arXiv subjects

Can Cui

Publications and source records attributed to Can Cui.

At least 109 records · Page 6Linked to original sources

arXiv2023

Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging

The segment anything model (SAM) was released as a foundation model for image segmentation. The promptable segmentation model was trained by over 1 billion masks on 11M licensed and privacy-respecting images. The model supports zero-shot image segmentation with various segmentation prompts (e.g., points, boxes, masks). It makes the SAM attractive for medical image analysis, especially for digital pathology where the training data are rare. In this study, we evaluate the zero-shot segmentation performance of SAM model on representative segmentation tasks on whole slide imaging (WSI), including (1) tumor segmentation, (2) non-tumor tissue segmentation, (3) cell nuclei segmentation. Core Results: The results suggest that the zero-shot SAM model achieves remarkable segmentation performance for large connected objects. However, it does not consistently achieve satisfying performance for dense instance object segmentation, even with 20 prompts (clicks/boxes) on each image. We also summarized the identified limitations for digital pathology: (1) image resolution, (2) multiple scales, (3) prompt selection, and (4) model fine-tuning. In the future, the few-shot fine-tuning with images from downstream pathological segmentation tasks might help the model to achieve better performance in dense object segmentation.

eess.IV↗

arXiv2023

CAusal and collaborative proxy-tasKs lEarning for Semi-Supervised Domain Adaptation

Semi-supervised domain adaptation (SSDA) adapts a learner to a new domain by effectively utilizing source domain data and a few labeled target samples. It is a practical yet under-investigated research topic. In this paper, we analyze the SSDA problem from two perspectives that have previously been overlooked, and correspondingly decompose it into two \emph{key subproblems}: \emph{robust domain adaptation (DA) learning} and \emph{maximal cross-domain data utilization}. \textbf{(i)} From a causal theoretical view, a robust DA model should distinguish the invariant ``concept'' (key clue to image label) from the nuisance of confounding factors across domains. To achieve this goal, we propose to generate \emph{concept-invariant samples} to enable the model to classify the samples through causal intervention, yielding improved generalization guarantees; \textbf{(ii)} Based on the robust DA theory, we aim to exploit the maximal utilization of rich source domain data and a few labeled target samples to boost SSDA further. Consequently, we propose a collaboratively debiasing learning framework that utilizes two complementary semi-supervised learning (SSL) classifiers to mutually exchange their unbiased knowledge, which helps unleash the potential of source and target domain training data, thereby producing more convincing pseudo-labels. Such obtained labels facilitate cross-domain feature alignment and duly improve the invariant concept learning. In our experimental study, we show that the proposed model significantly outperforms SOTA methods in terms of effectiveness and generalisability on SSDA datasets.

cs.CV↗

arXiv2023

Distributionally Robust Chance-Constrained Optimization for Hierarchical UAV-based MEC

Multi-access edge computing (MEC) is regarded as a promising technology in the sixth-generation communication. However, the antenna gain is always affected by the environment when unmanned aerial vehicles (UAVs) are served as MEC platforms, resulting in unexpected channel errors. In order to deal with the problem and reduce the power consumption in the UAV-based MEC, we jointly optimize the access scheme and power allocation in the hierarchical UAV-based MEC. Specifically, UAVs are deployed in the lower layer to collect data from ground users. Moreover, a UAV with powerful computation ability is deployed in the upper layer to assist with computing. The goal is to guarantee the quality of service and minimize the total power consumption. We consider the errors caused by various perturbations in realistic circumstances and formulate a distributionally robust chance-constrained optimization problem with an uncertainty set. The problem with chance constraints is intractable. To tackle this issue, we utilize the conditional value-at-risk method to reformulate the problem into a semidefinite programming form. Then, a joint algorithm for access scheme and power allocation is designed. Finally, we conduct simulations to demonstrate the efficiency of the proposed algorithm.

cs.NI↗

arXiv2023

Deep Multi-modal Fusion of Image and Non-image Data in Disease Diagnosis and Prognosis: A Review

The rapid development of diagnostic technologies in healthcare is leading to higher requirements for physicians to handle and integrate the heterogeneous, yet complementary data that are produced during routine practice. For instance, the personalized diagnosis and treatment planning for a single cancer patient relies on the various images (e.g., radiological, pathological, and camera images) and non-image data (e.g., clinical data and genomic data). However, such decision-making procedures can be subjective, qualitative, and have large inter-subject variabilities. With the recent advances in multi-modal deep learning technologies, an increasingly large number of efforts have been devoted to a key question: how do we extract and aggregate multi-modal information to ultimately provide more objective, quantitative computer-aided clinical decision making? This paper reviews the recent studies on dealing with such a question. Briefly, this review will include the (1) overview of current multi-modal learning workflows, (2) summarization of multi-modal fusion methods, (3) discussion of the performance, (4) applications in disease diagnosis and prognosis, and (5) challenges and future directions.

cs.LG↗

arXiv2023

Omni-Seg: A Scale-aware Dynamic Network for Renal Pathological Image Segmentation

Comprehensive semantic segmentation on renal pathological images is challenging due to the heterogeneous scales of the objects. For example, on a whole slide image (WSI), the cross-sectional areas of glomeruli can be 64 times larger than that of the peritubular capillaries, making it impractical to segment both objects on the same patch, at the same scale. To handle this scaling issue, prior studies have typically trained multiple segmentation networks in order to match the optimal pixel resolution of heterogeneous tissue types. This multi-network solution is resource-intensive and fails to model the spatial relationship between tissue types. In this paper, we propose the Omni-Seg+ network, a scale-aware dynamic neural network that achieves multi-object (six tissue types) and multi-scale (5X to 40X scale) pathological image segmentation via a single neural network. The contribution of this paper is three-fold: (1) a novel scale-aware controller is proposed to generalize the dynamic neural network from single-scale to multi-scale; (2) semi-supervised consistency regularization of pseudo-labels is introduced to model the inter-scale correlation of unannotated tissue types into a single end-to-end learning paradigm; and (3) superior scale-aware generalization is evidenced by directly applying a model trained on human kidney images to mouse kidney images, without retraining. By learning from ~150,000 human pathological image patches from six tissue types at three different resolutions, our approach achieved superior segmentation performance according to human visual assessment and evaluation of image-omics (i.e., spatial transcriptomics). The official implementation is available at https://github.com/ddrrnn123/Omni-Seg.

eess.IV↗

arXiv2022

Matching Estimators of Causal Effects in Clustered Observational Studies with Application to Quantifying the Impact of Marine Protected Areas on Biodiversity

Marine conservation preserves fish biodiversity, protects marine and coastal ecosystems, and supports climate resilience and adaptation. Despite the importance of establishing marine protected areas (MPAs), research on the effectiveness of MPAs with different conservation policies is limited due to the lack of quantitative MPA information. In this paper, leveraging a global MPA database, we investigate the causal impact of MPA policies on fish biodiversity. To address challenges posed by this clustered and confounded observational study, we construct a matching estimator of the average treatment effect and a cluster-weighted bootstrap method for variance estimation. We establish the theoretical guarantees of the matching estimator and its variance estimator. Under our proposed matching framework, we recommend matching on both cluster-level and unit-level covariates to achieve efficiency. The simulation results demonstrate that our matching strategy minimizes the bias and achieves the nominal confidence interval coverage. Applying our proposed matching method to compare different MPA policies reveals that the no-take policy is more effective than the multi-use policy in preserving fish biodiversity.

stat.ME↗

arXiv2022

Turbulence in outer protoplanetary disks: MRI or VSI?

The outer protoplanetary disks (PPDs) can be subject to the magnetorotational instability (MRI) and the vertical shear instability (VSI). While both processes can drive turbulence in the disk, existing numerical simulations have studied them separately. In this paper, we conduct global 3D non-ideal magnetohydrodynamic (MHD) simulations for outer PPDs with ambipolar diffusion and instantaneous cooling, and hence conductive to both instabilities. Given the range of ambipolar Elsässer numbers ($Am$) explored, it is found that the VSI turbulence dominates over the MRI when ambipolar diffusion is strong ($Am=0.1$); the VSI and MRI can co-exist for $Am=1$; and the VSI is overwhelmed by the MRI when ambipolar diffusion is weak ($Am=10$). Angular momentum transport process is primarily driven by MHD winds, while viscous accretion due to MRI and/or VSI turbulence makes a moderate contribution in most cases. Spontaneous magnetic flux concentration and formation of annular substructures remain robust in strong ambipolar diffusion dominated disks ($Am\leq1$) with the presence of the VSI. Ambipolar diffusion is the major contributor to the magnetic flux concentration phenomenon rather than advection.

astro-ph.EP↗

arXiv2022

Millimeter Gap Contrast as a Probe for Turbulence Level in Protoplanetary Disks

Turbulent motions are believed to regulate angular momentum transport and influence dust evolution in protoplanetary disks. Measuring the strength of turbulence is challenging through gas line observations because of the requirement for high spatial and spectral resolution data, and an exquisite determination of the temperature. In this work, taking the well-known HD 163296 disk as an example, we investigated the contrast of gaps identified in high angular resolution continuum images as a probe for the level of turbulence. With self-consistent radiative transfer models, we simultaneously analyzed the radial brightness profiles along the disk major and minor axes, and the azimuthal brightness profiles of the B67 and B100 rings. By fitting all the gap contrasts measured from these profiles, we constrained the gas-to-dust scale height ratio $Λ$ to be $3.0_{-0.8}^{+0.3}$, $1.2_{-0.1}^{+0.1}$ and ${\ge}\,6.5$ for the D48, B67 and B100 regions, respectively. The varying gas-to-dust scale height ratios indicate that the degree of dust settling changes with radius. The inferred values for $Λ$ translate into a turbulence level of $α_{\rm turb}\,{<}\,3\times10^{-3}$ in the D48 and B100 regions, which is consistent with previous upper limits set by gas line observations. However, turbulent motions in the B67 ring are strong with $α_{\rm turb}\,{\sim}1.2\,{\times}\,10^{-2}$. Due to the degeneracy between $Λ$ and the depth of dust surface density drops, the turbulence strength in the D86 gap region is not constrained.

astro-ph.EP↗

arXiv2022

Cross-scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images

Multi-instance learning (MIL) is widely used in the computer-aided interpretation of pathological Whole Slide Images (WSIs) to solve the lack of pixel-wise or patch-wise annotations. Often, this approach directly applies "natural image driven" MIL algorithms which overlook the multi-scale (i.e. pyramidal) nature of WSIs. Off-the-shelf MIL algorithms are typically deployed on a single-scale of WSIs (e.g., 20x magnification), while human pathologists usually aggregate the global and local patterns in a multi-scale manner (e.g., by zooming in and out between different magnifications). In this study, we propose a novel cross-scale attention mechanism to explicitly aggregate inter-scale interactions into a single MIL network for Crohn's Disease (CD), which is a form of inflammatory bowel disease. The contribution of this paper is two-fold: (1) a cross-scale attention mechanism is proposed to aggregate features from different resolutions with multi-scale interaction; and (2) differential multi-scale attention visualizations are generated to localize explainable lesion patterns. By training ~250,000 H&E-stained Ascending Colon (AC) patches from 20 CD patient and 30 healthy control samples at different scales, our approach achieved a superior Area under the Curve (AUC) score of 0.8924 compared with baseline models. The official implementation is publicly available at https://github.com/hrlblab/CS-MIL.

cs.CV↗

arXiv2022

Survival Prediction of Brain Cancer with Incomplete Radiology, Pathology, Genomics, and Demographic Data

Integrating cross-department multi-modal data (e.g., radiological, pathological, genomic, and clinical data) is ubiquitous in brain cancer diagnosis and survival prediction. To date, such an integration is typically conducted by human physicians (and panels of experts), which can be subjective and semi-quantitative. Recent advances in multi-modal deep learning, however, have opened a door to leverage such a process to a more objective and quantitative manner. Unfortunately, the prior arts of using four modalities on brain cancer survival prediction are limited by a "complete modalities" setting (i.e., with all modalities available). Thus, there are still open questions on how to effectively predict brain cancer survival from the incomplete radiological, pathological, genomic, and demographic data (e.g., one or more modalities might not be collected for a patient). For instance, should we use both complete and incomplete data, and more importantly, how to use those data? To answer the preceding questions, we generalize the multi-modal learning on cross-department multi-modal data to a missing data setting. Our contribution is three-fold: 1) We introduce optimal multi-modal learning with missing data (MMD) pipeline with optimized hardware consumption and computational efficiency; 2) We extend multi-modal learning on radiological, pathological, genomic, and demographic data into missing data scenarios; 3) a large-scale public dataset (with 962 patients) is collected to systematically evaluate glioma tumor survival prediction using four modalities. The proposed method improved the C-index of survival prediction from 0.7624 to 0.8053.

cs.LG↗

arXiv2022

ModDrop++: A Dynamic Filter Network with Intra-subject Co-training for Multiple Sclerosis Lesion Segmentation with Missing Modalities

Multiple Sclerosis (MS) is a chronic neuroinflammatory disease and multi-modality MRIs are routinely used to monitor MS lesions. Many automatic MS lesion segmentation models have been developed and have reached human-level performance. However, most established methods assume the MRI modalities used during training are also available during testing, which is not guaranteed in clinical practice. Previously, a training strategy termed Modality Dropout (ModDrop) has been applied to MS lesion segmentation to achieve the state-of-the-art performance with missing modality. In this paper, we present a novel method dubbed ModDrop++ to train a unified network adaptive to an arbitrary number of input MRI sequences. ModDrop++ upgrades the main idea of ModDrop in two key ways. First, we devise a plug-and-play dynamic head and adopt a filter scaling strategy to improve the expressiveness of the network. Second, we design a co-training strategy to leverage the intra-subject relation between full modality and missing modality. Specifically, the intra-subject co-training strategy aims to guide the dynamic head to generate similar feature representations between the full- and missing-modality data from the same subject. We use two public MS datasets to show the superiority of ModDrop++. Source code and trained models are available at https://github.com/han-liu/ModDropPlusPlus.

eess.IV↗

arXiv2022

Wavelike nature of the vertical shear instability in global protoplanetary disks

The vertical shear instability (VSI) is a robust phenomenon in irradiated protoplanetary disks (PPDs). The majority of previous numerical simulations have focused on the turbulent properties of its saturated state. However, the saturation of the VSI manifests as large-scale coherent radially travelling inertial waves. In this paper, we study inertial-wave-disk interactions and their impact on VSI saturation. Inertial-wave linear theory is developed and applied to a representative global 2D simulation using the Athena++ code. It is found that the VSI saturates by separating the disk into several radial wave zones roughly demarcated by corotation resonances (turning points); this structure also manifests in modest radial variations in the vertical turbulence strength. Future numerical work should employ large radial domains to accommodate this radial structure of the VSI, while concurrently adopting sufficiently fine resolutions to resolve the parametric instability that attacks the saturated VSI inertial waves.

astro-ph.EP↗

arXiv2022

Learned Coarse Models for Efficient Turbulence Simulation

Turbulence simulation with classical numerical solvers requires high-resolution grids to accurately resolve dynamics. Here we train learned simulators at low spatial and temporal resolutions to capture turbulent dynamics generated at high resolution. We show that our proposed model can simulate turbulent dynamics more accurately than classical numerical solvers at the comparably low resolutions across various scientifically relevant metrics. Our model is trained end-to-end from data and is capable of learning a range of challenging chaotic and turbulent dynamics at low resolution, including trajectories generated by the state-of-the-art Athena++ engine. We show that our simpler, general-purpose architecture outperforms various more specialized, turbulence-specific architectures from the learned turbulence simulation literature. In general, we see that learned simulators yield unstable trajectories; however, we show that tuning training noise and temporal downsampling solves this problem. We also find that while generalization beyond the training distribution is a challenge for learned models, training noise, added loss constraints, and dataset augmentation can help. Broadly, we conclude that our learned simulator outperforms traditional solvers run on coarser grids, and emphasize that simple design choices can offer stability and robust generalization.

physics.flu-dyn↗

arXiv2022

Omni-Seg: A Single Dynamic Network for Multi-label Renal Pathology Image Segmentation using Partially Labeled Data

Computer-assisted quantitative analysis on Giga-pixel pathology images has provided a new avenue in histology examination. The innovations have been largely focused on cancer pathology (i.e., tumor segmentation and characterization). In non-cancer pathology, the learning algorithms can be asked to examine more comprehensive tissue types simultaneously, as a multi-label setting. The prior arts typically needed to train multiple segmentation networks in order to match the domain-specific knowledge for heterogeneous tissue types (e.g., glomerular tuft, glomerular unit, proximal tubular, distal tubular, peritubular capillaries, and arteries). In this paper, we propose a dynamic single segmentation network (Omni-Seg) that learns to segment multiple tissue types using partially labeled images (i.e., only one tissue type is labeled for each training image) for renal pathology. By learning from ~150,000 patch-wise pathological images from six tissue types, the proposed Omni-Seg network achieved superior segmentation accuracy and less resource consumption when compared to the previous the multiple-network and multi-head design. In the testing stage, the proposed method obtains "completely labeled" tissue segmentation results using only "partially labeled" training images. The source code is available at https://github.com/ddrrnn123/Omni-Seg

eess.IV↗

arXiv2022

Shape-Dependent Multi-Weight Magnetic Artificial Synapses for Neuromorphic Computing

In neuromorphic computing, artificial synapses provide a multi-weight conductance state that is set based on inputs from neurons, analogous to the brain. Additional properties of the synapse beyond multiple weights can be needed, and can depend on the application, requiring the need for generating different synapse behaviors from the same materials. Here, we measure artificial synapses based on magnetic materials that use a magnetic tunnel junction and a magnetic domain wall. By fabricating lithographic notches in a domain wall track underneath a single magnetic tunnel junction, we achieve 4-5 stable resistance states that can be repeatably controlled electrically using spin orbit torque. We analyze the effect of geometry on the synapse behavior, showing that a trapezoidal device has asymmetric weight updates with high controllability, while a straight device has higher stochasticity, but with stable resistance levels. The device data is input into neuromorphic computing simulators to show the usefulness of application-specific synaptic functions. Implementing an artificial neural network applied on streamed Fashion-MNIST data, we show that the trapezoidal magnetic synapse can be used as a metaplastic function for efficient online learning. Implementing a convolutional neural network for CIFAR-100 image recognition, we show that the straight magnetic synapse achieves near-ideal inference accuracy, due to the stability of its resistance levels. This work shows multi-weight magnetic synapses are a feasible technology for neuromorphic computing and provides design guidelines for emerging artificial synapse technologies.

cond-mat.mes-hall↗

arXiv2022

A Survey on Deep Reinforcement Learning for Data Processing and Analytics

Data processing and analytics are fundamental and pervasive. Algorithms play a vital role in data processing and analytics where many algorithm designs have incorporated heuristics and general rules from human knowledge and experience to improve their effectiveness. Recently, reinforcement learning, deep reinforcement learning (DRL) in particular, is increasingly explored and exploited in many areas because it can learn better strategies in complicated environments it is interacting with than statically designed algorithms. Motivated by this trend, we provide a comprehensive review of recent works focusing on utilizing DRL to improve data processing and analytics. First, we present an introduction to key concepts, theories, and methods in DRL. Next, we discuss DRL deployment on database systems, facilitating data processing and analytics in various aspects, including data organization, scheduling, tuning, and indexing. Then, we survey the application of DRL in data processing and analytics, ranging from data preparation, natural language processing to healthcare, fintech, etc. Finally, we discuss important open challenges and future research directions of using DRL in data processing and analytics.

cs.LG↗

arXiv2022

Unsupervised Domain Adaptation for Vestibular Schwannoma and Cochlea Segmentation via Semi-supervised Learning and Label Fusion

Automatic methods to segment the vestibular schwannoma (VS) tumors and the cochlea from magnetic resonance imaging (MRI) are critical to VS treatment planning. Although supervised methods have achieved satisfactory performance in VS segmentation, they require full annotations by experts, which is laborious and time-consuming. In this work, we aim to tackle the VS and cochlea segmentation problem in an unsupervised domain adaptation setting. Our proposed method leverages both the image-level domain alignment to minimize the domain divergence and semi-supervised training to further boost the performance. Furthermore, we propose to fuse the labels predicted from multiple models via noisy label correction. In the MICCAI 2021 crossMoDA challenge, our results on the final evaluation leaderboard showed that our proposed method has achieved promising segmentation performance with mean dice score of 79.9% and 82.5% and ASSD of 1.29 mm and 0.18 mm for VS tumor and cochlea, respectively. The cochlea ASSD achieved by our method has outperformed all other competing methods as well as the supervised nnU-Net.

cs.CV↗

arXiv2022

The saturation of the VSI in protoplanetary disks via parametric instability

The vertical shear instability (VSI) is a robust and potentially important phenomenon in irradiated protoplanetary disks (PPDs), yet the mechanism by which it saturates remains poorly understood. Global simulations suggest that the non-linear evolution of the VSI is dominated by radially propagating inertial wavetrains (called `body modes'), but these are known to be susceptible to a parametric instability. In this paper, we propose that the global VSI saturates via this secondary instability, which initiates a redistribution of energy from the large scales to smaller-scale inertial waves, and finally into a turbulent cascade. We present an analytic theory of the instability in a simple idealised model that captures the main physical and mathematical details of the problem. In addition, we conduct numerical simulations with the SNOOPY code to consolidate the theory. Once the parametric instability prevails, the VSI is likely far more disordered and incoherent than current global simulations suggest. We also argue that it is challenging to capture parametric instability in global simulations unless the radial resolution is very fine, possibly $\sim 300$ grid cells per scale height in radius.

astro-ph.EP↗