arXiv subjects

Chenyu Wang

Publications and source records attributed to Chenyu Wang.

At least 109 records · Page 6Linked to original sources

arXiv2024

How Much Data are Enough? Investigating Dataset Requirements for Patch-Based Brain MRI Segmentation Tasks

Training deep neural networks reliably requires access to large-scale datasets. However, obtaining such datasets can be challenging, especially in the context of neuroimaging analysis tasks, where the cost associated with image acquisition and annotation can be prohibitive. To mitigate both the time and financial costs associated with model development, a clear understanding of the amount of data required to train a satisfactory model is crucial. This paper focuses on an early stage phase of deep learning research, prior to model development, and proposes a strategic framework for estimating the amount of annotated data required to train patch-based segmentation networks. This framework includes the establishment of performance expectations using a novel Minor Boundary Adjustment for Threshold (MinBAT) method, and standardizing patch selection through the ROI-based Expanded Patch Selection (REPS) method. Our experiments demonstrate that tasks involving regions of interest (ROIs) with different sizes or shapes may yield variably acceptable Dice Similarity Coefficient (DSC) scores. By setting an acceptable DSC as the target, the required amount of training data can be estimated and even predicted as data accumulates. This approach could assist researchers and engineers in estimating the cost associated with data collection and annotation when defining a new segmentation task based on deep neural networks, ultimately contributing to their efficient translation to real-world applications.

cs.CV↗

arXiv2024

Unveiling Memorization in Code Models

The availability of large-scale datasets, advanced architectures, and powerful computational resources have led to effective code models that automate diverse software engineering activities. The datasets usually consist of billions of lines of code from both open-source and private repositories. A code model memorizes and produces source code verbatim, which potentially contains vulnerabilities, sensitive information, or code with strict licenses, leading to potential security and privacy issues. This paper investigates an important problem: to what extent do code models memorize their training data? We conduct an empirical study to explore memorization in large pre-trained code models. Our study highlights that simply extracting 20,000 outputs (each having 512 tokens) from a code model can produce over 40,125 code snippets that are memorized from the training data. To provide a better understanding, we build a taxonomy of memorized contents with 3 categories and 14 subcategories. The results show that the prompts sent to the code models affect the distribution of memorized contents. We identify several key factors of memorization. Specifically, given the same architecture, larger models suffer more from memorization problems. A code model produces more memorization when it is allowed to generate longer outputs. We also find a strong positive correlation between the number of an output's occurrences in the training data and that in the generated outputs, which indicates that a potential way to reduce memorization is to remove duplicates in the training data. We then identify effective metrics that infer whether an output contains memorization accurately. We also make suggestions to deal with memorization.

cs.SE↗

arXiv2023

Removing Biases from Molecular Representations via Information Maximization

High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological activity of a drug. Since large-scale screens have to be divided into multiple experiments, a key difficulty is dealing with batch effects, which can introduce systematic errors and non-biological associations in the data. We propose InfoCORE, an Information maximization approach for COnfounder REmoval, to effectively deal with batch effects and obtain refined molecular representations. InfoCORE establishes a variational lower bound on the conditional mutual information of the latent representations given a batch identifier. It adaptively reweighs samples to equalize their implied batch distribution. Extensive experiments on drug screening data reveal InfoCORE's superior performance in a multitude of tasks including molecular property prediction and molecule-phenotype retrieval. Additionally, we show results for how InfoCORE offers a versatile framework and resolves general distribution shifts and issues of data fairness by minimizing correlation with spurious features or removing sensitive attributes. The code is available at https://github.com/uhlerlab/InfoCORE.

cs.LG↗

arXiv2023

Passively stable 0.7-octave microcombs in thin-film lithium niobate microresonators

Optical frequency comb based on microresonator (microcomb) is an integrated coherent light source and has the potential to promise a high-precision frequency standard, and self-reference and long-term stable microcomb is the key to this realization. Here, we demonstrated a 0.7-octave spectrum Kerr comb via dispersion engineering in a thin film lithium niobate microresonator, and the single soliton state can be accessed passively with long-term stability over 3 hours. With such a robust broadband coherent comb source using thin film lithium niobate, fully stabilized microcomb can be expected for massive practical applications.

physics.optics↗

arXiv2023

Improving Multiple Sclerosis Lesion Segmentation Across Clinical Sites: A Federated Learning Approach with Noise-Resilient Training

Accurately measuring the evolution of Multiple Sclerosis (MS) with magnetic resonance imaging (MRI) critically informs understanding of disease progression and helps to direct therapeutic strategy. Deep learning models have shown promise for automatically segmenting MS lesions, but the scarcity of accurately annotated data hinders progress in this area. Obtaining sufficient data from a single clinical site is challenging and does not address the heterogeneous need for model robustness. Conversely, the collection of data from multiple sites introduces data privacy concerns and potential label noise due to varying annotation standards. To address this dilemma, we explore the use of the federated learning framework while considering label noise. Our approach enables collaboration among multiple clinical sites without compromising data privacy under a federated learning paradigm that incorporates a noise-robust training strategy based on label correction. Specifically, we introduce a Decoupled Hard Label Correction (DHLC) strategy that considers the imbalanced distribution and fuzzy boundaries of MS lesions, enabling the correction of false annotations based on prediction confidence. We also introduce a Centrally Enhanced Label Correction (CELC) strategy, which leverages the aggregated central model as a correction teacher for all sites, enhancing the reliability of the correction process. Extensive experiments conducted on two multi-site datasets demonstrate the effectiveness and robustness of our proposed methods, indicating their potential for clinical applications in multi-site collaborations.

eess.IV↗

arXiv2023

A hybrid Decoder-DeepONet operator regression framework for unaligned observation data

Deep neural operators (DNOs) have been utilized to approximate nonlinear mappings between function spaces. However, DNOs face the challenge of increased dimensionality and computational cost associated with unaligned observation data. In this study, we propose a hybrid Decoder-DeepONet operator regression framework to handle unaligned data effectively. Additionally, we introduce a Multi-Decoder-DeepONet, which utilizes an average field of training data as input augmentation. The consistencies of the frameworks with the operator approximation theory are provided, on the basis of the universal approximation theorem. Two numerical experiments, Darcy problem and flow-field around an airfoil, are conducted to validate the efficiency and accuracy of the proposed methods. Results illustrate the advantages of Decoder-DeepONet and Multi-Decoder-DeepONet in handling unaligned observation data and showcase their potentials in improving prediction accuracy.

cs.LG↗

arXiv2023

Are We Ready to Embrace Generative AI for Software Q&A?

Stack Overflow, the world's largest software Q&A (SQA) website, is facing a significant traffic drop due to the emergence of generative AI techniques. ChatGPT is banned by Stack Overflow after only 6 days from its release. The main reason provided by the official Stack Overflow is that the answers generated by ChatGPT are of low quality. To verify this, we conduct a comparative evaluation of human-written and ChatGPT-generated answers. Our methodology employs both automatic comparison and a manual study. Our results suggest that human-written and ChatGPT-generated answers are semantically similar, however, human-written answers outperform ChatGPT-generated ones consistently across multiple aspects, specifically by 10% on the overall score. We release the data, analysis scripts, and detailed results at https://anonymous.4open.science/r/GAI4SQA-FD5C.

cs.SE↗

arXiv2023

Coherent X-ray Spectroscopy Elucidates Nanoscale Dynamics of Plasma-Enhanced Thin-Film Growth

Sophisticated thin film growth techniques increasingly rely on the addition of a plasma component to open or widen a processing window, particularly at low temperatures. However, the addition of the plasma into the growth environment also complicates the surface dynamical evolution. Taking advantage of continued increases in accelerator-based X-ray source brilliance, this real-time study uses X-ray Photon Correlation Spectroscopy (XPCS) to elucidate the nanoscale surface dynamics during Plasma-Enhanced Atomic Layer Deposition (PE-ALD) of an epitaxial indium nitride film. XPCS examines the evolution of the coherent X-ray scattering speckle pattern, which is a fingerprint of the unique sample microstructure at each moment in time. In PE-ALD, ultrathin films are synthesized from repeated cycles of alternating self-limited surface reactions induced by temporally-separated pulses of material precursor and plasma reactant, allowing the influence of each on the evolving morphology to be examined. During the heteroepitaxial 3D growth examined here, sudden changes in surface structure during initial film growth, consistent with numerous overlapping stress-relief events, are observed. When the film becomes continuous, the nanoscale surface morphology abruptly becomes long-lived with correlation time spanning the period of the experiment. Throughout the growth experiment, there is a consistent repeating pattern of correlations associated with the cyclic growth process, which is modeled as transitions between different surface states. The plasma exposure does not simply freeze in a structure that is then built upon in subsequent cycles, but rather there is considerable surface evolution during all phases of the growth cycle.

cond-mat.mtrl-sci↗

arXiv2023

Precise Few-shot Fat-free Thigh Muscle Segmentation in T1-weighted MRI

Precise thigh muscle volumes are crucial to monitor the motor functionality of patients with diseases that may result in various degrees of thigh muscle loss. T1-weighted MRI is the default surrogate to obtain thigh muscle masks due to its contrast between muscle and fat signals. Deep learning approaches have recently been widely used to obtain these masks through segmentation. However, due to the insufficient amount of precise annotations, thigh muscle masks generated by deep learning approaches tend to misclassify intra-muscular fat (IMF) as muscle impacting the analysis of muscle volumetrics. As IMF is infiltrated inside the muscle, human annotations require expertise and time. Thus, precise muscle masks where IMF is excluded are limited in practice. To alleviate this, we propose a few-shot segmentation framework to generate thigh muscle masks excluding IMF. In our framework, we design a novel pseudo-label correction and evaluation scheme, together with a new noise robust loss for exploiting high certainty areas. The proposed framework only takes $1\%$ of the fine-annotated training dataset, and achieves comparable performance with fully supervised methods according to the experimental results.

eess.IV↗

arXiv2023

What Do Users Ask in Open-Source AI Repositories? An Empirical Study of GitHub Issues

Artificial Intelligence systems, which benefit from the availability of large-scale datasets and increasing computational power, have become effective solutions to various critical tasks, such as natural language understanding, speech recognition, and image processing. The advancement of these AI systems is inseparable from open-source software (OSS). This paper presents an empirical study that investigates the issues in the repositories of open-source AI repositories to assist developers in understanding problems during the process of employing AI systems. We collect 576 repositories from the PapersWithCode platform. Among these repositories, we find 24,953 issues by utilizing GitHub REST APIs. Our empirical study includes three phases. First, we manually analyze these issues to categorize the problems that developers are likely to encounter in open-source AI repositories. Specifically, we provide a taxonomy of 13 categories related to AI systems. The two most common issues are runtime errors (23.18%) and unclear instructions (19.53%). Second, we see that 67.5% of issues are closed. We also find that half of these issues resolve within four days. Moreover, issue management features, e.g., label and assign, are not widely adopted in open-source AI repositories. In particular, only 7.81% and 5.9% of repositories label issues and assign these issues to assignees, respectively. Finally, we empirically show that employing GitHub issue management features and writing issues with detailed descriptions facilitate the resolution of issues. Based on our findings, we make recommendations for developers to help better manage the issues of open-source AI repositories and improve their quality.

cs.SE↗

arXiv2023

Learning from pseudo-labels: deep networks improve consistency in longitudinal brain volume estimation

Brain atrophy is an important biomarker for monitoring neurodegeneration and disease progression in conditions such as multiple sclerosis (MS). An accurate and robust quantitative measurement of brain volume change is paramount for translational research and clinical applications. This paper presents a deep learning based method, DeepBVC, for longitudinal brain volume change measurement using 3D T1-weighted MRI scans. Trained with the intermediate outputs from SIENA, DeepBVC is designed to take into account the variance caused by different scanners and acquisition protocols. Compared with SIENA, DeepBVC demonstrates higher consistency in terms of volume change estimation across multiple time points in MS subjects; and greater stability and superior performance in scan-rescan experiments. Moreover, the results also show that DeepBVC is insensitive to acquisition variance in terms of imaging contrast, voxel resolution, random bias field and signal-to-noise ratio. Measurement robustness, automation and processing speed suggest a broad potential of DeepBVC in both research and clinical quantitative neuroimaging applications.

q-bio.QM↗

arXiv2023

GRB 220408B: A Three-Episode Burst from a Precessing Jet

Jet precession has previously been proposed to explain the apparently repeating features in the light curves of a few gamma-ray bursts (GRBs). In this {\it Letter}, we further apply the precession model to a bright GRB 220408B by examining both its temporal and spectral consistency with the predictions of the model. As one of the recently confirmed GRBs observed by our GRID CubeSat mission, GRB 220408B is noteworthy as it exhibits three apparently similar emission episodes. Furthermore, the similarities are reinforced by their strong temporal correlations and similar features in terms of spectral evolution and spectral lags. Our analysis demonstrates that these features can be well explained by the modulated emission of a Fast-Rise-Exponential-Decay (FRED) shape light curve intrinsically produced by a precessing jet with a precession period of $18.4 \pm 0.2$ seconds, a nutation period of $11.1 \pm 0.2$ seconds and viewed off-axis. This study provides a straightforward explanation for the complex yet similar multi-episode GRB light curves.

astro-ph.HE↗

arXiv2022

Accurate Instance-Level CAD Model Retrieval in a Large-Scale Database

We present a new solution to the fine-grained retrieval of clean CAD models from a large-scale database in order to recover detailed object shape geometries for RGBD scans. Unlike previous work simply indexing into a moderately small database using an object shape descriptor and accepting the top retrieval result, we argue that in the case of a large-scale database a more accurate model may be found within a neighborhood of the descriptor. More importantly, we propose that the distinctiveness deficiency of shape descriptors at the instance level can be compensated by a geometry-based re-ranking of its neighborhood. Our approach first leverages the discriminative power of learned representations to distinguish between different categories of models and then uses a novel robust point set distance metric to re-rank the CAD neighborhood, enabling fine-grained retrieval in a large shape database. Evaluation on a real-world dataset shows that our geometry-based re-ranking is a conceptually simple but highly effective method that can lead to a significant improvement in retrieval accuracy compared to the state-of-the-art.

cs.CV↗

arXiv2022

VECtor: A Versatile Event-Centric Benchmark for Multi-Sensor SLAM

Event cameras have recently gained in popularity as they hold strong potential to complement regular cameras in situations of high dynamics or challenging illumination. An important problem that may benefit from the addition of an event camera is given by Simultaneous Localization And Mapping (SLAM). However, in order to ensure progress on event-inclusive multi-sensor SLAM, novel benchmark sequences are needed. Our contribution is the first complete set of benchmark datasets captured with a multi-sensor setup containing an event-based stereo camera, a regular stereo camera, multiple depth sensors, and an inertial measurement unit. The setup is fully hardware-synchronized and underwent accurate extrinsic calibration. All sequences come with ground truth data captured by highly accurate external reference devices such as a motion capture system. Individual sequences include both small and large-scale environments, and cover the specific challenges targeted by dynamic vision sensors.

cs.RO↗

arXiv2022

DELTA: Dynamically Optimizing GPU Memory beyond Tensor Recomputation

The further development of deep neural networks is hampered by the limited GPU memory resource. Therefore, the optimization of GPU memory resources is highly demanded. Swapping and recomputation are commonly applied to make better use of GPU memory in deep learning. However, as an emerging domain, several challenges remain:1)The efficiency of recomputation is limited for both static and dynamic methods. 2)Swapping requires offloading parameters manually, which incurs a great time cost. 3) There is no such dynamic and fine-grained method that involves tensor swapping together with tensor recomputation nowadays. To remedy the above issues, we propose a novel scheduler manager named DELTA(Dynamic tEnsor offLoad and recompuTAtion). To the best of our knowledge, we are the first to make a reasonable dynamic runtime scheduler on the combination of tensor swapping and tensor recomputation without user oversight. In DELTA, we propose a filter algorithm to select the optimal tensors to be released out of GPU memory and present a director algorithm to select a proper action for each of these tensors. Furthermore, prefetching and overlapping are deliberately considered to overcome the time cost caused by swapping and recomputing tensors. Experimental results show that DELTA not only saves 40%-70% of GPU memory, surpassing the state-of-the-art method to a great extent but also gets comparable convergence results as the baseline with acceptable time delay. Also, DELTA gains 2.04$\times$ maximum batchsize when training ResNet-50 and 2.25$\times$ when training ResNet-101 compared with the baseline. Besides, comparisons between the swapping cost and recomputation cost in our experiments demonstrate the importance of making a reasonable dynamic scheduler on tensor swapping and tensor recomputation, which refutes the arguments in some related work that swapping should be the first and best choice.

cs.LG↗

arXiv2022

MS Lesion Segmentation: Revisiting Weighting Mechanisms for Federated Learning

Federated learning (FL) has been widely employed for medical image analysis to facilitate multi-client collaborative learning without sharing raw data. Despite great success, FL's performance is limited for multiple sclerosis (MS) lesion segmentation tasks, due to variance in lesion characteristics imparted by different scanners and acquisition parameters. In this work, we propose the first FL MS lesion segmentation framework via two effective re-weighting mechanisms. Specifically, a learnable weight is assigned to each local node during the aggregation process, based on its segmentation performance. In addition, the segmentation loss function in each client is also re-weighted according to the lesion volume for the data during training. Comparison experiments on two FL MS segmentation scenarios using public and clinical datasets have demonstrated the effectiveness of the proposed method by outperforming other FL methods significantly. Furthermore, the segmentation performance of FL incorporating our proposed aggregation mechanism can exceed centralised training with all the raw data. The extensive evaluation also indicated the superiority of our method when estimating brain volume differences estimation after lesion inpainting.

eess.IV↗

arXiv2022

Precise Indoor Positioning Based on UWB and Deep Learning

We examined UWB-based indoor location in conjunction with a fingerprint technique in this work. We built a connection between the measured and real distances for the UWB indoor positioning system. This connection is used to produce a distance database that may be used to generate fringerprints. We created a BP neural network to classify the target node to the relevant fringerpint using the distance database. Our suggested deep learning technology considerably enhances location accuracy when compared to existing trilateration systems.

eess.SP↗

arXiv2022

Multiple Sclerosis Lesion Analysis in Brain Magnetic Resonance Images: Techniques and Clinical Applications

Multiple sclerosis (MS) is a chronic inflammatory and degenerative disease of the central nervous system, characterized by the appearance of focal lesions in the white and gray matter that topographically correlate with an individual patient's neurological symptoms and signs. Magnetic resonance imaging (MRI) provides detailed in-vivo structural information, permitting the quantification and categorization of MS lesions that critically inform disease management. Traditionally, MS lesions have been manually annotated on 2D MRI slices, a process that is inefficient and prone to inter-/intra-observer errors. Recently, automated statistical imaging analysis techniques have been proposed to detect and segment MS lesions based on MRI voxel intensity. However, their effectiveness is limited by the heterogeneity of both MRI data acquisition techniques and the appearance of MS lesions. By learning complex lesion representations directly from images, deep learning techniques have achieved remarkable breakthroughs in the MS lesion segmentation task. Here, we provide a comprehensive review of state-of-the-art automatic statistical and deep-learning MS segmentation methods and discuss current and future clinical applications. Further, we review technical strategies, such as domain adaptation, to enhance MS lesion segmentation in real-world clinical settings.

cs.CV↗