OpenRaiser/Intern-Atlas huggingface dataset:
Map3D: Registration Based Multi-Object Tracking on 3D Serial Whole Slide Images
Venue: arXiv cs.CV 2021
Year: 2021

There has been a long pursuit for precise and reproducible glomerular quantification on renal pathology to leverage both research and practice. When digitizing the biopsy tissue samples using whole slide imaging (WSI), a set of serial sections from the same tissue can be acquired as a stack of images, similar to frames in a video. In radiology, the stack of images (e.g., computed tomography) are naturally used to provide 3D context for organs, tissues, and tumors. In pathology, it is appealing to do a similar 3D assessment. However, the 3D identification and association of large-scale glomeruli on renal pathology is challenging due to large tissue deformation, missing tissues, and artifacts from WSI. In this paper, we propose a novel Multi-object Association for Pathology in 3D (Map3D) method for automatically identifying and associating large-scale cross-sections of 3D objects from routine serial sectioning and WSI. The innovations of the Map3D method are three-fold: (1) the large-scale glomerular association is formed as a new multi-object tracking (MOT) perspective; (2) the quality-aware whole series registration is proposed to not only provide affinity estimation but also offer automatic kidney-wise quality assurance (QA) for registration; (3) a dual-path association method is proposed to tackle the large deformation, missing tissues, and artifacts during tracking. To the best of our knowledge, the Map3D method is the first approach that enables automatic and large-scale glomerular association across 3D serial sectioning using WSI. Our proposed method Map3D achieved MOTA= 44.6, which is 12.1% higher than the non deep learning benchmarks.
Adversarial Attack Vulnerability of Medical Image Analysis Systems: Unexplored Factors
Venue: arXiv cs.CR 2021
Year: 2021

Adversarial attacks are considered a potentially serious security threat for machine learning systems. Medical image analysis (MedIA) systems have recently been argued to be vulnerable to adversarial attacks due to strong financial incentives and the associated technological infrastructure. In this paper, we study previously unexplored factors affecting adversarial attack vulnerability of deep learning MedIA systems in three medical domains: ophthalmology, radiology, and pathology. We focus on adversarial black-box settings, in which the attacker does not have full access to the target model and usually uses another model, commonly referred to as surrogate model, to craft adversarial examples. We consider this to be the most realistic scenario for MedIA systems. Firstly, we study the effect of weight initialization (ImageNet vs. random) on the transferability of adversarial attacks from the surrogate model to the target model. Secondly, we study the influence of differences in development data between target and surrogate models. We further study the interaction of weight initialization and data differences with differences in model architecture. All experiments were done with a perturbation degree tuned to ensure maximal transferability at minimal visual perceptibility of the attacks. Our experiments show that pre-training may dramatically increase the transferability of adversarial examples, even when the target and surrogate's architectures are different: the larger the performance gain using pre-training, the larger the transferability. Differences in the development data between target and surrogate models considerably decrease the performance of the attack; this decrease is further amplified by difference in the model architecture. We believe these factors should be considered when developing security-critical MedIA systems planned to be deployed in clinical practice.
Anti-Transfer Learning for Task Invariance in Convolutional Neural Networks for Speech Processing
Venue: arXiv cs.LG 2021
Year: 2021

We introduce the novel concept of anti-transfer learning for speech processing with convolutional neural networks. While transfer learning assumes that the learning process for a target task will benefit from re-using representations learned for another task, anti-transfer avoids the learning of representations that have been learned for an orthogonal task, i.e., one that is not relevant and potentially misleading for the target task, such as speaker identity for speech recognition or speech content for emotion recognition. In anti-transfer learning, we penalize similarity between activations of a network being trained and another one previously trained on an orthogonal task, which yields more suitable representations. This leads to better generalization and provides a degree of control over correlations that are spurious or undesirable, e.g. to avoid social bias. We have implemented anti-transfer for convolutional neural networks in different configurations with several similarity metrics and aggregation functions, which we evaluate and analyze with several speech and audio tasks and settings, using six datasets. We show that anti-transfer actually leads to the intended invariance to the orthogonal task and to more appropriate features for the target task at hand. Anti-transfer learning consistently improves classification accuracy in all test cases. While anti-transfer creates computation and memory cost at training time, there is relatively little computation cost when using pre-trained models for orthogonal tasks. Anti-transfer is widely applicable and particularly useful where a specific invariance is desirable or where trained models are available and labeled data for orthogonal tasks are difficult to obtain.
An Unsupervised Information-Theoretic Perceptual Quality Metric
Venue: arXiv cs.CV 2021
Year: 2021

Tractable models of human perception have proved to be challenging to build. Hand-designed models such as MS-SSIM remain popular predictors of human image quality judgements due to their simplicity and speed. Recent modern deep learning approaches can perform better, but they rely on supervised data which can be costly to gather: large sets of class labels such as ImageNet, image quality ratings, or both. We combine recent advances in information-theoretic objective functions with a computational architecture informed by the physiology of the human visual system and unsupervised training on pairs of video frames, yielding our Perceptual Information Metric (PIM). We show that PIM is competitive with supervised metrics on the recent and challenging BAPPS image quality assessment dataset and outperforms them in predicting the ranking of image compression methods in CLIC 2020. We also perform qualitative experiments using the ImageNet-C dataset, and establish that PIM is robust with respect to architectural details.
BioDynaMo: a general platform for scalable agent-based simulation
Venue: arXiv cs.CE 2021
Year: 2021

Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results: We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a general-purpose and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology, and epidemiology. For each use case we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baseline. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research. Availability: BioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in supplementary information. Contact: lukas.breitwieser@inf.ethz.ch, a.s.hesam@tudelft.nl, omutlu@ethz.ch, r.bauer@surrey.ac.uk Supplementary information: Available at https://doi.org/10.5281/zenodo.4501515
Evading Curse of Dimensionality in Unconstrained Private GLMs via Private Gradient Descent
Venue: arXiv cs.CR 2021
Year: 2021

We revisit the well-studied problem of differentially private empirical risk minimization (ERM). We show that for unconstrained convex generalized linear models (GLMs), one can obtain an excess empirical risk of $\tilde O\left(\sqrt{\texttt{rank}}/εn\right)$, where ${\texttt{rank}}$ is the rank of the feature matrix in the GLM problem, $n$ is the number of data samples, and $ε$ is the privacy parameter. This bound is attained via differentially private gradient descent (DP-GD). Furthermore, via the first lower bound for unconstrained private ERM, we show that our upper bound is tight. In sharp contrast to the constrained ERM setting, there is no dependence on the dimensionality of the ambient model space ($p$). (Notice that ${\texttt{rank}}\leq \min\{n, p\}$.) Besides, we obtain an analogous excess population risk bound which depends on ${\texttt{rank}}$ instead of $p$. For the smooth non-convex GLM setting (i.e., where the objective function is non-convex but preserves the GLM structure), we further show that DP-GD attains a dimension-independent convergence of $\tilde O\left(\sqrt{\texttt{rank}}/εn\right)$ to a first-order-stationary-point of the underlying objective. Finally, we show that for convex GLMs, a variant of DP-GD commonly used in practice (which involves clipping the individual gradients) also exhibits the same dimension-independent convergence to the minimum of a well-defined objective. To that end, we provide a structural lemma that characterizes the effect of clipping on the optimization profile of DP-GD.
The Smoothed Possibility of Social Choice
Venue: arXiv cs.GT 2021
Year: 2021

We develop a framework that leverages the smoothed complexity analysis by Spielman and Teng to circumvent paradoxes and impossibility theorems in social choice, motivated by modern applications of social choice powered by AI and ML. For Condrocet's paradox, we prove that the smoothed likelihood of the paradox either vanishes at an exponential rate as the number of agents increases, or does not vanish at all. For the ANR impossibility on the non-existence of voting rules that simultaneously satisfy anonymity, neutrality, and resolvability, we characterize the rate for the impossibility to vanish, to be either polynomially fast or exponentially fast. We also propose a novel easy-to-compute tie-breaking mechanism that optimally preserves anonymity and neutrality for even number of alternatives in natural settings. Our results illustrate the smoothed possibility of social choice -- even though the paradox and the impossibility theorem hold in the worst case, they may not be a big concern in practice.
Longitudinal Self-Supervised Learning
Venue: arXiv cs.LG 2021
Year: 2021

Machine learning analysis of longitudinal neuroimaging data is typically based on supervised learning, which requires a large number of ground-truth labels to be informative. As ground-truth labels are often missing or expensive to obtain in neuroscience, we avoid them in our analysis by combing factor disentanglement with self-supervised learning to identify changes and consistencies across the multiple MRIs acquired of each individual over time. Specifically, we propose a new definition of disentanglement by formulating a multivariate mapping between factors (e.g., brain age) associated with an MRI and a latent image representation. Then, factors that evolve across acquisitions of longitudinal sequences are disentangled from that mapping by self-supervised learning in such a way that changes in a single factor induce change along one direction in the representation space. We implement this model, named Longitudinal Self-Supervised Learning (LSSL), via a standard autoencoding structure with a cosine loss to disentangle brain age from the image representation. We apply LSSL to two longitudinal neuroimaging studies to highlight its strength in extracting the brain-age information from MRI and revealing informative characteristics associated with neurodegenerative and neuropsychological disorders. Moreover, the representations learned by LSSL facilitate supervised classification by recording faster convergence and higher (or similar) prediction accuracy compared to several other representation learning techniques.
Non-convergence of stochastic gradient descent in the training of deep neural networks
Venue: arXiv cs.LG 2021
Year: 2021

Deep neural networks have successfully been trained in various application areas with stochastic gradient descent. However, there exists no rigorous mathematical explanation why this works so well. The training of neural networks with stochastic gradient descent has four different discretization parameters: (i) the network architecture; (ii) the amount of training data; (iii) the number of gradient steps; and (iv) the number of randomly initialized gradient trajectories. While it can be shown that the approximation error converges to zero if all four parameters are sent to infinity in the right order, we demonstrate in this paper that stochastic gradient descent fails to converge for ReLU networks if their depth is much larger than their width and the number of random initializations does not increase to infinity fast enough.
Fourier Sparse Leverage Scores and Approximate Kernel Learning
Venue: arXiv cs.DS 2021
Year: 2021

We prove new explicit upper bounds on the leverage scores of Fourier sparse functions under both the Gaussian and Laplace measures. In particular, we study $s$-sparse functions of the form $f(x) = \sum_{j=1}^s a_j e^{i λ_j x}$ for coefficients $a_j \in \mathbb{C}$ and frequencies $λ_j \in \mathbb{R}$. Bounding Fourier sparse leverage scores under various measures is of pure mathematical interest in approximation theory, and our work extends existing results for the uniform measure [Erd17,CP19a]. Practically, our bounds are motivated by two important applications in machine learning: 1. Kernel Approximation. They yield a new random Fourier features algorithm for approximating Gaussian and Cauchy (rational quadratic) kernel matrices. For low-dimensional data, our method uses a near optimal number of features, and its runtime is polynomial in the $statistical\ dimension$ of the approximated kernel matrix. It is the first "oblivious sketching method" with this property for any kernel besides the polynomial kernel, resolving an open question of [AKM+17,AKK+20b]. 2. Active Learning. They can be used as non-uniform sampling distributions for robust active learning when data follows a Gaussian or Laplace distribution. Using the framework of [AKM+19], we provide essentially optimal results for bandlimited and multiband interpolation, and Gaussian process regression. These results generalize existing work that only applies to uniformly distributed data.
Mean-Field Approximation to Gaussian-Softmax Integral with Application to Uncertainty Estimation
Venue: arXiv cs.LG 2021
Year: 2021

Many methods have been proposed to quantify the predictive uncertainty associated with the outputs of deep neural networks. Among them, ensemble methods often lead to state-of-the-art results, though they require modifications to the training procedures and are computationally costly for both training and inference. In this paper, we propose a new single-model based approach. The main idea is inspired by the observation that we can "simulate" an ensemble of models by drawing from a Gaussian distribution, with a form similar to those from the asymptotic normality theory, infinitesimal Jackknife, Laplacian approximation to Bayesian neural networks, and trajectories in stochastic gradient descents. However, instead of using each model in the "ensemble" to predict and then aggregating their predictions, we integrate the Gaussian distribution and the softmax outputs of the neural networks. We use a mean-field approximation formula to compute this analytically intractable integral. The proposed approach has several appealing properties: it functions as an ensemble without requiring multiple models, and it enables closed-form approximate inference using only the first and second moments of the Gaussian. Empirically, the proposed approach performs competitively when compared to state-of-the-art methods, including deep ensembles, temperature scaling, dropout and Bayesian NNs, on standard uncertainty estimation tasks. It also outperforms many methods on out-of-distribution detection.
SDCOR: Scalable Density-based Clustering for Local Outlier Detection in Massive-Scale Datasets
Venue: arXiv cs.LG 2021
Year: 2021

This paper presents a batch-wise density-based clustering approach for local outlier detection in massive-scale datasets. Unlike the well-known traditional algorithms, which assume that all the data is memory-resident, our proposed method is scalable and processes the input data chunk-by-chunk within the confines of a limited memory buffer. A temporary clustering model is built at the first phase; then, it is gradually updated by analyzing consecutive memory loads of points. Subsequently, at the end of scalable clustering, the approximate structure of the original clusters is obtained. Finally, by another scan of the entire dataset and using a suitable criterion, an outlying score is assigned to each object called SDCOR (Scalable Density-based Clustering Outlierness Ratio). Evaluations on real-life and synthetic datasets demonstrate that the proposed method has a low linear time complexity and is more effective and efficient compared to best-known conventional density-based methods, which need to load all data into the memory; and also, to some fast distance-based methods, which can perform on data resident in the disk.
v2e: From Video Frames to Realistic DVS Events
Venue: arXiv cs.CV 2021
Year: 2021

To help meet the increasing need for dynamic vision sensor (DVS) event camera data, this paper proposes the v2e toolbox that generates realistic synthetic DVS events from intensity frames. It also clarifies incorrect claims about DVS motion blur and latency characteristics in recent literature. Unlike other toolboxes, v2e includes pixel-level Gaussian event threshold mismatch, finite intensity-dependent bandwidth, and intensity-dependent noise. Realistic DVS events are useful in training networks for uncontrolled lighting conditions. The use of v2e synthetic events is demonstrated in two experiments. The first experiment is object recognition with N-Caltech 101 dataset. Results show that pretraining on various v2e lighting conditions improves generalization when transferred on real DVS data for a ResNet model. The second experiment shows that for night driving, a car detector trained with v2e events shows an average accuracy improvement of 40% compared to the YOLOv3 trained on intensity frames.
Dual T: Reducing Estimation Error for Transition Matrix in Label-noise Learning
Venue: arXiv cs.LG 2021
Year: 2021

The transition matrix, denoting the transition relationship from clean labels to noisy labels, is essential to build statistically consistent classifiers in label-noise learning. Existing methods for estimating the transition matrix rely heavily on estimating the noisy class posterior. However, the estimation error for noisy class posterior could be large due to the randomness of label noise, which would lead the transition matrix to be poorly estimated. Therefore, in this paper, we aim to solve this problem by exploiting the divide-and-conquer paradigm. Specifically, we introduce an intermediate class to avoid directly estimating the noisy class posterior. By this intermediate class, the original transition matrix can then be factorized into the product of two easy-to-estimate transition matrices. We term the proposed method the dual-T estimator. Both theoretical analyses and empirical results illustrate the effectiveness of the dual-T estimator for estimating transition matrices, leading to better classification performances.
Benchmarking Multi-Agent Deep Reinforcement Learning Algorithms in Cooperative Tasks
Venue: arXiv cs.LG 2021
Year: 2021

Multi-agent deep reinforcement learning (MARL) suffers from a lack of commonly-used evaluation tasks and criteria, making comparisons between approaches difficult. In this work, we provide a systematic evaluation and comparison of three different classes of MARL algorithms (independent learning, centralised multi-agent policy gradient, value decomposition) in a diverse range of cooperative multi-agent learning tasks. Our experiments serve as a reference for the expected performance of algorithms across different learning tasks, and we provide insights regarding the effectiveness of different learning approaches. We open-source EPyMARL, which extends the PyMARL codebase to include additional algorithms and allow for flexible configuration of algorithm implementation details such as parameter sharing. Finally, we open-source two environments for multi-agent research which focus on coordination under sparse rewards.
Optimal Transport for Conditional Domain Matching and Label Shift
Venue: arXiv cs.LG 2021
Year: 2021

We address the problem of unsupervised domain adaptation under the setting of generalized target shift (joint class-conditional and label shifts). For this framework, we theoretically show that, for good generalization, it is necessary to learn a latent representation in which both marginals and class-conditional distributions are aligned across domains. For this sake, we propose a learning problem that minimizes importance weighted loss in the source domain and a Wasserstein distance between weighted marginals. For a proper weighting, we provide an estimator of target label proportion by blending mixture estimation and optimal matching by optimal transport. This estimation comes with theoretical guarantees of correctness under mild assumptions. Our experimental results show that our method performs better on average than competitors across a range domain adaptation problems including \emph{digits},\emph{VisDA} and \emph{Office}. Code for this paper is available at \url{https://github.com/arakotom/mars_domain_adaptation}.
COVID-19 Vaccine Acceptance in the US and UK in the Early Phase of the Pandemic: AI-Generated Vaccines Hesitancy for Minors, and the Role of Governments
Venue: arXiv cs.CY 2021
Year: 2021

This study presents survey results of the public's willingness to get vaccinated against COVID-19 during an early phase of the pandemic and examines factors that could influence vaccine acceptance based on a between-subjects design. A representative quota sample of 572 adults in the US and UK participated in an online survey. First, the participants' medical use tendencies and initial vaccine acceptance were assessed; then, short vignettes were provided to evaluate their changes in attitude towards COVID-19 vaccines. For data analysis, ANOVA and post hoc pairwise comparisons were used. The participants were more reluctant to vaccinate their children than themselves and the elderly. The use of artificial intelligence (AI) in vaccine development did not influence vaccine acceptance. Vignettes that explicitly stated the high effectiveness of vaccines led to an increase in vaccine acceptance. Our study suggests public policies emphasizing the vaccine effectiveness against the virus could lead to higher vaccination rates. We also discuss the public's expectations of governments concerning vaccine safety and present a series of implications based on our findings.