Long-term stability and physical consistency are critical properties for AI-based weather models if they are going to be used for subseasonal-to-seasonal forecasts or beyond, e.g., climate change projection. However, current AI-based weather models can only provide short-term forecasts accurately since they become unstable or physically inconsistent when time-integrated beyond a few weeks or a few months. Either they exhibit numerical blow-up or hallucinate unrealistic dynamics of the atmospheric variables, akin to the current class of autoregressive large language models. The cause of the instabilities is unknown, and the methods that are used to improve their stability horizons are ad-hoc and lack rigorous theory. In this paper, we reveal that the universal causal mechanism for these instabilities in any turbulent flow is due to \textit{spectral bias} wherein, \textit{any} deep learning architecture is biased to learn only the large-scale dynamics and ignores the small scales completely. We further elucidate how turbulence physics and the absence of convergence in deep learning-based time-integrators amplify this bias, leading to unstable error propagation. Finally, using the quasi-geostrophic flow and European Center for Medium-Range Weather Forecasting (ECMWF) Reanalysis data as test cases, we bridge the gap between deep learning theory and numerical analysis to propose one mitigative solution to such unphysical behavior. We develop long-term physically-consistent data-driven models for the climate system and demonstrate accurate short-term forecasts, and hundreds of years of time-integration with accurate mean and variability.
Next generation cars embed intelligent assessment of car driving safety through innovative solutions often based on usage of artificial intelligence. The safety driving monitoring can be carried out using several methodologies widely treated in scientific literature. In this context, the author proposes an innovative approach that uses ad-hoc bio-sensing system suitable to reconstruct the physio-based attentional status of the car driver. To reconstruct the car driver physiological status, the author proposed the use of a bio-sensing probe consisting of a coupled LEDs at Near infrared (NiR) spectrum with a photodetector. This probe placed over the monitored subject allows to detect a physiological signal called PhotoPlethysmoGraphy (PPG). The PPG signal formation is regulated by the change in oxygenated and non-oxygenated hemoglobin concentration in the monitored subject bloodstream which will be directly connected to cardiac activity in turn regulated by the Autonomic Nervous System (ANS) that characterizes the subject's attention level. This so designed car driver drowsiness monitoring will be combined with further driving safety assessment based on correlated intelligent driving scenario understanding.
Effective quantification of uncertainty is an essential and still missing step towards a greater adoption of deep-learning approaches in different applications, including mission-critical ones. In particular, investigations on the predictive uncertainty of deep-learning models describing non-linear dynamical systems are very limited to date. This paper is aimed at filling this gap and presents preliminary results on uncertainty quantification for system identification with neural state-space models. We frame the learning problem in a Bayesian probabilistic setting and obtain posterior distributions for the neural network's weights and outputs through approximate inference techniques. Based on the posterior, we construct credible intervals on the outputs and define a surprise index which can effectively diagnose usage of the model in a potentially dangerous out-of-distribution regime, where predictions cannot be trusted.
Accurate delineation of key waveforms in an ECG is a critical step in extracting relevant features to support the diagnosis and treatment of heart conditions. Although deep learning based methods using segmentation models to locate P, QRS, and T waves have shown promising results, their ability to handle arrhythmias has not been studied in any detail. In this paper we investigate the effect of arrhythmias on delineation quality and develop strategies to improve performance in such cases. We introduce a U-Net-like segmentation model for ECG delineation with a particular focus on diverse arrhythmias. This is followed by a post-processing algorithm which removes noise and automatically determines the boundaries of P, QRS, and T waves. Our model has been trained on a diverse dataset and evaluated against the LUDB and QTDB datasets to show strong performance, with F1-scores exceeding 99% for QRS and T waves, and over 97% for P waves in the LUDB dataset. Furthermore, we assess various models across a wide array of arrhythmias and observe that models with a strong performance on standard benchmarks may still perform poorly on arrhythmias that are underrepresented in these benchmarks, such as tachycardias. We propose solutions to address this discrepancy.
Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020. Breast imaging plays a significant role in early diagnosis and intervention to improve the outcome of breast cancer patients. In the past decade, deep learning has shown remarkable progress in breast cancer imaging analysis, holding great promise in interpreting the rich information and complex context of breast imaging modalities. Considering the rapid improvement in deep learning technology and the increasing severity of breast cancer, it is critical to summarize past progress and identify future challenges to be addressed. This paper provides an extensive review of deep learning-based breast cancer imaging research, covering studies on mammogram, ultrasound, magnetic resonance imaging, and digital pathology images over the past decade. The major deep learning methods and applications on imaging-based screening, diagnosis, treatment response prediction, and prognosis are elaborated and discussed. Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging.
The ability of convolutional neural networks (CNNs) to recognize objects regardless of their position in the image is due to the translation-equivariance of the convolutional operation. Group-equivariant CNNs transfer this equivariance to other transformations of the input. Dealing appropriately with objects and object parts of different scale is challenging, and scale can vary for multiple reasons such as the underlying object size or the resolution of the imaging modality. In this paper, we propose a scale-equivariant convolutional network layer for three-dimensional data that guarantees scale-equivariance in 3D CNNs. Scale-equivariance lifts the burden of having to learn each possible scale separately, allowing the neural network to focus on higher-level learning goals, which leads to better results and better data-efficiency. We provide an overview of the theoretical foundations and scientific work on scale-equivariant neural networks in the two-dimensional domain. We then transfer the concepts from 2D to the three-dimensional space and create a scale-equivariant convolutional layer for 3D data. Using the proposed scale-equivariant layer, we create a scale-equivariant U-Net for medical image segmentation and compare it with a non-scale-equivariant baseline method. Our experiments demonstrate the effectiveness of the proposed method in achieving scale-equivariance for 3D medical image analysis. We publish our code at https://github.com/wimmerth/scale-equivariant-3d-convnet for further research and application.
Multivariate time series classification (MTSC) is an important data mining task, which can be effectively solved by popular deep learning technology. Unfortunately, the existing deep learning-based methods neglect the hidden dependencies in different dimensions and also rarely consider the unique dynamic features of time series, which lack sufficient feature extraction capability to obtain satisfactory classification accuracy. To address this problem, we propose a novel temporal dynamic graph neural network (TodyNet) that can extract hidden spatio-temporal dependencies without undefined graph structure. It enables information flow among isolated but implicit interdependent variables and captures the associations between different time slots by dynamic graph mechanism, which further improves the classification performance of the model. Meanwhile, the hierarchical representations of graphs cannot be learned due to the limitation of GNNs. Thus, we also design a temporal graph pooling layer to obtain a global graph-level representation for graph learning with learnable temporal parameters. The dynamic graph, graph information propagation, and temporal convolution are jointly learned in an end-to-end framework. The experiments on 26 UEA benchmark datasets illustrate that the proposed TodyNet outperforms existing deep learning-based methods in the MTSC tasks.
The consumption of microbial-contaminated food and water is responsible for the deaths of millions of people annually. Smartphone-based microscopy systems are portable, low-cost, and more accessible alternatives for the detection of Giardia and Cryptosporidium than traditional brightfield microscopes. However, the images from smartphone microscopes are noisier and require manual cyst identification by trained technicians, usually unavailable in resource-limited settings. Automatic detection of (oo)cysts using deep-learning-based object detection could offer a solution for this limitation. We evaluate the performance of four state-of-the-art object detectors to detect (oo)cysts of Giardia and Cryptosporidium on a custom dataset that includes both smartphone and brightfield microscopic images from vegetable samples. Faster RCNN, RetinaNet, You Only Look Once (YOLOv8s), and Deformable Detection Transformer (Deformable DETR) deep-learning models were employed to explore their efficacy and limitations. Our results show that while the deep-learning models perform better with the brightfield microscopy image dataset than the smartphone microscopy image dataset, the smartphone microscopy predictions are still comparable to the prediction performance of non-experts. Also, we publicly release brightfield and smartphone microscopy datasets with the benchmark results for the detection of Giardia and Cryptosporidium, independently captured on reference (or standard lab setting) and vegetable samples. Our code and dataset are available at https://github.com/naamiinepal/smartphone_microscopy and https://doi.org/10.5281/zenodo.7813183, respectively.
Predictions made by deep learning models are prone to data perturbations, adversarial attacks, and out-of-distribution inputs. To build a trusted AI system, it is therefore critical to accurately quantify the prediction uncertainties. While current efforts focus on improving uncertainty quantification accuracy and efficiency, there is a need to identify uncertainty sources and take actions to mitigate their effects on predictions. Therefore, we propose to develop explainable and actionable Bayesian deep learning methods to not only perform accurate uncertainty quantification but also explain the uncertainties, identify their sources, and propose strategies to mitigate the uncertainty impacts. Specifically, we introduce a gradient-based uncertainty attribution method to identify the most problematic regions of the input that contribute to the prediction uncertainty. Compared to existing methods, the proposed UA-Backprop has competitive accuracy, relaxed assumptions, and high efficiency. Moreover, we propose an uncertainty mitigation strategy that leverages the attribution results as attention to further improve the model performance. Both qualitative and quantitative evaluations are conducted to demonstrate the effectiveness of our proposed methods.
The architecture of a deep neural network is defined explicitly in terms of the number of layers, the width of each layer and the general network topology. Existing optimisation frameworks neglect this information in favour of implicit architectural information (e.g. second-order methods) or architecture-agnostic distance functions (e.g. mirror descent). Meanwhile, the most popular optimiser in practice, Adam, is based on heuristics. This paper builds a new framework for deriving optimisation algorithms that explicitly leverage neural architecture. The theory extends mirror descent to non-convex composite objective functions: the idea is to transform a Bregman divergence to account for the non-linear structure of neural architecture. Working through the details for deep fully-connected networks yields automatic gradient descent: a first-order optimiser without any hyperparameters. Automatic gradient descent trains both fully-connected and convolutional networks out-of-the-box and at ImageNet scale. A PyTorch implementation is available at https://github.com/jxbz/agd and also in Appendix B. Overall, the paper supplies a rigorous theoretical foundation for a next-generation of architecture-dependent optimisers that work automatically and without hyperparameters.
Deep Learning (DL) can predict biomarkers from cancer histopathology. Several clinically approved applications use this technology. Most approaches, however, predict categorical labels, whereas biomarkers are often continuous measurements. We hypothesized that regression-based DL outperforms classification-based DL. Therefore, we developed and evaluated a new self-supervised attention-based weakly supervised regression method that predicts continuous biomarkers directly from images in 11,671 patients across nine cancer types. We tested our method for multiple clinically and biologically relevant biomarkers: homologous repair deficiency (HRD) score, a clinically used pan-cancer biomarker, as well as markers of key biological processes in the tumor microenvironment. Using regression significantly enhances the accuracy of biomarker prediction, while also improving the interpretability of the results over classification. In a large cohort of colorectal cancer patients, regression-based prediction scores provide a higher prognostic value than classification-based scores. Our open-source regression approach offers a promising alternative for continuous biomarker analysis in computational pathology.
Deep learning models can be fooled by small $l_p$-norm adversarial perturbations and natural perturbations in terms of attributes. Although the robustness against each perturbation has been explored, it remains a challenge to address the robustness against joint perturbations effectively. In this paper, we study the robustness of deep learning models against joint perturbations by proposing a novel attack mechanism named Semantic-Preserving Adversarial (SPA) attack, which can then be used to enhance adversarial training. Specifically, we introduce an attribute manipulator to generate natural and human-comprehensible perturbations and a noise generator to generate diverse adversarial noises. Based on such combined noises, we optimize both the attribute value and the diversity variable to generate jointly-perturbed samples. For robust training, we adversarially train the deep learning model against the generated joint perturbations. Empirical results on four benchmarks show that the SPA attack causes a larger performance decline with small $l_{\infty}$ norm-ball constraints compared to existing approaches. Furthermore, our SPA-enhanced training outperforms existing defense methods against such joint perturbations.
Compiled binary executables are often the only available artifact in reverse engineering, malware analysis, and software systems maintenance. Unfortunately, the lack of semantic information like variable types makes comprehending binaries difficult. In efforts to improve the comprehensibility of binaries, researchers have recently used machine learning techniques to predict semantic information contained in the original source code. Chen et al. implemented DIRTY, a Transformer-based Encoder-Decoder architecture capable of augmenting decompiled code with variable names and types by leveraging decompiler output tokens and variable size information. Chen et al. were able to demonstrate a substantial increase in name and type extraction accuracy on Hex-Rays decompiler outputs compared to existing static analysis and AI-based techniques. We extend the original DIRTY results by re-training the DIRTY model on a dataset produced by the open-source Ghidra decompiler. Although Chen et al. concluded that Ghidra was not a suitable decompiler candidate due to its difficulty in parsing and incorporating DWARF symbols during analysis, we demonstrate that straightforward parsing of variable data generated by Ghidra results in similar retyping performance. We hope this work inspires further interest and adoption of the Ghidra decompiler for use in research projects.
Deep learning has gained immense popularity in the Earth sciences as it enables us to formulate purely data-driven models of complex Earth system processes. Deep learning-based weather prediction (DLWP) models have made significant progress in the last few years, achieving forecast skills comparable to established numerical weather prediction models with comparatively lesser computational costs. In order to train accurate, reliable, and tractable DLWP models with several millions of parameters, the model design needs to incorporate suitable inductive biases that encode structural assumptions about the data and the modelled processes. When chosen appropriately, these biases enable faster learning and better generalisation to unseen data. Although inductive biases play a crucial role in successful DLWP models, they are often not stated explicitly and their contribution to model performance remains unclear. Here, we review and analyse the inductive biases of state-of-the-art DLWP models with respect to five key design elements: data selection, learning objective, loss function, architecture, and optimisation method. We identify the most important inductive biases and highlight potential avenues towards more efficient and probabilistic DLWP models.
The vulnerability in the algorithm supply chain of deep learning has imposed new challenges to image retrieval systems in the downstream. Among a variety of techniques, deep hashing is gaining popularity. As it inherits the algorithmic backend from deep learning, a handful of attacks are recently proposed to disrupt normal image retrieval. Unfortunately, the defense strategies in softmax classification are not readily available to be applied in the image retrieval domain. In this paper, we propose an efficient and unsupervised scheme to identify unique adversarial behaviors in the hamming space. In particular, we design three criteria from the perspectives of hamming distance, quantization loss and denoising to defend against both untargeted and targeted attacks, which collectively limit the adversarial space. The extensive experiments on four datasets demonstrate 2-23% improvements of detection rates with minimum computational overhead for real-time image queries.
Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source options exist for deploying models in an interactive interface. Experimenting with different deep learning approaches typically requires switching software libraries and reprocessing data, reducing the feasibility and practicality of experimenting with new architectures. We developed a flexible deep learning library for histopathology called Slideflow, a package which supports a broad array of deep learning methods for digital pathology and includes a fast whole-slide interface for deploying trained models. Slideflow includes unique tools for whole-slide image data processing, efficient stain normalization and augmentation, weakly-supervised whole-slide classification, uncertainty quantification, feature generation, feature space analysis, and explainability. Whole-slide image processing is highly optimized, enabling whole-slide tile extraction at 40X magnification in 2.5 seconds per slide. The framework-agnostic data processing pipeline enables rapid experimentation with new methods built with either Tensorflow or PyTorch, and the graphical user interface supports real-time visualization of slides, predictions, heatmaps, and feature space characteristics on a variety of hardware devices, including ARM-based devices such as the Raspberry Pi.
Micropaleontology in geosciences focuses on studying the evolution of microfossils (e.g., foraminifera) through geological records to reconstruct past environmental and climatic conditions. This field heavily relies on visual recognition of microfossil features, making it suitable for computer vision technology, specifically deep convolutional neural networks (CNNs), to automate and optimize microfossil identification and classification. However, the application of deep learning in micropaleontology is hindered by limited availability of high-quality, high-resolution labeled fossil images and the significant manual labeling effort required by experts. To address these challenges, we propose a novel deep learning workflow combining hierarchical vision transformers with style-based generative adversarial network algorithms to efficiently acquire and synthetically generate realistic high-resolution labeled datasets of micropaleontology in large volumes. Our study shows that this workflow can generate high-resolution images with a high signal-to-noise ratio (39.1 dB) and realistic synthetic images with a Frechet inception distance similarity score of 14.88. Additionally, our workflow provides a large volume of self-labeled datasets for model benchmarking and various downstream visual tasks, including fossil classification and segmentation. For the first time, we performed few-shot semantic segmentation of different foraminifera chambers on both generated and synthetic images with high accuracy. This novel meta-learning approach is only possible with the availability of high-resolution, high-volume labeled datasets. Our deep learning-based workflow shows promise in advancing and optimizing micropaleontological research and other visual-dependent geological analyses.
Knowledge graphs (KGs) store rich facts about the real world. In this paper, we study KG alignment, which aims to find alignment between not only entities but also relations and classes in different KGs. Alignment at the entity level can cross-fertilize alignment at the schema level. We propose a new KG alignment approach, called DAAKG, based on deep learning and active learning. With deep learning, it learns the embeddings of entities, relations and classes, and jointly aligns them in a semi-supervised manner. With active learning, it estimates how likely an entity, relation or class pair can be inferred, and selects the best batch for human labeling. We design two approximation algorithms for efficient solution to batch selection. Our experiments on benchmark datasets show the superior accuracy and generalization of DAAKG and validate the effectiveness of all its modules.
This paper presents a deep learning-based pipeline for categorizing Bengali toxic comments, in which at first a binary classification model is used to determine whether a comment is toxic or not, and then a multi-label classifier is employed to determine which toxicity type the comment belongs to. For this purpose, we have prepared a manually labeled dataset consisting of 16,073 instances among which 8,488 are Toxic and any toxic comment may correspond to one or more of the six toxic categories - vulgar, hate, religious, threat, troll, and insult simultaneously. Long Short Term Memory (LSTM) with BERT Embedding achieved 89.42% accuracy for the binary classification task while as a multi-label classifier, a combination of Convolutional Neural Network and Bi-directional Long Short Term Memory (CNN-BiLSTM) with attention mechanism achieved 78.92% accuracy and 0.86 as weighted F1-score. To explain the predictions and interpret the word feature importance during classification by the proposed models, we utilized Local Interpretable Model-Agnostic Explanations (LIME) framework. We have made our dataset public and can be accessed at - https://github.com/deepu099cse/Multi-Labeled-Bengali-Toxic-Comments-Classification
Multiple Sclerosis (MS) is a chronic disease developed in human brain and spinal cord, which can cause permanent damage or deterioration of the nerves. The severity of MS disease is monitored by the Expanded Disability Status Scale (EDSS), composed of several functional sub-scores. Early and accurate classification of MS disease severity is critical for slowing down or preventing disease progression via applying early therapeutic intervention strategies. Recent advances in deep learning and the wide use of Electronic Health Records (EHR) creates opportunities to apply data-driven and predictive modeling tools for this goal. Previous studies focusing on using single-modal machine learning and deep learning algorithms were limited in terms of prediction accuracy due to the data insufficiency or model simplicity. In this paper, we proposed an idea of using patients' multimodal longitudinal and longitudinal EHR data to predict multiple sclerosis disease severity at the hospital visit. This work has two important contributions. First, we describe a pilot effort to leverage structured EHR data, neuroimaging data and clinical notes to build a multi-modal deep learning framework to predict patient's MS disease severity. The proposed pipeline demonstrates up to 25% increase in terms of the area under the Area Under the Receiver Operating Characteristic curve (AUROC) compared to models using single-modal data. Second, the study also provides insights regarding the amount useful signal embedded in each data modality with respect to MS disease prediction, which may improve data collection processes.