arXiv subjects

Hongwei Li

Publications and source records attributed to Hongwei Li.

At least 109 records · Page 6Linked to original sources

arXiv2022

Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings

Human ratings are abstract representations of segmentation quality. To approximate human quality ratings on scarce expert data, we train surrogate quality estimation models. We evaluate on a complex multi-class segmentation problem, specifically glioma segmentation, following the BraTS annotation protocol. The training data features quality ratings from 15 expert neuroradiologists on a scale ranging from 1 to 6 stars for various computer-generated and manual 3D annotations. Even though the networks operate on 2D images and with scarce training data, we can approximate segmentation quality within a margin of error comparable to human intra-rater reliability. Segmentation quality prediction has broad applications. While an understanding of segmentation quality is imperative for successful clinical translation of automatic segmentation quality algorithms, it can play an essential role in training new segmentation models. Due to the split-second inference times, it can be directly applied within a loss function or as a fully-automatic dataset curation mechanism in a federated learning setting.

cs.CV↗

arXiv2022

Adaptive Local Implicit Image Function for Arbitrary-scale Super-resolution

Image representation is critical for many visual tasks. Instead of representing images discretely with 2D arrays of pixels, a recent study, namely local implicit image function (LIIF), denotes images as a continuous function where pixel values are expansion by using the corresponding coordinates as inputs. Due to its continuous nature, LIIF can be adopted for arbitrary-scale image super-resolution tasks, resulting in a single effective and efficient model for various up-scaling factors. However, LIIF often suffers from structural distortions and ringing artifacts around edges, mostly because all pixels share the same model, thus ignoring the local properties of the image. In this paper, we propose a novel adaptive local image function (A-LIIF) to alleviate this problem. Specifically, our A-LIIF consists of two main components: an encoder and a expansion network. The former captures cross-scale image features, while the latter models the continuous up-scaling function by a weighted combination of multiple local implicit image functions. Accordingly, our A-LIIF can reconstruct the high-frequency textures and structures more accurately. Experiments on multiple benchmark datasets verify the effectiveness of our method. Our codes are available at \url{https://github.com/LeeHW-THU/A-LIIF}.

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arXiv2022

What Makes for Automatic Reconstruction of Pulmonary Segments

3D reconstruction of pulmonary segments plays an important role in surgical treatment planning of lung cancer, which facilitates preservation of pulmonary function and helps ensure low recurrence rates. However, automatic reconstruction of pulmonary segments remains unexplored in the era of deep learning. In this paper, we investigate what makes for automatic reconstruction of pulmonary segments. First and foremost, we formulate, clinically and geometrically, the anatomical definitions of pulmonary segments, and propose evaluation metrics adhering to these definitions. Second, we propose ImPulSe (Implicit Pulmonary Segment), a deep implicit surface model designed for pulmonary segment reconstruction. The automatic reconstruction of pulmonary segments by ImPulSe is accurate in metrics and visually appealing. Compared with canonical segmentation methods, ImPulSe outputs continuous predictions of arbitrary resolutions with higher training efficiency and fewer parameters. Lastly, we experiment with different network inputs to analyze what matters in the task of pulmonary segment reconstruction. Our code is available at https://github.com/M3DV/ImPulSe.

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arXiv2022

Privacy-preserving Decentralized Deep Learning with Multiparty Homomorphic Encryption

Decentralized deep learning plays a key role in collaborative model training due to its attractive properties, including tolerating high network latency and less prone to single-point failures. Unfortunately, such a training mode is more vulnerable to data privacy leaks compared to other distributed training frameworks. Existing efforts exclusively use differential privacy as the cornerstone to alleviate the data privacy threat. However, it is still not clear whether differential privacy can provide a satisfactory utility-privacy trade-off for model training, due to its inherent contradictions. To address this problem, we propose D-MHE, the first secure and efficient decentralized training framework with lossless precision. Inspired by the latest developments in the homomorphic encryption technology, we design a multiparty version of Brakerski-Fan-Vercauteren (BFV), one of the most advanced cryptosystems, and use it to implement private gradient updates of users'local models. D-MHE can reduce the communication complexity of general Secure Multiparty Computation (MPC) tasks from quadratic to linear in the number of users, making it very suitable and scalable for large-scale decentralized learning systems. Moreover, D-MHE provides strict semantic security protection even if the majority of users are dishonest with collusion. We conduct extensive experiments on MNIST and CIFAR-10 datasets to demonstrate the superiority of D-MHE in terms of model accuracy, computation and communication cost compared with existing schemes.

cs.CR↗

arXiv2022

Hercules: Boosting the Performance of Privacy-preserving Federated Learning

In this paper, we address the problem of privacy-preserving federated neural network training with $N$ users. We present Hercules, an efficient and high-precision training framework that can tolerate collusion of up to $N-1$ users. Hercules follows the POSEIDON framework proposed by Sav et al. (NDSS'21), but makes a qualitative leap in performance with the following contributions: (i) we design a novel parallel homomorphic computation method for matrix operations, which enables fast Single Instruction and Multiple Data (SIMD) operations over ciphertexts. For the multiplication of two $h\times h$ dimensional matrices, our method reduces the computation complexity from $O(h^3)$ to $O(h)$. This greatly improves the training efficiency of the neural network since the ciphertext computation is dominated by the convolution operations; (ii) we present an efficient approximation on the sign function based on the composite polynomial approximation. It is used to approximate non-polynomial functions (i.e., ReLU and max), with the optimal asymptotic complexity. Extensive experiments on various benchmark datasets (BCW, ESR, CREDIT, MNIST, SVHN, CIFAR-10 and CIFAR-100) show that compared with POSEIDON, Hercules obtains up to 4% increase in model accuracy, and up to 60$\times$ reduction in the computation and communication cost.

cs.CR↗

arXiv2022

Domain-Adaptive 3D Medical Image Synthesis: An Efficient Unsupervised Approach

Medical image synthesis has attracted increasing attention because it could generate missing image data, improving diagnosis and benefits many downstream tasks. However, so far the developed synthesis model is not adaptive to unseen data distribution that presents domain shift, limiting its applicability in clinical routine. This work focuses on exploring domain adaptation (DA) of 3D image-to-image synthesis models. First, we highlight the technical difference in DA between classification, segmentation and synthesis models. Second, we present a novel efficient adaptation approach based on 2D variational autoencoder which approximates 3D distributions. Third, we present empirical studies on the effect of the amount of adaptation data and the key hyper-parameters. Our results show that the proposed approach can significantly improve the synthesis accuracy on unseen domains in a 3D setting. The code is publicly available at https://github.com/WinstonHuTiger/2D_VAE_UDA_for_3D_sythesis

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arXiv2022

Fetal Brain Tissue Annotation and Segmentation Challenge Results

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

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arXiv2022

Selecting Regularization Parameters for nuclear norm type minimization problems

The reconstruction of low-rank matrix from its noisy observation finds its usage in many applications. It can be reformulated into a constrained nuclear norm minimization problem, where the bound $η$ of the constraint is explicitly given or can be estimated by the probability distribution of the noise. When the Lagrangian method is applied to find the minimizer, the solution can be obtained by the singular value thresholding operator where the thresholding parameter $λ$ is related to the Lagrangian multiplier. In this paper, we first show that the Frobenius norm of the discrepancy between the minimizer and the observed matrix is a strictly increasing function of $λ$. From that we derive a closed-form solution for $λ$ in terms of $η$. The result can be used to solve the constrained nuclear-norm-type minimization problem when $η$ is given. For the unconstrained nuclear-norm-type regularized problems, our result allows us to automatically choose a suitable regularization parameter by using the discrepancy principle. The regularization parameters obtained are comparable to (and sometimes better than) those obtained by Stein's unbiased risk estimator (SURE) approach while the cost of solving the minimization problem can be reduced by 11--18 times. Numerical experiments with both synthetic data and real MRI data are performed to validate the proposed approach.

math.OC↗

arXiv2022

VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.

cs.CV↗

arXiv2022

Relationformer: A Unified Framework for Image-to-Graph Generation

A comprehensive representation of an image requires understanding objects and their mutual relationship, especially in image-to-graph generation, e.g., road network extraction, blood-vessel network extraction, or scene graph generation. Traditionally, image-to-graph generation is addressed with a two-stage approach consisting of object detection followed by a separate relation prediction, which prevents simultaneous object-relation interaction. This work proposes a unified one-stage transformer-based framework, namely Relationformer, that jointly predicts objects and their relations. We leverage direct set-based object prediction and incorporate the interaction among the objects to learn an object-relation representation jointly. In addition to existing [obj]-tokens, we propose a novel learnable token, namely [rln]-token. Together with [obj]-tokens, [rln]-token exploits local and global semantic reasoning in an image through a series of mutual associations. In combination with the pair-wise [obj]-token, the [rln]-token contributes to a computationally efficient relation prediction. We achieve state-of-the-art performance on multiple, diverse and multi-domain datasets that demonstrate our approach's effectiveness and generalizability.

cs.CV↗

arXiv2022

CodeGen-Test: An Automatic Code Generation Model Integrating Program Test Information

Automatic code generation is to generate the program code according to the given natural language description. The current mainstream approach uses neural networks to encode natural language descriptions, and output abstract syntax trees (AST) at the decoder, then convert the AST into program code. While the generated code largely conforms to specific syntax rules, two problems are still ignored. One is missing program testing, an essential step in the process of complete code implementation; the other is only focusing on the syntax compliance of the generated code, while ignoring the more important program functional requirements. The paper proposes a CodeGen-Test model, which adds program testing steps and incorporates program testing information to iteratively generate code that meets the functional requirements of the program, thereby improving the quality of code generation. At the same time, the paper proposes a new evaluation metric, test accuracy (Test-Acc), which represents the proportion of passing program test in generated code. Different from the previous evaluation metric, which only evaluates the quality of code generation from the perspective of character similarity, the Test-Acc can evaluate the quality of code generation from the Program functions. Moreover, the paper evaluates the CodeGen-test model on a python data set "hearthstone legend". The experimental results show the proposed method can effectively improve the quality of generated code. Compared with the existing optimal model, CodeGen-Test model improves the Bleu value by 0.2%, Rouge-L value by 0.3% and Test-Acc by 6%.

cs.SE↗

arXiv2021

ComFeel: Productivity is a Matter of the Senses Too

Indoor environmental quality has been found to impact employees' productivity in the long run, yet it is unclear its meeting-level impact in the short term. We studied the relationship between sensorial pleasantness of a meeting's room and the meeting's productivity. By administering a 28-item questionnaire to 363 online participants, we indeed found that three factors captured 62% of people's experience of meetings: (a) productivity; (b) psychological safety; and (c) room pleasantness. To measure room pleasantness, we developed and deployed ComFeel, an indoor environmental sensing infrastructure, which captures light, temperature, and gas resistance readings through miniaturized and unobtrusive devices we built and named 'Geckos'. Across 29 real-world meetings, using ComFeel, we collected 1373 minutes of readings. For each of these meetings, we also collected whether each participant felt the meeting to have been productive, the setting to be psychologically safe, and the meeting room to be pleasant. As one expects, we found that, on average, the probability of a meeting being productive increased by 35% for each standard deviation increase in the psychological safety participants experienced. Importantly, that probability increased by as much as 25% for each increase in room pleasantness, confirming the significant short-term impact of the indoor environment on meetings' productivity.

cs.HC↗

arXiv2021

Cardiac Segmentation on Late Gadolinium Enhancement MRI: A Benchmark Study from Multi-Sequence Cardiac MR Segmentation Challenge

Accurate computing, analysis and modeling of the ventricles and myocardium from medical images are important, especially in the diagnosis and treatment management for patients suffering from myocardial infarction (MI). Late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) provides an important protocol to visualize MI. However, automated segmentation of LGE CMR is still challenging, due to the indistinguishable boundaries, heterogeneous intensity distribution and complex enhancement patterns of pathological myocardium from LGE CMR. Furthermore, compared with the other sequences LGE CMR images with gold standard labels are particularly limited, which represents another obstacle for developing novel algorithms for automatic segmentation of LGE CMR. This paper presents the selective results from the Multi-Sequence Cardiac MR (MS-CMR) Segmentation challenge, in conjunction with MICCAI 2019. The challenge offered a data set of paired MS-CMR images, including auxiliary CMR sequences as well as LGE CMR, from 45 patients who underwent cardiomyopathy. It was aimed to develop new algorithms, as well as benchmark existing ones for LGE CMR segmentation and compare them objectively. In addition, the paired MS-CMR images could enable algorithms to combine the complementary information from the other sequences for the segmentation of LGE CMR. Nine representative works were selected for evaluation and comparisons, among which three methods are unsupervised methods and the other six are supervised. The results showed that the average performance of the nine methods was comparable to the inter-observer variations. The success of these methods was mainly attributed to the inclusion of the auxiliary sequences from the MS-CMR images, which provide important label information for the training of deep neural networks.

eess.IV↗

arXiv2021

Imbalance-Aware Self-Supervised Learning for 3D Radiomic Representations

Radiomic representations can quantify properties of regions of interest in medical image data. Classically, they account for pre-defined statistics of shape, texture, and other low-level image features. Alternatively, deep learning-based representations are derived from supervised learning but require expensive annotations from experts and often suffer from overfitting and data imbalance issues. In this work, we address the challenge of learning representations of 3D medical images for an effective quantification under data imbalance. We propose a \emph{self-supervised} representation learning framework to learn high-level features of 3D volumes as a complement to existing radiomics features. Specifically, we demonstrate how to learn image representations in a self-supervised fashion using a 3D Siamese network. More importantly, we deal with data imbalance by exploiting two unsupervised strategies: a) sample re-weighting, and b) balancing the composition of training batches. When combining our learned self-supervised feature with traditional radiomics, we show significant improvement in brain tumor classification and lung cancer staging tasks covering MRI and CT imaging modalities.

cs.CV↗

arXiv2021

METGAN: Generative Tumour Inpainting and Modality Synthesis in Light Sheet Microscopy

Novel multimodal imaging methods are capable of generating extensive, super high resolution datasets for preclinical research. Yet, a massive lack of annotations prevents the broad use of deep learning to analyze such data. So far, existing generative models fail to mitigate this problem because of frequent labeling errors. In this paper, we introduce a novel generative method which leverages real anatomical information to generate realistic image-label pairs of tumours. We construct a dual-pathway generator, for the anatomical image and label, trained in a cycle-consistent setup, constrained by an independent, pretrained segmentor. The generated images yield significant quantitative improvement compared to existing methods. To validate the quality of synthesis, we train segmentation networks on a dataset augmented with the synthetic data, substantially improving the segmentation over baseline.

eess.IV↗

arXiv2021

Feedback Graph Attention Convolutional Network for Medical Image Enhancement

Artifacts, blur and noise are the common distortions degrading MRI images during the acquisition process, and deep neural networks have been demonstrated to help in improving image quality. To well exploit global structural information and texture details, we propose a novel biomedical image enhancement network, named Feedback Graph Attention Convolutional Network (FB-GACN). As a key innovation, we consider the global structure of an image by building a graph network from image sub-regions that we consider to be node features, linking them non-locally according to their similarity. The proposed model consists of three main parts: 1) The parallel graph similarity branch and content branch, where the graph similarity branch aims at exploiting the similarity and symmetry across different image sub-regions in low-resolution feature space and provides additional priors for the content branch to enhance texture details. 2) A feedback mechanism with a recurrent structure to refine low-level representations with high-level information and generate powerful high-level texture details by handling the feedback connections. 3) A reconstruction to remove the artifacts and recover super-resolution images by using the estimated sub-region correlation priors obtained from the graph similarity branch. We evaluate our method on two image enhancement tasks: i) cross-protocol super resolution of diffusion MRI; ii) artifact removal of FLAIR MR images. Experimental results demonstrate that the proposed algorithm outperforms the state-of-the-art methods.

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arXiv2021

Red-GAN: Attacking class imbalance via conditioned generation. Yet another perspective on medical image synthesis for skin lesion dermoscopy and brain tumor MRI

Exploiting learning algorithms under scarce data regimes is a limitation and a reality of the medical imaging field. In an attempt to mitigate the problem, we propose a data augmentation protocol based on generative adversarial networks. We condition the networks at a pixel-level (segmentation mask) and at a global-level information (acquisition environment or lesion type). Such conditioning provides immediate access to the image-label pairs while controlling global class specific appearance of the synthesized images. To stimulate synthesis of the features relevant for the segmentation task, an additional passive player in a form of segmentor is introduced into the adversarial game. We validate the approach on two medical datasets: BraTS, ISIC. By controlling the class distribution through injection of synthetic images into the training set we achieve control over the accuracy levels of the datasets' classes.

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arXiv2021

Mass production and characterization of 3-inch PMTs for the JUNO experiment

26,000 3-inch photomultiplier tubes (PMTs) have been produced for Jiangmen Underground Neutrino Observatory (JUNO) by the Hainan Zhanchuang Photonics Technology Co., Ltd (HZC) company in China and passed all acceptance tests with only 15 tubes rejected. The mass production began in 2018 and elapsed for about 2 years at a rate of $\sim$1,000~PMTs per month. The characterization of the PMTs was performed in the factory concurrently with production as a joint effort between HZC and JUNO. Fifteen performance parameters were tracked at different sampling rates, and novel working strategies were implemented to improve quality assurance. This constitutes the largest sample of 3-inch PMTs ever produced and studied in detail to date.

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