples of their convolution with a Gaussian kernel. Our results show that minimizing a continuous counterpart of the $\ell_1$ norm exactly recovers the true spikes if they are sufficiently separated, and the samples are sufficiently dense. In addition, we provide numerical evidence that our results extend to non-Gaussian kernels relevant to microscopy and telescopy.

math.NA↗

arXiv2020

Sparse Recovery Beyond Compressed Sensing: Separable Nonlinear Inverse Problems

Extracting information from nonlinear measurements is a fundamental challenge in data analysis. In this work, we consider separable inverse problems, where the data are modeled as a linear combination of functions that depend nonlinearly on certain parameters of interest. These parameters may represent neuronal activity in a human brain, frequencies of electromagnetic waves, fluorescent probes in a cell, or magnetic relaxation times of biological tissues. Separable nonlinear inverse problems can be reformulated as underdetermined sparse-recovery problems, and solved using convex programming. This approach has had empirical success in a variety of domains, from geophysics to medical imaging, but lacks a theoretical justification. In particular, compressed-sensing theory does not apply, because the measurement operators are deterministic and violate incoherence conditions such as the restricted-isometry property. Our main contribution is a theory for sparse recovery adapted to deterministic settings. We show that convex programming succeeds in recovering the parameters of interest, as long as their values are sufficiently distinct with respect to the correlation structure of the measurement operator. The theoretical results are illustrated through numerical experiments for two applications: heat-source localization and estimation of brain activity from electroencephalography data.

eess.SP↗

arXiv2020

Towards data-driven stroke rehabilitation via wearable sensors and deep learning

Recovery after stroke is often incomplete, but rehabilitation training may potentiate recovery by engaging endogenous neuroplasticity. In preclinical models of stroke, high doses of rehabilitation training are required to restore functional movement to the affected limbs of animals. In humans, however, the necessary dose of training to potentiate recovery is not known. This ignorance stems from the lack of objective, pragmatic approaches for measuring training doses in rehabilitation activities. Here, to develop a measurement approach, we took the critical first step of automatically identifying functional primitives, the basic building block of activities. Forty-eight individuals with chronic stroke performed a variety of rehabilitation activities while wearing inertial measurement units (IMUs) to capture upper body motion. Primitives were identified by human labelers, who labeled and segmented the associated IMU data. We performed automatic classification of these primitives using machine learning. We designed a convolutional neural network model that outperformed existing methods. The model includes an initial module to compute separate embeddings of different physical quantities in the sensor data. In addition, it replaces batch normalization (which performs normalization based on statistics computed from the training data) with instance normalization (which uses statistics computed from the test data). This increases robustness to possible distributional shifts when applying the method to new patients. With this approach, we attained an average classification accuracy of 70%. Thus, using a combination of IMU-based motion capture and deep learning, we were able to identify primitives automatically. This approach builds towards objectively-measured rehabilitation training, enabling the identification and counting of functional primitives that accrues to a training dose.

eess.SP↗

arXiv2020

On the design of convolutional neural networks for automatic detection of Alzheimer's disease

Early detection is a crucial goal in the study of Alzheimer's Disease (AD). In this work, we describe several techniques to boost the performance of 3D deep convolutional neural networks (CNNs) trained to detect AD using structural brain MRI scans. Specifically, we provide evidence that (1) instance normalization outperforms batch normalization, (2) early spatial downsampling negatively affects performance, (3) widening the model brings consistent gains while increasing the depth does not, and (4) incorporating age information yields moderate improvement. Together, these insights yield an increment of approximately 14% in test accuracy over existing models when distinguishing between patients with AD, mild cognitive impairment, and controls in the ADNI dataset. Similar performance is achieved on an independent dataset.

eess.IV↗

arXiv2020

Be Like Water: Robustness to Extraneous Variables Via Adaptive Feature Normalization

Extraneous variables are variables that are irrelevant for a certain task, but heavily affect the distribution of the available data. In this work, we show that the presence of such variables can degrade the performance of deep-learning models. We study three datasets where there is a strong influence of known extraneous variables: classification of upper-body movements in stroke patients, annotation of surgical activities, and recognition of corrupted images. Models trained with batch normalization learn features that are highly dependent on the extraneous variables. In batch normalization, the statistics used to normalize the features are learned from the training set and fixed at test time, which produces a mismatch in the presence of varying extraneous variables. We demonstrate that estimating the feature statistics adaptively during inference, as in instance normalization, addresses this issue, producing normalized features that are more robust to changes in the extraneous variables. This results in a significant gain in performance for different network architectures and choices of feature statistics.

cs.LG↗

arXiv2020

Robust and interpretable blind image denoising via bias-free convolutional neural networks

Deep convolutional networks often append additive constant ("bias") terms to their convolution operations, enabling a richer repertoire of functional mappings. Biases are also used to facilitate training, by subtracting mean response over batches of training images (a component of "batch normalization"). Recent state-of-the-art blind denoising methods (e.g., DnCNN) seem to require these terms for their success. Here, however, we show that these networks systematically overfit the noise levels for which they are trained: when deployed at noise levels outside the training range, performance degrades dramatically. In contrast, a bias-free architecture -- obtained by removing the constant terms in every layer of the network, including those used for batch normalization-- generalizes robustly across noise levels, while preserving state-of-the-art performance within the training range. Locally, the bias-free network acts linearly on the noisy image, enabling direct analysis of network behavior via standard linear-algebraic tools. These analyses provide interpretations of network functionality in terms of nonlinear adaptive filtering, and projection onto a union of low-dimensional subspaces, connecting the learning-based method to more traditional denoising methodology.

eess.IV↗

arXiv2019

Time-Series Analysis via Low-Rank Matrix Factorization Applied to Infant-Sleep Data

We propose a nonparametric model for time series with missing data based on low-rank matrix factorization. The model expresses each instance in a set of time series as a linear combination of a small number of shared basis functions. Constraining the functions and the corresponding coefficients to be nonnegative yields an interpretable low-dimensional representation of the data. A time-smoothing regularization term ensures that the model captures meaningful trends in the data, instead of overfitting short-term fluctuations. The low-dimensional representation makes it possible to detect outliers and cluster the time series according to the interpretable features extracted by the model, and also to perform forecasting via kernel regression. We apply our methodology to a large real-world dataset of infant-sleep data gathered by caregivers with a mobile-phone app. Our analysis automatically extracts daily-sleep patterns consistent with the existing literature. This allows us to compute sleep-development trends for the cohort, which characterize the emergence of circadian sleep and different napping habits. We apply our methodology to detect anomalous individuals, to cluster the cohort into groups with different sleeping tendencies, and to obtain improved predictions of future sleep behavior.

stat.ML↗

arXiv2019

A Learning-Based Framework for Line-Spectra Super-resolution

We propose a learning-based approach for estimating the spectrum of a multisinusoidal signal from a finite number of samples. A neural-network is trained to approximate the spectra of such signals on simulated data. The proposed methodology is very flexible: adapting to different signal and noise models only requires modifying the training data accordingly. Numerical experiments show that the approach performs competitively with classical methods designed for additive Gaussian noise at a range of noise levels, and is also effective in the presence of impulsive noise.

cs.LG↗

arXiv2018

Deconvolution of Point Sources: A Sampling Theorem and Robustness Guarantees

In this work we analyze a convex-programming method for estimating superpositions of point sources or spikes from nonuniform samples of their convolution with a known kernel. We consider a one-dimensional model where the kernel is either a Gaussian function or a Ricker wavelet, inspired by applications in geophysics and imaging. Our analysis establishes that minimizing a continuous counterpart of the $\ell_1$ norm achieves exact recovery of the original spikes as long as (1) the signal support satisfies a minimum-separation condition and (2) there are at least two samples close to every spike. In addition, we derive theoretical guarantees on the robustness of the approach to both dense and sparse additive noise.

math.OC↗