Contemporary deep learning models have demonstrated promising results across various applications within seismology and earthquake engineering. These models rely primarily on utilizing ground motion records for tasks such as earthquake event classification, localization, earthquake early warning systems, and structural health monitoring. However, the extent to which these models truly extract meaningful patterns from these complex time-series signals remains underexplored. In this study, our objective is to evaluate the degree to which auxiliary information, such as seismic phase arrival times or seismic station distribution within a network, dominates the process of deep learning from ground motion records, potentially hindering its effectiveness. Our experimental results reveal a strong dependence on the highly correlated Primary (P) and Secondary (S) phase arrival times. These findings expose a critical gap in the current research landscape, highlighting the lack of robust methodologies for deep learning from single-station ground motion recordings that do not rely on auxiliary inputs.
Knowledge tracing (KT) plays a crucial role in predicting students' future performance by analyzing their historical learning processes. Deep neural networks (DNNs) have shown great potential in solving the KT problem. However, there still exist some important challenges when applying deep learning techniques to model the KT process. The first challenge lies in taking the individual information of the question into modeling. This is crucial because, despite questions sharing the same knowledge component (KC), students' knowledge acquisition on homogeneous questions can vary significantly. The second challenge lies in interpreting the prediction results from existing deep learning-based KT models. In real-world applications, while it may not be necessary to have complete transparency and interpretability of the model parameters, it is crucial to present the model's prediction results in a manner that teachers find interpretable. This makes teachers accept the rationale behind the prediction results and utilize them to design teaching activities and tailored learning strategies for students. However, the inherent black-box nature of deep learning techniques often poses a hurdle for teachers to fully embrace the model's prediction results. To address these challenges, we propose a Question-centric Multi-experts Contrastive Learning framework for KT called Q-MCKT. We have provided all the datasets and code on our website at https://github.com/rattlesnakey/Q-MCKT.
We review current and emerging knowledge-informed and brain-inspired cognitive systems for realizing adversarial defenses, eXplainable Artificial Intelligence (XAI), and zero-shot or few-short learning. Data-driven deep learning models have achieved remarkable performance and demonstrated capabilities surpassing human experts in many applications. Yet, their inability to exploit domain knowledge leads to serious performance limitations in practical applications. In particular, deep learning systems are exposed to adversarial attacks, which can trick them into making glaringly incorrect decisions. Moreover, complex data-driven models typically lack interpretability or explainability, i.e., their decisions cannot be understood by human subjects. Furthermore, models are usually trained on standard datasets with a closed-world assumption. Hence, they struggle to generalize to unseen cases during inference in practical open-world environments, thus, raising the zero- or few-shot generalization problem. Although many conventional solutions exist, explicit domain knowledge, brain-inspired neural network and cognitive architectures offer powerful new dimensions towards alleviating these problems. Prior knowledge is represented in appropriate forms and incorporated in deep learning frameworks to improve performance. Brain-inspired cognition methods use computational models that mimic the human mind to enhance intelligent behavior in artificial agents and autonomous robots. Ultimately, these models achieve better explainability, higher adversarial robustness and data-efficient learning, and can, in turn, provide insights for cognitive science and neuroscience-that is, to deepen human understanding on how the brain works in general, and how it handles these problems.
Diabetes, resulting from inadequate insulin production or utilization, causes extensive harm to the body. Existing diagnostic methods are often invasive and come with drawbacks, such as cost constraints. Although there are machine learning models like Classwise k Nearest Neighbor (CkNN) and General Regression Neural Network (GRNN), they struggle with imbalanced data and result in under-performance. Leveraging advancements in sensor technology and machine learning, we propose a non-invasive diabetes diagnosis using a Back Propagation Neural Network (BPNN) with batch normalization, incorporating data re-sampling and normalization for class balancing. Our method addresses existing challenges such as limited performance associated with traditional machine learning. Experimental results on three datasets show significant improvements in overall accuracy, sensitivity, and specificity compared to traditional methods. Notably, we achieve accuracies of 89.81% in Pima diabetes dataset, 75.49% in CDC BRFSS2015 dataset, and 95.28% in Mesra Diabetes dataset. This underscores the potential of deep learning models for robust diabetes diagnosis. See project website https://steve-zeyu-zhang.github.io/DiabetesDiagnosis/
Human action recognition in videos is a critical task with significant implications for numerous applications, including surveillance, sports analytics, and healthcare. The challenge lies in creating models that are both precise in their recognition capabilities and efficient enough for practical use. This study conducts an in-depth analysis of various deep learning models to address this challenge. Utilizing a subset of the UCF101 Videos dataset, we focus on Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), and Two-Stream ConvNets. The research reveals that while CNNs effectively capture spatial features and RNNs encode temporal sequences, Two-Stream ConvNets exhibit superior performance by integrating spatial and temporal dimensions. These insights are distilled from the evaluation metrics of accuracy, precision, recall, and F1-score. The results of this study underscore the potential of composite models in achieving robust human action recognition and suggest avenues for future research in optimizing these models for real-world deployment.
The surgical environment imposes unique challenges to the intraoperative registration of organ shapes to their preoperatively-imaged geometry. Biomechanical model-based registration remains popular, while deep learning solutions remain limited due to the sparsity and variability of intraoperative measurements and the limited ground-truth deformation of an organ that can be obtained during the surgery. In this paper, we propose a novel \textit{hybrid} registration approach that leverage a linearized iterative boundary reconstruction (LIBR) method based on linear elastic biomechanics, and use deep neural networks to learn its residual to the ground-truth deformation (LIBR+). We further formulate a dual-branch spline-residual graph convolutional neural network (SR-GCN) to assimilate information from sparse and variable intraoperative measurements and effectively propagate it through the geometry of the 3D organ. Experiments on a large intraoperative liver registration dataset demonstrated the consistent improvements achieved by LIBR+ in comparison to existing rigid, biomechnical model-based non-rigid, and deep-learning based non-rigid approaches to intraoperative liver registration.
Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a powerful tool for protein modeling due to its ability to learn complex patterns and representations from large-scale protein data. This comprehensive survey aims to provide an overview of the recent advances in deep learning techniques applied to protein science. The survey begins by introducing the developments of deep learning based protein models and emphasizes the importance of protein representation learning in drug discovery, protein engineering, and function annotation. It then delves into the fundamentals of deep learning, including convolutional neural networks, recurrent neural networks, attention models, and graph neural networks in modeling protein sequences, structures, and functions, and explores how these techniques can be used to extract meaningful features and capture intricate relationships within protein data. Next, the survey presents various applications of deep learning in the field of proteins, including protein structure prediction, protein-protein interaction prediction, protein function prediction, etc. Furthermore, it highlights the challenges and limitations of these deep learning techniques and also discusses potential solutions and future directions for overcoming these challenges. This comprehensive survey provides a valuable resource for researchers and practitioners in the field of proteins who are interested in harnessing the power of deep learning techniques. By consolidating the latest advancements and discussing potential avenues for improvement, this review contributes to the ongoing progress in protein research and paves the way for future breakthroughs in the field.
Biophilia is an innate love for living things and nature itself that has been associated with a positive impact on mental health and well-being. This study explores the application of deep learning methods for the classification of Biophilic artwork, in order to learn and explain the different Biophilic characteristics present in a visual representation of a painting. Using the concept of Biophilia that postulates the deep connection of human beings with nature, we use an artificially intelligent algorithm to recognise the different patterns underlying the Biophilic features in an artwork. Our proposed method uses a lower-dimensional representation of an image and a decoder model to extract salient features of the image of each Biophilic trait, such as plants, water bodies, seasons, animals, etc., based on learnt factors such as shape, texture, and illumination. The proposed classification model is capable of extracting Biophilic artwork that not only helps artists, collectors, and researchers studying to interpret and exploit the effects of mental well-being on exposure to nature-inspired visual aesthetics but also enables a methodical exploration of the study of Biophilia and Biophilic artwork for aesthetic preferences. Using the proposed algorithms, we have also created a gallery of Biophilic collections comprising famous artworks from different European and American art galleries, which will soon be published on the Vieunite@ online community.
The escalating threat of adversarial attacks on deep learning models, particularly in security-critical fields, has underscored the need for robust deep learning systems. Conventional robustness evaluations have relied on adversarial accuracy, which measures a model's performance under a specific perturbation intensity. However, this singular metric does not fully encapsulate the overall resilience of a model against varying degrees of perturbation. To address this gap, we propose a new metric termed adversarial hypervolume, assessing the robustness of deep learning models comprehensively over a range of perturbation intensities from a multi-objective optimization standpoint. This metric allows for an in-depth comparison of defense mechanisms and recognizes the trivial improvements in robustness afforded by less potent defensive strategies. Additionally, we adopt a novel training algorithm that enhances adversarial robustness uniformly across various perturbation intensities, in contrast to methods narrowly focused on optimizing adversarial accuracy. Our extensive empirical studies validate the effectiveness of the adversarial hypervolume metric, demonstrating its ability to reveal subtle differences in robustness that adversarial accuracy overlooks. This research contributes a new measure of robustness and establishes a standard for assessing and benchmarking the resilience of current and future defensive models against adversarial threats.
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of large homo-oligomeric assemblies exhibit internal symmetry, posing a major challenge in structure determination. The performances of existing deep learning methods are limited since the symmetrical protein assembly usually has a long sequence, making structural computation infeasible. In addition, multiple identical subunits in symmetrical protein complex cause the issue of supervision ambiguity in label assignment, requiring a consistent structure modeling for the training. To tackle these problems, we propose a protein folding framework called SGNet to model protein-protein interactions in symmetrical assemblies. SGNet conducts feature extraction on a single subunit and generates the whole assembly using our proposed symmetry module, which largely mitigates computational problems caused by sequence length. Thanks to the elaborate design of modeling symmetry consistently, we can model all global symmetry types in quaternary protein structure prediction. Extensive experimental results on a benchmark of symmetrical protein complexes further demonstrate the effectiveness of our method.
EEG-based Emotion recognition holds significant promise for applications in human-computer interaction, medicine, and neuroscience. While deep learning has shown potential in this field, current approaches usually rely on large-scale high-quality labeled datasets, limiting the performance of deep learning. Self-supervised learning offers a solution by automatically generating labels, but its inter-subject generalizability remains under-explored. For this reason, our interest lies in offering a self-supervised learning paradigm with better inter-subject generalizability. Inspired by recent efforts in combining low-level and high-level tasks in deep learning, we propose a cascaded self-supervised architecture for EEG emotion recognition. Then, we introduce a low-level task, time-to-frequency reconstruction (TFR). This task leverages the inherent time-frequency relationship in EEG signals. Our architecture integrates it with the high-level contrastive learning modules, performing self-supervised learning for EEG-based emotion recognition. Experiment on DEAP and DREAMER datasets demonstrates superior performance of our method over similar works. The outcome results also highlight the indispensability of the TFR task and the robustness of our method to label scarcity, validating the effectiveness of the proposed method.
Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients. However, the inverse problem-solving aspect of these models presents a substantial challenge, either due to the high computational requirements of model-based approaches or the limited robustness of deep learning (DL) methods. We propose a novel framework that leverages the unique strengths of both approaches in a synergistic manner. Our method incorporates a DL ensemble for initial parameter estimation, facilitating efficient downstream evolutionary sampling initialized with this DL-based prior. We showcase the effectiveness of integrating a rapid deep-learning algorithm with a high-precision evolution strategy in estimating brain tumor cell concentrations from magnetic resonance images. The DL-Prior plays a pivotal role, significantly constraining the effective sampling-parameter space. This reduction results in a fivefold convergence acceleration and a Dice-score of 95%.
Digital transformation in the built environment generates vast data for developing data-driven models to optimize building operations. This study presents an integrated solution utilizing edge computing, digital twins, and deep learning to enhance the understanding of climate in buildings. Parametric digital twins, created using an ontology, ensure consistent data representation across diverse service systems equipped by different buildings. Based on created digital twins and collected data, deep learning methods are employed to develop predictive models for identifying patterns in indoor climate and providing insights. Both the parametric digital twin and deep learning models are deployed on edge for low latency and privacy compliance. As a demonstration, a case study was conducted in a historic building in \"Osterg\"otland, Sweden, to compare the performance of five deep learning architectures. The results indicate that the time-series dense encoder model exhibited strong competitiveness in performing multi-horizon forecasts of indoor temperature and relative humidity with low computational costs.
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.
This paper introduces a hypothesis space for deep learning that employs deep neural networks (DNNs). By treating a DNN as a function of two variables, the physical variable and parameter variable, we consider the primitive set of the DNNs for the parameter variable located in a set of the weight matrices and biases determined by a prescribed depth and widths of the DNNs. We then complete the linear span of the primitive DNN set in a weak* topology to construct a Banach space of functions of the physical variable. We prove that the Banach space so constructed is a reproducing kernel Banach space (RKBS) and construct its reproducing kernel. We investigate two learning models, regularized learning and minimum interpolation problem in the resulting RKBS, by establishing representer theorems for solutions of the learning models. The representer theorems unfold that solutions of these learning models can be expressed as linear combination of a finite number of kernel sessions determined by given data and the reproducing kernel.
In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions prevalent in chemical literature. To bridge this gap, we proposed MolNexTR, a novel image-to-graph deep learning model that collaborates to fuse the strengths of ConvNext, a powerful Convolutional Neural Network variant, and Vision-TRansformer. This integration facilitates a more detailed extraction of both local and global features from molecular images. MolNexTR can predict atoms and bonds simultaneously and understand their layout rules. It also excels at flexibly integrating symbolic chemistry principles to discern chirality and decipher abbreviated structures. We further incorporate a series of advanced algorithms, including an improved data augmentation module, an image contamination module, and a post-processing module for getting the final SMILES output. These modules cooperate to enhance the model's robustness to diverse styles of molecular images found in real literature. In our test sets, MolNexTR has demonstrated superior performance, achieving an accuracy rate of 81-97%, marking a significant advancement in the domain of molecular structure recognition.
Recently, deep learning (DL)-based methods have been proposed for the computational reduction of gadolinium-based contrast agents (GBCAs) to mitigate adverse side effects while preserving diagnostic value. Currently, the two main challenges for these approaches are the accurate prediction of contrast enhancement and the synthesis of realistic images. In this work, we address both challenges by utilizing the contrast signal encoded in the subtraction images of pre-contrast and post-contrast image pairs. To avoid the synthesis of any noise or artifacts and solely focus on contrast signal extraction and enhancement from low-dose subtraction images, we train our DL model using noise-free standard-dose subtraction images as targets. As a result, our model predicts the contrast enhancement signal only; thereby enabling synthesization of images beyond the standard dose. Furthermore, we adapt the embedding idea of recent diffusion-based models to condition our model on physical parameters affecting the contrast enhancement behavior. We demonstrate the effectiveness of our approach on synthetic and real datasets using various scanners, field strengths, and contrast agents.
Second-order optimization techniques have the potential to achieve faster convergence rates compared to first-order methods through the incorporation of second-order derivatives or statistics. However, their utilization in deep learning is limited due to their computational inefficiency. Various approaches have been proposed to address this issue, primarily centered on minimizing the size of the matrix to be inverted. Nevertheless, the necessity of performing the inverse operation iteratively persists. In this work, we present a fast natural gradient descent (FNGD) method that only requires inversion during the first epoch. Specifically, it is revealed that natural gradient descent (NGD) is essentially a weighted sum of per-sample gradients. Our novel approach further proposes to share these weighted coefficients across epochs without affecting empirical performance. Consequently, FNGD exhibits similarities to the average sum in first-order methods, leading to the computational complexity of FNGD being comparable to that of first-order methods. Extensive experiments on image classification and machine translation tasks demonstrate the efficiency of the proposed FNGD. For training ResNet-18 on CIFAR-100, FNGD can achieve a speedup of 2.07$\times$ compared with KFAC. For training Transformer on Multi30K, FNGD outperforms AdamW by 24 BLEU score while requiring almost the same training time.
This article investigates deep learning methodologies for single-modality clinical data analysis, as a crucial precursor to multi-modal medical research. Building on Guo JingYuan's work, the study refines clinical data processing through Compact Convolutional Transformer (CCT), Patch Up, and the innovative CamCenterLoss technique, establishing a foundation for future multimodal investigations. The proposed methodology demonstrates improved prediction accuracy and at tentiveness to critically ill patients compared to Guo JingYuan's ResNet and StageNet approaches. Novelty that using image-pretrained vision transformer backbone to perform transfer learning time-series clinical data.The study highlights the potential of CCT, Patch Up, and novel CamCenterLoss in processing single modality clinical data within deep learning frameworks, paving the way for future multimodal medical research and promoting precision and personalized healthcare
Performance is arguably the most crucial attribute that reflects the quality of a configurable software system. However, given the increasing scale and complexity of modern software, modeling and predicting how various configurations can impact performance becomes one of the major challenges in software maintenance. As such, performance is often modeled without having a thorough knowledge of the software system, but relying mainly on data, which fits precisely with the purpose of deep learning. In this paper, we conduct a comprehensive review exclusively on the topic of deep learning for performance learning of configurable software, covering 1,206 searched papers spanning six indexing services, based on which 99 primary papers were extracted and analyzed. Our results outline key statistics, taxonomy, strengths, weaknesses, and optimal usage scenarios for techniques related to the preparation of configuration data, the construction of deep learning performance models, the evaluation of these models, and their utilization in various software configuration-related tasks.We also identify the good practices and potentially problematic phenomena from the studies surveyed, together with a comprehensive summary of actionable suggestions and insights into future opportunities within the field. To promote open science, all the raw results of this survey can be accessed at our repository: https://github.com/ideas-labo/DCPL-SLR.