Synthetic Datasets Research Articles

CANARD: An approach for generating expressive correspondences based on competency questions for alignment

Ontology matching aims at making ontologies interoperable. While the field has fully developed in the last years, most approaches are still limited to the generation of simple correspondences. More expressiveness is, however, required to better address the different kinds of ontology heterogeneities. This paper presents CANARD (Complex Alignment Need and A-box based Relation Discovery), an approach for generating expressive correspondences that rely on the notion of competency questions for alignment (CQA). A CQA expresses the user knowledge needs in terms of alignment and aims at reducing the alignment space. The approach takes as input a set of CQAs as SPARQL queries over the source ontology. The generation of correspondences is performed by matching the subgraph from the source CQA to the similar surroundings of the instances from the target ontology. Evaluation is carried out on both synthetic and real-world datasets. The impact of several approach parameters is discussed. Experiments have showed that CANARD performs, overall, better on CQA coverage than precision and that using existing same:As links, between the instances of the source and target ontologies, gives better results than exact label matches of their labels. The use of CQA improved also both CQA coverage and precision with respect to using automatically generated queries. The reassessment of the counter-example increased significantly the precision, to the detriment of runtime. Finally, experiments on large datasets showed that CANARD is one of the few systems that can perform on large knowledge bases, but depends on regularly populated knowledge bases and the quality of instance links.

Measurement Guidance in Diffusion Models: Insight from Medical Image Synthesis.

In the field of healthcare, the acquisition of sample is usually restricted by multiple considerations, including cost, labor- intensive annotation, privacy concerns, and radiation hazards, therefore, synthesizing images-of-interest is an important tool to data augmentation. Diffusion models have recently attained state-of-the-art results in various synthesis tasks, and embedding energy functions has been proved that can effectively guide the pre-trained model to synthesize target samples. However, we notice that current method development and validation are still limited to improving indicators, such as Fréchet Inception Distance score (FID) and Inception Score (IS), and have not provided deeper investigations on downstream tasks, like disease grading and diagnosis. Moreover, existing classifier guidance which can be regarded as a special case of energy function can only has a singular effect on altering the distribution of the synthetic dataset. This may contribute to in-distribution synthetic sample that has limited help to downstream model optimization. All these limitations remind that we still have a long way to go to achieve controllable generation. In this work, we first conducted an analysis on previous guidance as well as its contributions on further applications from the perspective of data distribution. To synthesize samples which can help downstream applications, we then introduce uncertainty guidance in each sampling step and design an uncertainty-guided diffusion models. Extensive experiments on four medical datasets, with ten classic networks trained on the augmented sample sets provided a comprehensive evaluation on the practical contributions of our methodology. Furthermore, we provide a theoretical guarantee for general gradient guidance in diffusion models, which would benefit future research on investigating other forms of measurement guidance for specific generative tasks. Codes and models are available at: https://github.com/yangqy1110/MGDM.

Sub-One Quasi-Norm-Based k-Means Clustering Algorithm and Analyses

Recognizing the pivotal role of choosing an appropriate distance metric in designing the clustering algorithm, our focus is on innovating the k-means method by redefining the distance metric in its distortion. In this study, we introduce a novel k-means clustering algorithm utilizing a distance metric derived from the ℓp\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\ell _p$$\\end{document} quasi-norm with p∈(0,1)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$p\\in (0,1)$$\\end{document}. Through an illustrative example, we showcase the advantageous properties of the proposed distance metric compared to commonly used alternatives for revealing natural groupings in data. Subsequently, we present a novel k-means type heuristic by integrating this sub-one quasi-norm-based distance, offer a step-by-step iterative relocation scheme, and prove the convergence to the Kuhn-Tucker point. Finally, we empirically validate the effectiveness of our clustering method through experiments on synthetic and real-life datasets, both in their original form and with additional noise introduced. We also investigate the performance of the proposed method as a subroutine in a deep learning clustering algorithm. Our results demonstrate the efficacy of the proposed k-means algorithm in capturing distinctive patterns exhibited by certain data types.

DCDIMB: Dynamic Community-based Diversified Influence Maximization using Bridge Nodes

Influence maximization (IM) is the fundamental study of social network analysis. The IM problem finds the top k nodes that have maximum influence in the network. Most of the studies in IM focus on maximizing the number of activated nodes in the static social network. But in real life, social networks are dynamic in nature. This work addresses the diversification of activated nodes in the dynamic social network. This work proposes an objective function that maximizes the number of communities by utilizing bridge nodes. We also propose a diffusion model that considers the role of inactive nodes in influencing a node. We prove the submodularity, and monotonicity of the objective function under the proposed diffusion model. This work analyzes the impact of different ratios of bridge nodes in the seed set on real-world and synthetic datasets. Further, we prove the NP-Hardness of the objective function under the proposed diffusion model. The experiments are conducted on various real-world and synthetic datasets with known and unknown community information. The proposed work experimentally shows that the objective function gives the maximum number of communities considering bridge nodes compared to the benchmark algorithms.

Marginal land in China suitable for bioenergy crops under diverse socioeconomic and climate scenarios from 2020–2100

ABSTRACT Maximizing the development of renewable energy plays a critical role in mitigating the climate crisis. Marginal land provides space for the development of biomass energy; however, it remains unclear how the amount and spatial distribution of marginal land that is suitable for energy crop development will change in the future. Here, we project energy marginal land changes in China following the shared socioeconomic pathway (SSP) and/or representative concentration path (RCP). We provide datasets of marginal land, agriculturally suitable land, and potentially suitable for energy crops under historical scenarios and six future scenarios (i.e. SSP1–1.9, SSP1–2.6, SSP4–3.4, SSP2–4.5, SSP4–6.0, and SSP3–7.0) for the period 2020–2100, with a spatial resolution of 5 km. Under the six scenarios, from 2020–2100, the area of suitable marginal land ranged from 1.90–16.28 (Jatropha curcas L.) to 37.37–73.97 (Panicum virgatum L.) (×104 km2), depending on the choice of energy crops and climate scenario. Based on the growing suitability of eight important bioenergy crops—Ricinus communis L., Saccharum officinarum L., Pistacia chinensis Bunge, Panicum virgatum L., Jatropha curcas L., Miscanthus giganteus J., Manihot esculenta Crantz, and Sorghum bicolor Moench—our dataset can be used to identify suitable locations for specific energy crops. This new synthetic dataset could support the development of multiscenario-based solutions related to carbon neutrality, ecosystem services, and energy transition.

Deblur-GS: 3D Gaussian Splatting from Camera Motion Blurred Images

Novel view synthesis has undergone a revolution thanks to the radiance field method. The introduction of 3D Gaussian splatting (3DGS) has successfully addressed the issues of prolonged training times and slow rendering speeds associated with the Neural Radiance Field (NeRF), all while preserving the quality of reconstructions. However, 3DGS remains heavily reliant on the quality of input images and their initial camera pose initialization. In cases where input images are blurred, the reconstruction results suffer from blurriness and artifacts. In this paper, we propose the Deblur-GS method for reconstructing 3D Gaussian points to create a sharp radiance field from a camera motion blurred image set. We model the problem of motion blur as a joint optimization challenge involving camera trajectory estimation and time sampling. We cohesively optimize the parameters of the Gaussian points and the camera trajectory during the shutter time. Deblur-GS consistently achieves superior performance and rendering quality when compared to previous methods, as demonstrated in evaluations conducted on both synthetic and real datasets.

Data Validation Utilizing Expert Knowledge and Shape Constraints

Data validation is a primary concern in any data-driven application, as undetected data errors may negatively affect machine learning models and lead to suboptimal decisions. Data quality issues are usually detected manually by experts, which becomes infeasible and uneconomical for large volumes of data. To enable automated data validation, we propose “shape constraint-based data validation”, a novel approach based on machine learning that incorporates expert knowledge in the form of shape constraints. Shape constraints can be used to describe expected (multivariate and nonlinear) patterns in valid data, and enable the detection of invalid data which deviates from these expected patterns. Our approach can be divided into two steps: (1) shape-constrained prediction models are trained on data, and (2) their training error is analyzed to identify invalid data. The training error can be used as an indicator for invalid data because shape-constrained models can fit valid data better than invalid data. We evaluate the approach on a benchmark suite consisting of synthetic datasets, which we have published for benchmarking similar data validation approaches. Additionally, we demonstrate the capabilities of the proposed approach with a real-world dataset consisting of measurements from a friction test bench in an industrial setting. Our approach detects subtle data errors that are difficult to identify even for domain experts.

Optimized Python library for reconstruction of ensemble-based gene co-expression networks using multi-GPU

AbstractGene co-expression networks are valuable tools for discovering biologically relevant information within gene expression data. However, analysing large datasets presents challenges due to the identification of nonlinear gene–gene associations and the need to process an ever-growing number of gene pairs and their potential network connections. These challenges mean that some experiments are discarded because the techniques do not support these intense workloads. This paper presents pyEnGNet, a Python library that can generate gene co-expression networks in High-performance computing environments. To do this, pyEnGNet harnesses CPU and multi-GPU parallel computing resources, efficiently handling large datasets. These implementations have optimised memory management and processing, delivering timely results. We have used synthetic datasets to prove the runtime and intensive workload improvements. In addition, pyEnGNet was used in a real-life study of patients after allogeneic stem cell transplantation with invasive aspergillosis and was able to detect biological perspectives in the study.

Validating Synthetic Data for Perception in Autonomous Airport Navigation Tasks

Autonomous navigation within airport environments presents significant challenges, mostly due to the scarcity of accessible and labeled data for training autonomous systems. This study introduces an innovative approach to assess the performance of vision-based models trained on synthetic datasets, with the goal of determining whether simulated data can train and validate navigation operations in complex airport environments. The methodology includes a comparative analysis employing image processing techniques and object detection algorithms. A comparative analysis of two different datasets was conducted: a synthetic dataset that mirrors real airport scenarios, generated using the Microsoft Flight Simulator 2020®video game, and a real-world dataset. The results indicate that models trained on a combination of both real and synthetic images perform much better in terms of adaptability and accuracy compared to those trained only on one type of dataset. This analysis makes a significant contribution to the field of autonomous airport navigation and offers a cost-effective and practical solution to overcome the challenges of dataset acquisition and algorithm validation. It is thus believed that this study lays the groundwork for future advancements in the field.

Learning the effective order of a hypergraph dynamical system.

Dynamical systems on hypergraphs can display a rich set of behaviors not observable for systems with pairwise interactions. Given a distributed dynamical system with a putative hypergraph structure, an interesting question is thus how much of this hypergraph structure is actually necessary to faithfully replicate the observed dynamical behavior. To answer this question, we propose a method to determine the minimum order of a hypergraph necessary to approximate the corresponding dynamics accurately. Specifically, we develop a mathematical framework that allows us to determine this order when the type of dynamics is known. We use these ideas in conjunction with a hypergraph neural network to directly learn the dynamics itself and the resulting order of the hypergraph from both synthetic and real datasets consisting of observed system trajectories.

Structured Generation Method of 3D Synthetic Tree Models for Precision Assessment

Abstract. The technology for 3D reconstruction of tree models based on point clouds has been extensively researched, necessitating effective datasets for the study of branch and leaf separation, skeleton point extraction, and tree parameter extraction methods. However, existing datasets for 3D tree models face several challenges, including insufficient data volume for deep learning network training, low accuracy of model ground truth impeding effective method precision evaluation, and a lack of dataset richness to satisfy the needs of multi-type method assessments. In response to these challenges, This paper introduces, for the first time, a fully automated method for generating structured three-dimensional synthetic tree models, and constructs a large-scale 3D synthetic tree dataset enriched with comprehensive structural information. This method facilitates automated computation across several processes, including the mass generation of simulated trees, separation of branches and leaves, noise generation, extraction of skeleton points, and volume calculation. To validate the usability of this dataset across various applications, this paper employs state-of-the-art (SoTA) algorithms to verify the accuracy of methods in 3D tree model reconstruction and carbon stock calculation, thereby thoroughly demonstrating the dataset’s effectiveness.

Scuphr: A probabilistic framework for cell lineage tree reconstruction

Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method’s robustness is investigated using various synthetic datasets and a biological dataset of 18 cells.

Understanding Wireless ChannelsThrough NeRF2

Despite Maxwell's formulation of the electromagnetic wave laws over a century and a half ago, accurately modeling the transmission of RF signals within electrically complex environments continues to be a formidable challenge. This complexity arises from intricate interactions of RF signals with various obstacles, such as reflections and diffractions. Inspired by the effective utilization of neural networks in computer vision for representing optical fields, this paper introduces NeRF2, a novel neural radio-frequency radiance field. NeRF2 conceptualizes a continuous, volumetric scene function to interpret RF signal propagation. Uniquely, NeRF2, once trained with limited signal measurements, can predict the characteristics and reception of a signal at an arbitrary point, given the transmitter's location. Functioning as a physical-layer neural network, NeRF2 amalgamates learned statistical models with physical ray tracing to create synthetic datasets, tailored for the training needs of application-layer artificial neural networks (ANNs). This integration, termed "turbo-learning," combines authentic and synthetic datasets, significantly augmenting ANNs' training efficacy. Experimental results illustrate that turbo-learning can substantially improve performance, with an estimated 50% enhancement. The efficacy of NeRF2 is further underscored in its applications in indoor localization and 5G MIMO systems.

Learning content-aware feature fusion for guided depth map super-resolution

RGB-D data including paired RGB color images and depth maps is widely used in downstream computer vision tasks. However, compared with the acquisition of high-resolution color images, the depth maps captured by consumer-level sensors are always in low resolution. Within decades of research, the most state-of-the-art (SOTA) methods of depth map super-resolution cannot adaptively tune the guidance fusion for all feature positions by channel-wise feature concatenation with spatially sharing convolutional kernels. This paper proposes JTFNet to resolve this issue, which simulates the traditional Joint Trilateral Filter (JTF). Specifically, a novel JTF block is introduced to adaptively tune the fusion pattern between the color features and the depth features for all feature positions. Moreover, based on the variant of JTF block whose target features and guidance features are in the cross-scale shape, the fusion for depth features is performed in a bi-directional way. Therefore, the error accumulation along scales can be effectively mitigated by iteratively HR feature guidance. Compared with the SOTA methods, the sufficient experiment is conducted on the mainstream synthetic datasets and real datasets, i.e., Middlebury, NYU and ToF-Mark, which shows remarkable improvement of our JTFNet.

DAE-GAN: Underwater Image Super-Resolution Based on Symmetric Degradation Attention Enhanced Generative Adversarial Network

Underwater images often exhibit detail blurring and color distortion due to light scattering, impurities, and other influences, obscuring essential textures and details. This presents a challenge for existing super-resolution techniques in identifying and extracting effective features, making high-quality reconstruction difficult. This research aims to innovate underwater image super-resolution technology to tackle this challenge. Initially, an underwater image degradation model was created by integrating random subsampling, Gaussian blur, mixed noise, and suspended particle simulation to generate a highly realistic synthetic dataset, thereby training the network to adapt to various degradation factors. Subsequently, to enhance the network’s capability to extract key features, improvements were made based on the symmetrically structured blind super-resolution generative adversarial network (BSRGAN) model architecture. An attention mechanism based on energy functions was introduced within the generator to assess the importance of each pixel, and a weighted fusion strategy of adversarial loss, reconstruction loss, and perceptual loss was utilized to improve the quality of image reconstruction. Experimental results demonstrated that the proposed method achieved significant improvements in peak signal-to-noise ratio (PSNR) and underwater image quality measure (UIQM) by 0.85 dB and 0.19, respectively, significantly enhancing the visual perception quality and indicating its feasibility in super-resolution applications.

Two-stage fine-tuning with ChatGPT data augmentation for learning class-imbalanced data

Classification of long-tailed distributed data is a challenging problem, which suffers from serious class imbalance and hence poor performance on tail classes, which have only a few samples. Owing to this paucity of samples, learning on the tail classes is especially challenging for fine-tuning when transferring a pretrained model to a downstream task. In this work, we present a simple modification of standard fine-tuning to cope with these challenges. Specifically, we propose a two-stage fine-tuning. In Stage 1, we fine-tune the final layer of the pretrained model with class-balanced augmented data, generated using ChatGPT. As a large generative language model, ChatGPT is capable of generating novel and contextually similar responses to a given prompt, which makes it an excellent candidate for data augmentation. In Stage 2, we perform the standard fine-tuning. Our modification has several benefits: (1) it leverages pretrained representations by only fine-tuning a small portion of the model parameters while keeping the rest untouched; (2) it allows the model to learn an initial representation of the specific task; and importantly (3) it protects the learning of tail classes from being at a disadvantage during the model updating. We conduct extensive experiments on synthetic datasets of both two-class and multi-class tasks of text classification as well as a real-world application to ADME (i.e., absorption, distribution, metabolism, and excretion) semantic drug labeling. The experimental results show that the proposed two-stage fine-tuning outperforms vanilla fine-tuning and state-of-the-art methods on the above datasets.

Suppressing label noise in medical image classification using mixup attention and self-supervised learning

Deep neural networks (DNNs) have been widely applied in medical image classification and achieve remarkable classification performance. These achievements heavily depend on large-scale accurately annotated training data. However, label noise is inevitably introduced in the medical image annotation, as the labeling process heavily relies on the expertise and experience of annotators. Meanwhile, DNNs suffer from overfitting noisy labels, degrading the performance of models. Therefore, in this work, we innovatively devise a noise-robust training approach to mitigate the adverse effects of noisy labels in medical image classification. Specifically, we incorporate contrastive learning and intra-group mixup attention strategies into vanilla supervised learning. The contrastive learning for feature extractor helps to enhance visual representation of DNNs. The intra-group mixup attention module constructs groups and assigns self-attention weights for group-wise samples, and subsequently interpolates massive noisy-suppressed samples through weighted mixup operation. We conduct comparative experiments on both synthetic and real-world noisy medical datasets under various noise levels. Rigorous experiments validate that our noise-robust method with contrastive learning and mixup attention can effectively handle with label noise, and is superior to state-of-the-art methods. An ablation study also shows that both components contribute to boost model performance. The proposed method demonstrates its capability of curb label noise and has certain potential toward real-world clinic applications.

Learning-based lens wavefront aberration recovery

Wavefront aberration describes the deviation of a wavefront in an imaging system from a desired perfect shape, such as a plane or a sphere, which may be caused by a variety of factors, such as imperfections in optical equipment, atmospheric turbulence, and the physical properties of imaging subjects and medium. Measuring the wavefront aberration of an imaging system is a crucial part of modern optics and optical engineering, with a variety of applications such as adaptive optics, optical testing, microscopy, laser system design, and ophthalmology. While there are dedicated wavefront sensors that aim to measure the phase of light, they often exhibit some drawbacks, such as higher cost and limited spatial resolution compared to regular intensity measurement. In this paper, we introduce a lightweight and practical learning-based method, named LWNet, to recover the wavefront aberration for an imaging system from a single intensity measurement. Specifically, LWNet takes a measured point spread function (PSF) as input and recovers the wavefront aberration with a two-stage network. The first stage network estimates an initial wavefront aberration via supervised learning, and the second stage network further optimizes the wavefront aberration via self-supervised learning by enforcing the statistical priors and physical constraints of wavefront aberrations via Zernike decomposition. For supervised learning, we created a synthetic PSF-wavefront aberration dataset via ray tracing of 88 lenses. Experimental results show that even trained with simulated data, LWNet works well for wavefront aberration estimation of real imaging systems and consistently outperforms prior learning-based methods.

Effects of the spatial resolution of the Virtual Epileptic Patient on the identification of epileptogenic networks

Abstract Digital twins play an increasing role in clinical decision making. This study evaluates a digital brain twin approach in presurgical evaluation, the Virtual Epileptic Patient (VEP), which estimates the epileptogenic zone in patients with drug-resistant epilepsy. We built the personalized digital brain twins of 14 patients and a series of synthetic dataset by considering different spatial configurations of the epileptogenic and/or propagation zone networks (EZN and PZN, respectively). Brain source signals were simulated with a high spatial resolution neural field model (NFM) composed of 81942 nodes, embedding both long-range (between brain regions) and short-range (within brain regions) coupling. Brain signals were then projected to stereotactic electroencephalographic (SEEG) contacts with an accurate forward solution. An inversion procedure based on a low spatial resolution neural mass model (NMM) composed of 162 nodes was applied to estimate the excitability of each region in each simulation. The ensuing estimated EZN/PZN was compared to the simulated ground truth by means of classification metrics. Overall, we observed correct but degraded performance when using an NMM to estimate the EZN from data simulated with an NFM, which was significant for the simplest spatial configurations. We quantified the reduced performance and demonstrated that the oversimplification of the forward problem is its principal cause. We showed that the absence of local coupling in the NMM affects the inversion process by an overestimation of the excitability, representing a significant clinical impact when using this procedure in the context of presurgical planning. In conclusion, this study highlighted the importance to shift from an NMM towards a full NFM modeling approach for the estimation of EZN, with a particularly relevant need when considering the most complex clinical cases.

Diagnostic Tool for Early Detection of Rheumatic Disorders Using Machine Learning Algorithm and Predictive Models

Background: Rheumatic diseases are chronic diseases that affect joints, tendons, ligaments, bones, muscles, and other vital organs. Detection of rheumatic diseases is a complex process that requires careful analysis of heterogeneous content from clinical examinations, patient history, and laboratory investigations. Machine learning techniques have made it possible to integrate such techniques into the complex diagnostic process to identify inherent features that lead to disease formation, development, and progression for remedial measures. Methods: An automated diagnostic tool using a multilayer neural network computational engine is presented to detect rheumatic disorders and the type of underlying disorder for therapeutic strategies. Rheumatic disorders considered are rheumatoid arthritis, osteoarthritis, and systemic lupus erythematosus. The detection system was trained and tested using 70% and 30% respectively of labelled synthetic dataset of 100,000 records containing both single and multiple disorders. Results: The detection system was able to detect and predict underlying disorders with accuracy of 97.48%, sensitivity of 96.80%, and specificity of 97.50%. Conclusion: The good performance suggests that this solution is robust enough and can be implemented for screening patients for intervention measures. This is a much-needed solution in environments with limited specialists, as the solution promotes task-shifting from the specialist level to the primary healthcare physicians.