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Annotating biomedical images for supervised learning is a complex and labor-intensive task due to data diversity and its intricate nature. In this paper, we propose an innovative method, the efficient one-pass selective annotation (EPOSA), that significantly reduces the annotation burden while maintaining robust model performance. Our approach employs a variational autoencoder (VAE) to extract salient features from unannotated images, which are subsequently clustered using the DBSCAN algorithm. This process groups similar images together, forming distinct clusters. We then use a two-stage sample selection algorithm, called representative selection (RepSel), to form a selected dataset. The first stage is a Markov Chain Monte Carlo (MCMC) sampling technique to select representative samples from each cluster for annotations. This selection process is the second stage, which is guided by the principle of maximizing intra-cluster mutual information and minimizing inter-cluster mutual information. This ensures a diverse set of features for model training and minimizes outlier inclusion. The selected samples are used to train a VGG-16 network for image classification. Experimental results on the Med-MNIST dataset demonstrate that our proposed EPOSA outperforms random selection and other state-of-the-art methods under the same annotation budget, presenting a promising direction for efficient and effective annotation in medical image analysis., Comment: We found that the idea and results of this paper were not mature enough to go public, after discussion with all co-authors, we decide to withdraw this paper

Deep learning based medical image recognition systems often require a substantial amount of training data with expert annotations, which can be expensive and time-consuming to obtain. Recently, synthetic augmentation techniques have been proposed to mitigate the issue by generating realistic images conditioned on class labels. However, the effectiveness of these methods heavily depends on the representation capability of the trained generative model, which cannot be guaranteed without sufficient labeled training data. To further reduce the dependency on annotated data, we propose a synthetic augmentation method called HistoDiffusion, which can be pre-trained on large-scale unlabeled datasets and later applied to a small-scale labeled dataset for augmented training. In particular, we train a latent diffusion model (LDM) on diverse unlabeled datasets to learn common features and generate realistic images without conditional inputs. Then, we fine-tune the model with classifier guidance in latent space on an unseen labeled dataset so that the model can synthesize images of specific categories. Additionally, we adopt a selective mechanism to only add synthetic samples with high confidence of matching to target labels. We evaluate our proposed method by pre-training on three histopathology datasets and testing on a histopathology dataset of colorectal cancer (CRC) excluded from the pre-training datasets. With HistoDiffusion augmentation, the classification accuracy of a backbone classifier is remarkably improved by 6.4% using a small set of the original labels. Our code is available at https://github.com/karenyyy/HistoDiffAug., Comment: MICCAI 2023

The realization of quantum gates in topological quantum computation still confronts significant challenges in both fundamental and practical aspects. Here, we propose a deterministic and fully topologically protected measurement-based scheme to realize the issue of implementing Clifford quantum gates on the Majorana qubits. Our scheme is based on rigorous proof that the single-qubit gate can be performed by leveraging the neighboring Majorana qubit but not disturbing its carried quantum information, eliminating the need for ancillary Majorana zero modes (MZMs) in topological quantum computing. Benefiting from the ancilla-free construction, we show the minimum measurement sequences with four steps to achieve two-qubit Clifford gates by constructing their geometric visualization. To avoid the uncertainty of the measurement-only strategy, we propose manipulating the MZMs in their parameter space to correct the undesired measurement outcomes while maintaining complete topological protection, as demonstrated in a concrete Majorana platform. Our scheme identifies the minimal operations of measurement-based topological and deterministic Clifford gates and offers an ancilla-free design of topological quantum computation., Comment: 5 pages, 3 figures and appendix

Recent advances in deep generative models have led to the development of methods capable of synthesizing high-quality, realistic images. These models pose threats to society due to their potential misuse. Prior research attempted to mitigate these threats by detecting generated images, but the varying traces left by different generative models make it challenging to create a universal detector capable of generalizing to new, unseen generative models. In this paper, we propose to inject a universal adversarial signature into an arbitrary pre-trained generative model, in order to make its generated contents more detectable and traceable. First, the imperceptible optimal signature for each image can be found by a signature injector through adversarial training. Subsequently, the signature can be incorporated into an arbitrary generator by fine-tuning it with the images processed by the signature injector. In this way, the detector corresponding to the signature can be reused for any fine-tuned generator for tracking the generator identity. The proposed method is validated on the FFHQ and ImageNet datasets with various state-of-the-art generative models, consistently showing a promising detection rate. Code will be made publicly available at \url{https://github.com/zengxianyu/genwm}.

The meninges, located between the skull and brain, are composed of three membrane layers: the pia, the arachnoid, and the dura. Reconstruction of these layers can aid in studying volume differences between patients with neurodegenerative diseases and normal aging subjects. In this work, we use convolutional neural networks (CNNs) to reconstruct surfaces representing meningeal layer boundaries from magnetic resonance (MR) images. We first use the CNNs to predict the signed distance functions (SDFs) representing these surfaces while preserving their anatomical ordering. The marching cubes algorithm is then used to generate continuous surface representations; both the subarachnoid space (SAS) and the intracranial volume (ICV) are computed from these surfaces. The proposed method is compared to a state-of-the-art deformable model-based reconstruction method, and we show that our method can reconstruct smoother and more accurate surfaces using less computation time. Finally, we conduct experiments with volumetric analysis on both subjects with multiple sclerosis and healthy controls. For healthy and MS subjects, ICVs and SAS volumes are found to be significantly correlated to sex (p<0.01) and age (p<0.03) changes, respectively., Comment: ISBI 2023 Oral

Data-driven thalamic nuclei parcellation depends on high-quality manual annotations. However, the small size and low contrast changes among thalamic nuclei, yield annotations that are often incomplete, noisy, or ambiguously labelled. To train a robust thalamic nuclei parcellation model with noisy annotations, we propose a label propagation algorithm based on random walker to refine the annotations before model training. A two-step model was trained to generate first the whole thalamus and then the nuclei masks. We conducted experiments on a mild traumatic brain injury~(mTBI) dataset with noisy thalamic nuclei annotations. Our model outperforms current state-of-the-art thalamic nuclei parcellations by a clear margin. We believe our method can also facilitate the training of other parcellation models with noisy labels.

Recently, with the development of deep learning, a number of Just Noticeable Difference (JND) datasets have been built for JND modeling. However, all the existing JND datasets only label the JND points based on the level of compression distortion. Hence, JND models learned from such datasets can only be used for image/video compression. As known, JND is a major characteristic of the human visual system (HVS), which reflects the maximum visual distortion that the HVS can tolerate. Hence, a generalized JND modeling should take more kinds of distortion types into account. To benefit JND modeling, this work establishes a generalized JND dataset with a coarse-to-fine JND selection, which contains 106 source images and 1,642 JND maps, covering 25 distortion types. To this end, we proposed a coarse JND candidate selection scheme to select the distorted images from the existing Image Quality Assessment (IQA) datasets as JND candidates instead of generating JND maps ourselves. Then, a fine JND selection is carried out on the JND candidates with a crowdsourced subjective assessment.

Normal pressure hydrocephalus~(NPH) is a brain disorder associated with enlarged ventricles and multiple cognitive and motor symptoms. The degree of ventricular enlargement can be measured using magnetic resonance images~(MRIs) and characterized quantitatively using the Evan's ratio (ER). Automatic computation of ER is desired to avoid the extra time and variations associated with manual measurements on MRI. Because shunt surgery is often used to treat NPH, it is necessary that this process be robust to image artifacts caused by the shunt and related implants. In this paper, we propose a 3D regions-of-interest aware (ROI-aware) network for segmenting the ventricles. The method achieves state-of-the-art performance on both pre-surgery MRIs and post-surgery MRIs with artifacts. Based on our segmentation results, we also describe an automated approach to compute ER from these results. Experimental results on multiple datasets demonstrate the potential of the proposed method to assist clinicians in the diagnosis and management of NPH.

Image quality control (IQC) can be used in automated magnetic resonance (MR) image analysis to exclude erroneous results caused by poorly acquired or artifact-laden images. Existing IQC methods for MR imaging generally require human effort to craft meaningful features or label large datasets for supervised training. The involvement of human labor can be burdensome and biased, as labeling MR images based on their quality is a subjective task. In this paper, we propose an automatic IQC method that evaluates the extent of artifacts in MR images without supervision. In particular, we design an artifact encoding network that learns representations of artifacts based on contrastive learning. We then use a normalizing flow to estimate the density of learned representations for unsupervised classification. Our experiments on large-scale multi-cohort MR datasets show that the proposed method accurately detects images with high levels of artifacts, which can inform downstream analysis tasks about potentially flawed data., Comment: Accepted at the International Society for Optics and Photonics - Medical Imaging (SPIE-MI) 2023

The thalamus is a subcortical gray matter structure that plays a key role in relaying sensory and motor signals within the brain. Its nuclei can atrophy or otherwise be affected by neurological disease and injuries including mild traumatic brain injury. Segmenting both the thalamus and its nuclei is challenging because of the relatively low contrast within and around the thalamus in conventional magnetic resonance (MR) images. This paper explores imaging features to determine key tissue signatures that naturally cluster, from which we can parcellate thalamic nuclei. Tissue contrasts include T1-weighted and T2-weighted images, MR diffusion measurements including FA, mean diffusivity, Knutsson coefficients that represent fiber orientation, and synthetic multi-TI images derived from FGATIR and T1-weighted images. After registration of these contrasts and isolation of the thalamus, we use the uniform manifold approximation and projection (UMAP) method for dimensionality reduction to produce a low-dimensional representation of the data within the thalamus. Manual labeling of the thalamus provides labels for our UMAP embedding from which k nearest neighbors can be used to label new unseen voxels in that same UMAP embedding. N -fold cross-validation of the method reveals comparable performance to state-of-the-art methods for thalamic parcellation., Comment: 8 pages, 3 figures, 2023 SPIE-MI Image Processing

The lack of standardization is a prominent issue in magnetic resonance (MR) imaging. This often causes undesired contrast variations in the acquired images due to differences in hardware and acquisition parameters. In recent years, image synthesis-based MR harmonization with disentanglement has been proposed to compensate for the undesired contrast variations. Despite the success of existing methods, we argue that three major improvements can be made. First, most existing methods are built upon the assumption that multi-contrast MR images of the same subject share the same anatomy. This assumption is questionable, since different MR contrasts are specialized to highlight different anatomical features. Second, these methods often require a fixed set of MR contrasts for training (e.g., both T1-weighted and T2-weighted images), limiting their applicability. Lastly, existing methods are generally sensitive to imaging artifacts. In this paper, we present Harmonization with Attention-based Contrast, Anatomy, and Artifact Awareness (HACA3), a novel approach to address these three issues. HACA3 incorporates an anatomy fusion module that accounts for the inherent anatomical differences between MR contrasts. Furthermore, HACA3 is also robust to imaging artifacts and can be trained and applied to any set of MR contrasts. HACA3 is developed and evaluated on diverse MR datasets acquired from 21 sites with varying field strengths, scanner platforms, and acquisition protocols. Experiments show that HACA3 achieves state-of-the-art performance under multiple image quality metrics. We also demonstrate the applicability and versatility of HACA3 on downstream tasks including white matter lesion segmentation and longitudinal volumetric analyses.

In real-world decision-making, uncertainty is important yet difficult to handle. Stochastic dominance provides a theoretically sound approach for comparing uncertain quantities, but optimization with stochastic dominance constraints is often computationally expensive, which limits practical applicability. In this paper, we develop a simple yet efficient approach for the problem, the Light Stochastic Dominance Solver (light-SD), that leverages useful properties of the Lagrangian. We recast the inner optimization in the Lagrangian as a learning problem for surrogate approximation, which bypasses apparent intractability and leads to tractable updates or even closed-form solutions for gradient calculations. We prove convergence of the algorithm and test it empirically. The proposed light-SD demonstrates superior performance on several representative problems ranging from finance to supply chain management., Comment: Accepted to the 26th International Conference on Artificial Intelligence and Statistics (AISTATS 2023)

General movement assessment (GMA) of infant movement videos (IMVs) is an effective method for early detection of cerebral palsy (CP) in infants. We demonstrate in this paper that end-to-end trainable neural networks for image sequence recognition can be applied to achieve good results in GMA, and more importantly, augmenting raw video with infant body parsing and pose estimation information can significantly improve performance. To solve the problem of efficiently utilizing partially labeled IMVs for body parsing, we propose a semi-supervised model, termed SiamParseNet (SPN), which consists of two branches, one for intra-frame body parts segmentation and another for inter-frame label propagation. During training, the two branches are jointly trained by alternating between using input pairs of only labeled frames and input of both labeled and unlabeled frames. We also investigate training data augmentation by proposing a factorized video generative adversarial network (FVGAN) to synthesize novel labeled frames for training. When testing, we employ a multi-source inference mechanism, where the final result for a test frame is either obtained via the segmentation branch or via propagation from a nearby key frame. We conduct extensive experiments for body parsing using SPN on two infant movement video datasets, where SPN coupled with FVGAN achieves state-of-the-art performance. We further demonstrate that SPN can be easily adapted to the infant pose estimation task with superior performance. Last but not least, we explore the clinical application of our method for GMA. We collected a new clinical IMV dataset with GMA annotations, and our experiments show that SPN models for body parsing and pose estimation trained on the first two datasets generalize well to the new clinical dataset and their results can significantly boost the CRNN-based GMA prediction performance., Comment: Elsevier Medical Image Analysis 2022

In this paper, we propose a novel dual-branch Transformation-Synthesis network (TS-Net), for video motion retargeting. Given one subject video and one driving video, TS-Net can produce a new plausible video with the subject appearance of the subject video and motion pattern of the driving video. TS-Net consists of a warp-based transformation branch and a warp-free synthesis branch. The novel design of dual branches combines the strengths of deformation-grid-based transformation and warp-free generation for better identity preservation and robustness to occlusion in the synthesized videos. A mask-aware similarity module is further introduced to the transformation branch to reduce computational overhead. Experimental results on face and dance datasets show that TS-Net achieves better performance in video motion retargeting than several state-of-the-art models as well as its single-branch variants. Our code is available at https://github.com/nihaomiao/WACV23_TSNet., Comment: WACV 2023

Images obtained under low-light conditions will seriously affect the quality of the images. Solving the problem of poor low-light image quality can effectively improve the visual quality of images and better improve the usability of computer vision. In addition, it has very important applications in many fields. This paper proposes a DEANet based on Retinex for low-light image enhancement. It combines the frequency information and content information of the image into three sub-networks: decomposition network, enhancement network and adjustment network. These three sub-networks are respectively used for decomposition, denoising, contrast enhancement and detail preservation, adjustment, and image generation. Our model has good robust results for all low-light images. The model is trained on the public data set LOL, and the experimental results show that our method is better than the existing state-of-the-art methods in terms of vision and quality., Comment: 8 pages, 7 figures

In 2D multi-slice magnetic resonance (MR) acquisition, the through-plane signals are typically of lower resolution than the in-plane signals. While contemporary super-resolution (SR) methods aim to recover the underlying high-resolution volume, the estimated high-frequency information is implicit via end-to-end data-driven training rather than being explicitly stated and sought. To address this, we reframe the SR problem statement in terms of perfect reconstruction filter banks, enabling us to identify and directly estimate the missing information. In this work, we propose a two-stage approach to approximate the completion of a perfect reconstruction filter bank corresponding to the anisotropic acquisition of a particular scan. In stage 1, we estimate the missing filters using gradient descent and in stage 2, we use deep networks to learn the mapping from coarse coefficients to detail coefficients. In addition, the proposed formulation does not rely on external training data, circumventing the need for domain shift correction. Under our approach, SR performance is improved particularly in "slice gap" scenarios, likely due to the constrained solution space imposed by the framework.

Significant improvement has been made on just noticeable difference (JND) modelling due to the development of deep neural networks, especially for the recently developed unsupervised-JND generation models. However, they have a major drawback that the generated JND is assessed in the real-world signal domain instead of in the perceptual domain in the human brain. There is an obvious difference when JND is assessed in such two domains since the visual signal in the real world is encoded before it is delivered into the brain with the human visual system (HVS). Hence, we propose an HVS-inspired signal degradation network for JND estimation. To achieve this, we carefully analyze the HVS perceptual process in JND subjective viewing to obtain relevant insights, and then design an HVS-inspired signal degradation (HVS-SD) network to represent the signal degradation in the HVS. On the one hand, the well learnt HVS-SD enables us to assess the JND in the perceptual domain. On the other hand, it provides more accurate prior information for better guiding JND generation. Additionally, considering the requirement that reasonable JND should not lead to visual attention shifting, a visual attention loss is proposed to control JND generation. Experimental results demonstrate that the proposed method achieves the SOTA performance for accurately estimating the redundancy of the HVS. Source code will be available at https://github.com/jianjin008/HVS-SD-JND., Comment: Submit to IEEE Transactions on Cybernetics

The automatic generation of floorplans given user inputs has great potential in architectural design and has recently been explored in the computer vision community. However, the majority of existing methods synthesize floorplans in the format of rasterized images, which are difficult to edit or customize. In this paper, we aim to synthesize floorplans as sequences of 1-D vectors, which eases user interaction and design customization. To generate high fidelity vectorized floorplans, we propose a novel two-stage framework, including a draft stage and a multi-round refining stage. In the first stage, we encode the room connectivity graph input by users with a graph convolutional network (GCN), then apply an autoregressive transformer network to generate an initial floorplan sequence. To polish the initial design and generate more visually appealing floorplans, we further propose a novel panoptic refinement network(PRN) composed of a GCN and a transformer network. The PRN takes the initial generated sequence as input and refines the floorplan design while encouraging the correct room connectivity with our proposed geometric loss. We have conducted extensive experiments on a real-world floorplan dataset, and the results show that our method achieves state-of-the-art performance under different settings and evaluation metrics., Comment: ECCV 2022

Nonvolatile phase change random access memory (PCRAM) is regarded as one of promising candidates for emerging mass storage in the era of Big Data. However, relatively high programming energy hurdles the further reduction of power consumption in PCRAM. Utilizing narrow edge-contact of graphene can effectively reduce the active volume of phase change material in each cell, and therefore realize low-power operation. Here, we demonstrate that a write energy can be reduced to about ~53.7 fJ in a cell with ~3 nm-wide graphene nanoribbon (GNR) as edge-contact, whose cross-sectional area is only ~1 nm2. It is found that the cycle endurance exhibits an obvious dependence on the bias polarity in the cell with structure asymmetry. If a positive bias was applied to graphene electrode, the endurance can be extended at least one order longer than the case with reversal of polarity. The work represents a great technological advance for the low power PCRAM and could benefit for in-memory computing in future., Comment: 14 pages, 4 figures

Accurate infarct segmentation in non-contrast CT (NCCT) images is a crucial step toward computer-aided acute ischemic stroke (AIS) assessment. In clinical practice, bilateral symmetric comparison of brain hemispheres is usually used to locate pathological abnormalities. Recent research has explored asymmetries to assist with AIS segmentation. However, most previous symmetry-based work mixed different types of asymmetries when evaluating their contribution to AIS. In this paper, we propose a novel Asymmetry Disentanglement Network (ADN) to automatically separate pathological asymmetries and intrinsic anatomical asymmetries in NCCTs for more effective and interpretable AIS segmentation. ADN first performs asymmetry disentanglement based on input NCCTs, which produces different types of 3D asymmetry maps. Then a synthetic, intrinsic-asymmetry-compensated and pathology-asymmetry-salient NCCT volume is generated and later used as input to a segmentation network. The training of ADN incorporates domain knowledge and adopts a tissue-type aware regularization loss function to encourage clinically-meaningful pathological asymmetry extraction. Coupled with an unsupervised 3D transformation network, ADN achieves state-of-the-art AIS segmentation performance on a public NCCT dataset. In addition to the superior performance, we believe the learned clinically-interpretable asymmetry maps can also provide insights towards a better understanding of AIS assessment. Our code is available at https://github.com/nihaomiao/MICCAI22_ADN., Comment: MICCAI 2022

Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture device coupled with label-free Raman Spectroscopy holds the promise of fast detection by rapidly obtaining the Raman signature of a virus followed by a machine learning approach applied to recognize the virus based on its Raman spectrum, which is used as a fingerprint. We present such a machine learning approach for analyzing Raman spectra of human and avian viruses. A Convolutional Neural Network (CNN) classifier specifically designed for spectral data achieves very high accuracy for a variety of virus type or subtype identification tasks. In particular, it achieves 99% accuracy for classifying influenza virus type A vs. type B, 96% accuracy for classifying four subtypes of influenza A, 95% accuracy for differentiating enveloped and non-enveloped viruses, and 99% accuracy for differentiating avian coronavirus (infectious bronchitis virus, IBV) from other avian viruses. Furthermore, interpretation of neural net responses in the trained CNN model using a full-gradient algorithm highlights Raman spectral ranges that are most important to virus identification. By correlating ML-selected salient Raman ranges with the signature ranges of known biomolecules and chemical functional groups (for example, amide, amino acid, carboxylic acid), we verify that our ML model effectively recognizes the Raman signatures of proteins, lipids and other vital functional groups present in different viruses and uses a weighted combination of these signatures to identify viruses., Comment: 23 pages, 8 figures

Disentangling anatomical and contrast information from medical images has gained attention recently, demonstrating benefits for various image analysis tasks. Current methods learn disentangled representations using either paired multi-modal images with the same underlying anatomy or auxiliary labels (e.g., manual delineations) to provide inductive bias for disentanglement. However, these requirements could significantly increase the time and cost in data collection and limit the applicability of these methods when such data are not available. Moreover, these methods generally do not guarantee disentanglement. In this paper, we present a novel framework that learns theoretically and practically superior disentanglement from single modality magnetic resonance images. Moreover, we propose a new information-based metric to quantitatively evaluate disentanglement. Comparisons over existing disentangling methods demonstrate that the proposed method achieves superior performance in both disentanglement and cross-domain image-to-image translation tasks.

With the advancement of deep learning techniques, major cloud providers and niche machine learning service providers start to offer their cloud-based machine learning tools, also known as machine learning as a service (MLaaS), to the public. According to our measurement, for the same task, these MLaaSes from different providers have varying performance due to the proprietary datasets, models, etc. Federating different MLaaSes together allows us to improve the analytic performance further. However, naively aggregating results from different MLaaSes not only incurs significant momentary cost but also may lead to sub-optimal performance gain due to the introduction of possible false-positive results. In this paper, we propose Armol, a framework to federate the right selection of MLaaS providers to achieve the best possible analytic performance. We first design a word grouping algorithm to unify the output labels across different providers. We then present a deep combinatorial reinforcement learning based-approach to maximize the accuracy while minimizing the cost. The predictions from the selected providers are then aggregated together using carefully chosen ensemble strategies. The real-world trace-driven evaluation further demonstrates that Armol is able to achieve the same accuracy results with $67\%$ less inference cost.