Recent advances in deep learning models for sequence classification have greatly improved their classification accuracy, specially when large training sets are available. However, several works have suggested that under some settings the predictions made by these models are poorly calibrated. In this work we study binary sequence classification problems and we look at model calibration from a different perspective by asking the question: Are deep learning models capable of learning the underlying target class distribution? We focus on sparse sequence classification, that is problems in which the target class is rare and compare three deep learning sequence classification models. We develop an evaluation that measures how well a classifier is learning the target class distribution. In addition, our evaluation disentangles good performance achieved by mere compression of the training sequences versus performance achieved by proper model generalization. Our results suggest that in this binary setting the deep-learning models are indeed able to learn the underlying class distribution in a non-trivial manner, i.e. by proper generalization beyond data compression.
The goal of Bayesian deep learning is to provide uncertainty quantification via the posterior distribution. However, exact inference over the weight space is computationally intractable due to the ultra-high dimensions of the neural network. Variational inference (VI) is a promising approach, but naive application on weight space does not scale well and often underperform on predictive accuracy. In this paper, we propose a new adaptive variational Bayesian algorithm to train neural networks on weight space that achieves high predictive accuracy. By showing that there is an equivalence to Stochastic Gradient Hamiltonian Monte Carlo(SGHMC) with preconditioning matrix, we then propose an MCMC within EM algorithm, which incorporates the spike-and-slab prior to capture the sparsity of the neural network. The EM-MCMC algorithm allows us to perform optimization and model pruning within one-shot. We evaluate our methods on CIFAR-10, CIFAR-100 and ImageNet datasets, and demonstrate that our dense model can reach the state-of-the-art performance and our sparse model perform very well compared to previously proposed pruning schemes.
Mass Spectrometry Imaging (MSI), using traditional rectilinear scanning, takes hours to days for high spatial resolution acquisitions. Given that most pixels within a sample's field of view are often neither relevant to underlying biological structures nor chemically informative, MSI presents as a prime candidate for integration with sparse and dynamic sampling algorithms. During a scan, stochastic models determine which locations probabilistically contain information critical to the generation of low-error reconstructions. Decreasing the number of required physical measurements thereby minimizes overall acquisition times. A Deep Learning Approach for Dynamic Sampling (DLADS), utilizing a Convolutional Neural Network (CNN) and encapsulating molecular mass intensity distributions within a third dimension, demonstrates a simulated 70% throughput improvement for Nanospray Desorption Electrospray Ionization (nano-DESI) MSI tissues. Evaluations are conducted between DLADS and a Supervised Learning Approach for Dynamic Sampling, with Least-Squares regression (SLADS-LS) and a Multi-Layer Perceptron (MLP) network (SLADS-Net). When compared with SLADS-LS, limited to a single m/z channel, as well as multichannel SLADS-LS and SLADS-Net, DLADS respectively improves regression performance by 36.7%, 7.0%, and 6.2%, resulting in gains to reconstruction quality of 6.0%, 2.1%, and 3.4% for acquisition of targeted m/z.
Plant phenotyping refers to a quantitative description of the plants properties, however in image-based phenotyping analysis, our focus is primarily on the plants anatomical, ontogenetical and physiological properties.This technique reinforced by the success of Deep Learning in the field of image based analysis is applicable to a wide range of research areas making high-throughput screens of plants possible, reducing the time and effort needed for phenotypic characterization.In this study, we use Deep Learning methods (supervised and unsupervised learning based approaches) to semantically segment grapevine leaves images in order to develop an automated object detection (through segmentation) system for leaf phenotyping which will yield information regarding their structure and function.In these directions we studied several deep learning approaches with promising results as well as we reported some future challenging tasks in the area of precision agriculture.Our work contributes to plant lifecycle monitoring through which dynamic traits such as growth and development can be captured and quantified, targeted intervention and selective application of agrochemicals and grapevine variety identification which are key prerequisites in sustainable agriculture.
Forecasting global precipitation patterns and, in particular, extreme precipitation events is of critical importance to preparing for and adapting to climate change. Making accurate high-resolution precipitation forecasts using traditional physical models remains a major challenge in operational weather forecasting as they incur substantial computational costs and struggle to achieve sufficient forecast skill. Recently, deep-learning-based models have shown great promise in closing the gap with numerical weather prediction (NWP) models in terms of precipitation forecast skill, opening up exciting new avenues for precipitation modeling. However, it is challenging for these deep learning models to fully resolve the fine-scale structures of precipitation phenomena and adequately characterize the extremes of the long-tailed precipitation distribution. In this work, we present several improvements to the architecture and training process of a current state-of-the art deep learning precipitation model (FourCastNet) using a novel generative adversarial network (GAN) to better capture fine scales and extremes. Our improvements achieve superior performance in capturing the extreme percentiles of global precipitation, while comparable to state-of-the-art NWP models in terms of forecast skill at 1--2 day lead times. Together, these improvements set a new state-of-the-art in global precipitation forecasting.
Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.
Cloud computing is used in many different research areas thanks to its high computing power and network capacity. Data security, cost-effectiveness, and flexibility of working options for remote workers have made this technology even more attractive today. Today, servers in cloud computing should protect themselves from threats more intelligently and provide security by preventing a new threat. A new deep learning model based on convolutional neural networks and recurrent neural networks for intrusion detection has been developed for cloud security in this study. The proposed model was trained and tested using NSL-KDD train dataset. With our deep learning model, any detected and not approved traffic is prevented from reaching the server in the cloud. The proposed system has 99.86% accuracy for five-class classification, which is the best result comparative to studies in the literature.
Weather extremes are a major societal and economic hazard, claiming thousands of lives and causing billions of dollars in damage every year. Under climate change, their impact and intensity are expected to worsen significantly. Unfortunately, general circulation models (GCMs), which are currently the primary tool for climate projections, cannot characterize weather extremes accurately. To address this, we present a multi-resolution deep-learning framework that, firstly, corrects a GCM's biases by matching low-order and tail statistics of its output with observations at coarse scales; and secondly, increases the level of detail of the debiased GCM output by reconstructing the finer scales as a function of the coarse scales. We use the proposed framework to generate statistically realistic realizations of the climate over Western Europe from a simple GCM corrected using observational atmospheric reanalysis. We also discuss implications for probabilistic risk assessment of natural disasters in a changing climate.
An article published on Medical News Today in June 2022 presented a fundamental question in its title: Can an earlobe crease predict heart attacks? The author explained that end arteries supply the heart and ears. In other words, if they lose blood supply, no other arteries can take over, resulting in tissue damage. Consequently, some earlobes have a diagonal crease, line, or deep fold that resembles a wrinkle. In this paper, we take a step toward detecting this specific marker, commonly known as DELC or Frank's Sign. For this reason, we have made the first DELC dataset available to the public. In addition, we have investigated the performance of numerous cutting-edge backbones on annotated photos. Experimentally, we demonstrate that it is possible to solve this challenge by combining pre-trained encoders with a customized classifier to achieve 97.7% accuracy. Moreover, we have analyzed the backbone trade-off between performance and size, estimating MobileNet as the most promising encoder.
We develop a novel deep learning method for uncertainty quantification in stochastic partial differential equations based on Bayesian neural network (BNN) and Hamiltonian Monte Carlo (HMC). A BNN efficiently learns the posterior distribution of the parameters in deep neural networks by performing Bayesian inference on the network parameters. The posterior distribution is efficiently sampled using HMC to quantify uncertainties in the system. Several numerical examples are shown for both forward and inverse problems in high dimension to demonstrate the effectiveness of the proposed method for uncertainty quantification. These also show promising results that the computational cost is almost independent of the dimension of the problem demonstrating the potential of the method for tackling the so-called curse of dimensionality.
The COVID-19 pandemic has affected countries across the world, demanding drastic public health policies to mitigate the spread of infection, leading to economic crisis as a collateral damage. In this work, we investigated the impact of human mobility (described via international commercial flights) on COVID-19 infection dynamics at the global scale. For this, we developed a graph neural network-based framework referred to as Dynamic Connectivity GraphSAGE (DCSAGE), which operates over spatiotemporal graphs and is well-suited for dynamically changing adjacency information. To obtain insights on the relative impact of different geographical locations, due to their associated air traffic, on the evolution of the pandemic, we conducted local sensitivity analysis on our model through node perturbation experiments. From our analyses, we identified Western Europe, North America, and Middle East as the leading geographical locations fueling the pandemic, attributed to the enormity of air traffic originating or transiting through these regions. We used these observations to identify tangible air traffic reduction strategies that can have a high impact on controlling the pandemic, with minimal interference to human mobility. Our work provides a robust deep learning-based tool to study global pandemics and is of key relevance to policy makers to take informed decisions regarding air traffic restrictions during future outbreaks.
Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine learning, has been applied to macromolecular structures. This review provides an overview of the recent applications of geometric deep learning in bioorganic and medicinal chemistry, highlighting its potential for structure-based drug discovery and design. Emphasis is placed on molecular property prediction, ligand binding site and pose prediction, and structure-based de novo molecular design. The current challenges and opportunities are highlighted, and a forecast of the future of geometric deep learning for drug discovery is presented.
We introduce an $r-$adaptive algorithm to solve Partial Differential Equations using a Deep Neural Network. The proposed method restricts to tensor product meshes and optimizes the boundary node locations in one dimension, from which we build two- or three-dimensional meshes. The method allows the definition of fixed interfaces to design conforming meshes, and enables changes in the topology, i.e., some nodes can jump across fixed interfaces. The method simultaneously optimizes the node locations and the PDE solution values over the resulting mesh. To numerically illustrate the performance of our proposed $r-$adaptive method, we apply it in combination with a collocation method, a Least Squares Method, and a Deep Ritz Method. We focus on the latter to solve one- and two-dimensional problems whose solutions are smooth, singular, and/or exhibit strong gradients.
Topology optimization (TO) is a method of deriving an optimal design that satisfies a given load and boundary conditions within a design domain. This method enables effective design without initial design, but has been limited in use due to high computational costs. At the same time, machine learning (ML) methodology including deep learning has made great progress in the 21st century, and accordingly, many studies have been conducted to enable effective and rapid optimization by applying ML to TO. Therefore, this study reviews and analyzes previous research on ML-based TO (MLTO). Two different perspectives of MLTO are used to review studies: (1) TO and (2) ML perspectives. The TO perspective addresses "why" to use ML for TO, while the ML perspective addresses "how" to apply ML to TO. In addition, the limitations of current MLTO research and future research directions are examined.
Diffusion magnetic resonance imaging (MRI) is the only imaging modality for non-invasive movement detection of in vivo water molecules, with significant clinical and research applications. Diffusion weighted imaging (DWI) MRI acquired by multi-shot techniques can achieve higher resolution, better signal-to-noise ratio, and lower geometric distortion than single-shot, but suffers from inter-shot motion-induced artifacts. These artifacts cannot be removed prospectively, leading to the absence of artifact-free training labels. Thus, the potential of deep learning in multi-shot DWI reconstruction remains largely untapped. To break the training data bottleneck, here, we propose a Physics-Informed Deep DWI reconstruction method (PIDD) to synthesize high-quality paired training data by leveraging the physical diffusion model (magnitude synthesis) and inter-shot motion-induced phase model (motion phase synthesis). The network is trained only once with 100,000 synthetic samples, achieving encouraging results on multiple realistic in vivo data reconstructions. Advantages over conventional methods include: (a) Better motion artifact suppression and reconstruction stability; (b) Outstanding generalization to multi-scenario reconstructions, including multi-resolution, multi-b-value, multi-under-sampling, multi-vendor, and multi-center; (c) Excellent clinical adaptability to patients with verifications by seven experienced doctors (p<0.001). In conclusion, PIDD presents a novel deep learning framework by exploiting the power of MRI physics, providing a cost-effective and explainable way to break the data bottleneck in deep learning medical imaging.
Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates reproducibility guidelines, especially so in the medical imaging field. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in this direction by advocating open access, and recently also recommending authors to make their code public - both aspects being adopted by the majority of the conference submissions. This helps the reproducibility of the methods, however, there is currently little or no support for further evaluation of these supplementary material, making them vulnerable to poor quality, which affects the impact of the entire submission. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but slightly adjusted guidelines on reproducibility and the quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories has not improved over the years, leaving room for improvement in every aspect of designing repositories. Merely 22% of all submissions contain a repository that were deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL.
Several recent works have addressed the ability of deep learning to disclose rich, hierarchical and discriminative models for the most diverse purposes. Specifically in the super-resolution field, Convolutional Neural Networks (CNNs) using different deep learning approaches attempt to recover realistic texture and fine grained details from low resolution images. In this work we explore the viability of these approaches for iris Super-Resolution (SR) in an iris recognition environment. For this, we test different architectures with and without a so called image re-projection to reduce artifacts applying it to different iris databases to verify the viability of the different CNNs for iris super-resolution. Results show that CNNs and image re-projection can improve the results specially for the accuracy of recognition systems using a complete different training database performing the transfer learning successfully.
Limited throughput is a key challenge in in-vivo deep-tissue imaging using nonlinear optical microscopy. Point scanning multiphoton microscopy, the current gold standard, is slow especially compared to the wide-field imaging modalities used for optically cleared or thin specimens. We recently introduced 'De-scattering with Excitation Patterning or DEEP', as a widefield alternative to point-scanning geometries. Using patterned multiphoton excitation, DEEP encodes spatial information inside tissue before scattering. However, to de-scatter at typical depths, hundreds of such patterned excitations are needed. In this work, we present DEEP$^2$, a deep learning based model, that can de-scatter images from just tens of patterned excitations instead of hundreds. Consequently, we improve DEEP's throughput by almost an order of magnitude. We demonstrate our method in multiple numerical and physical experiments including in-vivo cortical vasculature imaging up to four scattering lengths deep, in alive mice.
Since the 2004 DARPA Grand Challenge, the autonomous driving technology has witnessed nearly two decades of rapid development. Particularly, in recent years, with the application of new sensors and deep learning technologies extending to the autonomous field, the development of autonomous driving technology has continued to make breakthroughs. Thus, many carmakers and high-tech giants dedicated to research and system development of autonomous driving. However, as the foundation of autonomous driving, the deep learning technology faces many new security risks. The academic community has proposed deep learning countermeasures against the adversarial examples and AI backdoor, and has introduced them into the autonomous driving field for verification. Deep learning security matters to autonomous driving system security, and then matters to personal safety, which is an issue that deserves attention and research.This paper provides an summary of the concepts, developments and recent research in deep learning security technologies in autonomous driving. Firstly, we briefly introduce the deep learning framework and pipeline in the autonomous driving system, which mainly include the deep learning technologies and algorithms commonly used in this field. Moreover, we focus on the potential security threats of the deep learning based autonomous driving system in each functional layer in turn. We reviews the development of deep learning attack technologies to autonomous driving, investigates the State-of-the-Art algorithms, and reveals the potential risks. At last, we provides an outlook on deep learning security in the autonomous driving field and proposes recommendations for building a safe and trustworthy autonomous driving system.
As a booming research area in the past decade, deep learning technologies have been driven by big data collected and processed on an unprecedented scale. However, privacy concerns arise due to the potential leakage of sensitive information from the training data. Recent research has revealed that deep learning models are vulnerable to various privacy attacks, including membership inference attacks, attribute inference attacks, and gradient inversion attacks. Notably, the efficacy of these attacks varies from model to model. In this paper, we answer a fundamental question: Does model architecture affect model privacy? By investigating representative model architectures from convolutional neural networks (CNNs) to Transformers, we demonstrate that Transformers generally exhibit higher vulnerability to privacy attacks than CNNs. Additionally, we identify the micro design of activation layers, stem layers, and LN layers, as major factors contributing to the resilience of CNNs against privacy attacks, while the presence of attention modules is another main factor that exacerbates the privacy vulnerability of Transformers. Our discovery reveals valuable insights for deep learning models to defend against privacy attacks and inspires the research community to develop privacy-friendly model architectures.