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Published work

48 published item(s)

preprint2026arXiv

Compress Then Adapt? No, Do It Together via Task-aware Union of Subspaces

Adapting large pretrained models to diverse tasks is now routine, yet the two dominant strategies of parameter-efficient fine-tuning (PEFT) and low-rank compression are typically composed in sequence. This decoupled practice first compresses and then fine-tunes adapters, potentially misaligning the compressed subspace with downstream objectives and squandering a global parameter budget. To overcome this limitation, we introduce JACTUS (Joint Adaptation and Compression with a Task-aware Union of Subspaces), a single framework that unifies compression and adaptation. From a small calibration set, JACTUS estimates input and pre-activation gradient covariances, forms their orthogonal union with the pretrained weight subspace, performs a projected low-rank approximation inside this union, allocates rank globally by marginal gain per parameter, and trains only a compact core matrix. This explicitly mitigates the potential misalignment between the compressed subspace and downstream objectives by coupling the directions preserved for compression with those required for adaptation, yielding a deployable low-rank model that avoids retaining full frozen weights while enabling fast and robust tuning. On vision, JACTUS attains an average 89.2% accuracy on ViT-Base across eight datasets at 80% retained parameters, surpassing strong 100% PEFT baselines (e.g., DoRA 87.9%). On language, JACTUS achieves an 80.9% average on Llama2-7B commonsense QA at the same 80% retained-parameter budget, outperforming 100% PEFT (e.g., DoRA 79.7%) and exceeding prior compress-then-finetune pipelines under the same ratained-parameter budget. We will release code.

preprint2024arXiv

HOI4D: A 4D Egocentric Dataset for Category-Level Human-Object Interaction

We present HOI4D, a large-scale 4D egocentric dataset with rich annotations, to catalyze the research of category-level human-object interaction. HOI4D consists of 2.4M RGB-D egocentric video frames over 4000 sequences collected by 4 participants interacting with 800 different object instances from 16 categories over 610 different indoor rooms. Frame-wise annotations for panoptic segmentation, motion segmentation, 3D hand pose, category-level object pose and hand action have also been provided, together with reconstructed object meshes and scene point clouds. With HOI4D, we establish three benchmarking tasks to promote category-level HOI from 4D visual signals including semantic segmentation of 4D dynamic point cloud sequences, category-level object pose tracking, and egocentric action segmentation with diverse interaction targets. In-depth analysis shows HOI4D poses great challenges to existing methods and produces great research opportunities.

preprint2022arXiv

Dark Matter Halos in Interacting Dark Energy Models: Formation History, Density Profile, Spin and Shape

The interacting dark energy (IDE) model, which considers the interaction between dark energy and dark matter, provides a natural mechanism to alleviate the coincidence problem and can also relieve the observational tensions under the $Λ$CDM model. Previous studies have put constraints on IDE models by observations of cosmic expansion history, cosmic microwave background and large-scale structures. However, these data are not yet enough to distinguish IDE models from $Λ$CDM effectively. Because the non-linear structure formation contains rich cosmological information, it can provide additional means to differentiate alternative models. In this paper, based on a set of $N$-body simulations for IDE models, we investigate the formation histories and properties of dark matter halos, and compare with their $Λ$CDM counterparts. For the model with dark matter decaying into dark energy and the parameters being the best-fit values from previous constraints, the structure formation is markedly slowed down, and the halos have systematically lower mass, looser internal structure, higher spin and anisotropy. This is inconsistent with the observed structure formation, and thus this model can be safely ruled out from the perspective of non-linear structure formation. Moreover, we find that the ratio of halo concentrations between IDE and $Λ$CDM counterparts depends sensitively on the interaction parameter and is independent of halo mass. This can act as a powerful probe to constrain IDE models. Our results concretely demonstrate that the interaction of the two dark components can affect the halo formation considerably, and therefore the constraints from non-linear structures are indispensable.

preprint2022arXiv

Discovering novel systemic biomarkers in photos of the external eye

External eye photos were recently shown to reveal signs of diabetic retinal disease and elevated HbA1c. In this paper, we evaluate if external eye photos contain information about additional systemic medical conditions. We developed a deep learning system (DLS) that takes external eye photos as input and predicts multiple systemic parameters, such as those related to the liver (albumin, AST); kidney (eGFR estimated using the race-free 2021 CKD-EPI creatinine equation, the urine ACR); bone & mineral (calcium); thyroid (TSH); and blood count (Hgb, WBC, platelets). Development leveraged 151,237 images from 49,015 patients with diabetes undergoing diabetic eye screening in 11 sites across Los Angeles county, CA. Evaluation focused on 9 pre-specified systemic parameters and leveraged 3 validation sets (A, B, C) spanning 28,869 patients with and without diabetes undergoing eye screening in 3 independent sites in Los Angeles County, CA, and the greater Atlanta area, GA. We compared against baseline models incorporating available clinicodemographic variables (e.g. age, sex, race/ethnicity, years with diabetes). Relative to the baseline, the DLS achieved statistically significant superior performance at detecting AST>36, calcium<8.6, eGFR<60, Hgb<11, platelets<150, ACR>=300, and WBC<4 on validation set A (a patient population similar to the development sets), where the AUC of DLS exceeded that of the baseline by 5.2-19.4%. On validation sets B and C, with substantial patient population differences compared to the development sets, the DLS outperformed the baseline for ACR>=300 and Hgb<11 by 7.3-13.2%. Our findings provide further evidence that external eye photos contain important biomarkers of systemic health spanning multiple organ systems. Further work is needed to investigate whether and how these biomarkers can be translated into clinical impact.

preprint2022arXiv

EDN: Salient Object Detection via Extremely-Downsampled Network

Recent progress on salient object detection (SOD) mainly benefits from multi-scale learning, where the high-level and low-level features collaborate in locating salient objects and discovering fine details, respectively. However, most efforts are devoted to low-level feature learning by fusing multi-scale features or enhancing boundary representations. High-level features, which although have long proven effective for many other tasks, yet have been barely studied for SOD. In this paper, we tap into this gap and show that enhancing high- level features is essential for SOD as well. To this end, we introduce an Extremely-Downsampled Network (EDN), which employs an extreme downsampling technique to effectively learn a global view of the whole image, leading to accurate salient object localization. To accomplish better multi-level feature fusion, we construct the Scale-Correlated Pyramid Convolution (SCPC) to build an elegant decoder for recovering object details from the above extreme downsampling. Extensive experiments demonstrate that EDN achieves state-of-the-art performance with real-time speed. Our efficient EDN-Lite also achieves competitive performance with a speed of 316fps. Hence, this work is expected to spark some new thinking in SOD. Code is available at https://github.com/yuhuan-wu/EDN.

preprint2022arXiv

End-to-end Clinical Event Extraction from Chinese Electronic Health Record

Event extraction is an important work of medical text processing. According to the complex characteristics of medical text annotation, we use the end-to-end event extraction model to enhance the output formatting information of events. Through pre training and fine-tuning, we can extract the attributes of the four dimensions of medical text: anatomical position, subject word, description word and occurrence state. On the test set, the accuracy rate was 0.4511, the recall rate was 0.3928, and the F1 value was 0.42. The method of this model is simple, and it has won the second place in the task of mining clinical discovery events (task2) in the Chinese electronic medical record of the seventh China health information processing Conference (chip2021).

preprint2022arXiv

LEVEN: A Large-Scale Chinese Legal Event Detection Dataset

Recognizing facts is the most fundamental step in making judgments, hence detecting events in the legal documents is important to legal case analysis tasks. However, existing Legal Event Detection (LED) datasets only concern incomprehensive event types and have limited annotated data, which restricts the development of LED methods and their downstream applications. To alleviate these issues, we present LEVEN a large-scale Chinese LEgal eVENt detection dataset, with 8,116 legal documents and 150,977 human-annotated event mentions in 108 event types. Not only charge-related events, LEVEN also covers general events, which are critical for legal case understanding but neglected in existing LED datasets. To our knowledge, LEVEN is the largest LED dataset and has dozens of times the data scale of others, which shall significantly promote the training and evaluation of LED methods. The results of extensive experiments indicate that LED is challenging and needs further effort. Moreover, we simply utilize legal events as side information to promote downstream applications. The method achieves improvements of average 2.2 points precision in low-resource judgment prediction, and 1.5 points mean average precision in unsupervised case retrieval, which suggests the fundamentality of LED. The source code and dataset can be obtained from https://github.com/thunlp/LEVEN.

preprint2022arXiv

Mining Relations among Cross-Frame Affinities for Video Semantic Segmentation

The essence of video semantic segmentation (VSS) is how to leverage temporal information for prediction. Previous efforts are mainly devoted to developing new techniques to calculate the cross-frame affinities such as optical flow and attention. Instead, this paper contributes from a different angle by mining relations among cross-frame affinities, upon which better temporal information aggregation could be achieved. We explore relations among affinities in two aspects: single-scale intrinsic correlations and multi-scale relations. Inspired by traditional feature processing, we propose Single-scale Affinity Refinement (SAR) and Multi-scale Affinity Aggregation (MAA). To make it feasible to execute MAA, we propose a Selective Token Masking (STM) strategy to select a subset of consistent reference tokens for different scales when calculating affinities, which also improves the efficiency of our method. At last, the cross-frame affinities strengthened by SAR and MAA are adopted for adaptively aggregating temporal information. Our experiments demonstrate that the proposed method performs favorably against state-of-the-art VSS methods. The code is publicly available at https://github.com/GuoleiSun/VSS-MRCFA

preprint2022arXiv

MobileSal: Extremely Efficient RGB-D Salient Object Detection

The high computational cost of neural networks has prevented recent successes in RGB-D salient object detection (SOD) from benefiting real-world applications. Hence, this paper introduces a novel network, MobileSal, which focuses on efficient RGB-D SOD using mobile networks for deep feature extraction. However, mobile networks are less powerful in feature representation than cumbersome networks. To this end, we observe that the depth information of color images can strengthen the feature representation related to SOD if leveraged properly. Therefore, we propose an implicit depth restoration (IDR) technique to strengthen the mobile networks&#39; feature representation capability for RGB-D SOD. IDR is only adopted in the training phase and is omitted during testing, so it is computationally free. Besides, we propose compact pyramid refinement (CPR) for efficient multi-level feature aggregation to derive salient objects with clear boundaries. With IDR and CPR incorporated, MobileSal performs favorably against state-of-the-art methods on six challenging RGB-D SOD datasets with much faster speed (450fps for the input size of 320 $\times$ 320) and fewer parameters (6.5M). The code is released at https://mmcheng.net/mobilesal.

preprint2022arXiv

Mutual Learning for Domain Adaptation: Self-distillation Image Dehazing Network with Sample-cycle

Deep learning-based methods have made significant achievements for image dehazing. However, most of existing dehazing networks are concentrated on training models using simulated hazy images, resulting in generalization performance degradation when applied on real-world hazy images because of domain shift. In this paper, we propose a mutual learning dehazing framework for domain adaption. Specifically, we first devise two siamese networks: a teacher network in the synthetic domain and a student network in the real domain, and then optimize them in a mutual learning manner by leveraging EMA and joint loss. Moreover, we design a sample-cycle strategy based on density augmentation (HDA) module to introduce pseudo real-world image pairs provided by the student network into training for further improving the generalization performance. Extensive experiments on both synthetic and real-world dataset demonstrate that the propose mutual learning framework outperforms state-of-the-art dehazing techniques in terms of subjective and objective evaluation.

preprint2022arXiv

P2T: Pyramid Pooling Transformer for Scene Understanding

Recently, the vision transformer has achieved great success by pushing the state-of-the-art of various vision tasks. One of the most challenging problems in the vision transformer is that the large sequence length of image tokens leads to high computational cost (quadratic complexity). A popular solution to this problem is to use a single pooling operation to reduce the sequence length. This paper considers how to improve existing vision transformers, where the pooled feature extracted by a single pooling operation seems less powerful. To this end, we note that pyramid pooling has been demonstrated to be effective in various vision tasks owing to its powerful ability in context abstraction. However, pyramid pooling has not been explored in backbone network design. To bridge this gap, we propose to adapt pyramid pooling to Multi-Head Self-Attention (MHSA) in the vision transformer, simultaneously reducing the sequence length and capturing powerful contextual features. Plugged with our pooling-based MHSA, we build a universal vision transformer backbone, dubbed Pyramid Pooling Transformer (P2T). Extensive experiments demonstrate that, when applied P2T as the backbone network, it shows substantial superiority in various vision tasks such as image classification, semantic segmentation, object detection, and instance segmentation, compared to previous CNN- and transformer-based networks. The code will be released at https://github.com/yuhuan-wu/P2T.

preprint2022arXiv

Ret3D: Rethinking Object Relations for Efficient 3D Object Detection in Driving Scenes

Current efficient LiDAR-based detection frameworks are lacking in exploiting object relations, which naturally present in both spatial and temporal manners. To this end, we introduce a simple, efficient, and effective two-stage detector, termed as Ret3D. At the core of Ret3D is the utilization of novel intra-frame and inter-frame relation modules to capture the spatial and temporal relations accordingly. More Specifically, intra-frame relation module (IntraRM) encapsulates the intra-frame objects into a sparse graph and thus allows us to refine the object features through efficient message passing. On the other hand, inter-frame relation module (InterRM) densely connects each object in its corresponding tracked sequences dynamically, and leverages such temporal information to further enhance its representations efficiently through a lightweight transformer network. We instantiate our novel designs of IntraRM and InterRM with general center-based or anchor-based detectors and evaluate them on Waymo Open Dataset (WOD). With negligible extra overhead, Ret3D achieves the state-of-the-art performance, being 5.5% and 3.2% higher than the recent competitor in terms of the LEVEL 1 and LEVEL 2 mAPH metrics on vehicle detection, respectively.

preprint2022arXiv

Robust and Efficient Medical Imaging with Self-Supervision

Recent progress in Medical Artificial Intelligence (AI) has delivered systems that can reach clinical expert level performance. However, such systems tend to demonstrate sub-optimal &#34;out-of-distribution&#34; performance when evaluated in clinical settings different from the training environment. A common mitigation strategy is to develop separate systems for each clinical setting using site-specific data [1]. However, this quickly becomes impractical as medical data is time-consuming to acquire and expensive to annotate [2]. Thus, the problem of &#34;data-efficient generalization&#34; presents an ongoing difficulty for Medical AI development. Although progress in representation learning shows promise, their benefits have not been rigorously studied, specifically for out-of-distribution settings. To meet these challenges, we present REMEDIS, a unified representation learning strategy to improve robustness and data-efficiency of medical imaging AI. REMEDIS uses a generic combination of large-scale supervised transfer learning with self-supervised learning and requires little task-specific customization. We study a diverse range of medical imaging tasks and simulate three realistic application scenarios using retrospective data. REMEDIS exhibits significantly improved in-distribution performance with up to 11.5% relative improvement in diagnostic accuracy over a strong supervised baseline. More importantly, our strategy leads to strong data-efficient generalization of medical imaging AI, matching strong supervised baselines using between 1% to 33% of retraining data across tasks. These results suggest that REMEDIS can significantly accelerate the life-cycle of medical imaging AI development thereby presenting an important step forward for medical imaging AI to deliver broad impact.

preprint2022arXiv

Towards Efficient Single Image Dehazing and Desnowing

Removing adverse weather conditions like rain, fog, and snow from images is a challenging problem. Although the current recovery algorithms targeting a specific condition have made impressive progress, it is not flexible enough to deal with various degradation types. We propose an efficient and compact image restoration network named DAN-Net (Degradation-Adaptive Neural Network) to address this problem, which consists of multiple compact expert networks with one adaptive gated neural. A single expert network efficiently addresses specific degradation in nasty winter scenes relying on the compact architecture and three novel components. Based on the Mixture of Experts strategy, DAN-Net captures degradation information from each input image to adaptively modulate the outputs of task-specific expert networks to remove various adverse winter weather conditions. Specifically, it adopts a lightweight Adaptive Gated Neural Network to estimate gated attention maps of the input image, while different task-specific experts with the same topology are jointly dispatched to process the degraded image. Such novel image restoration pipeline handles different types of severe weather scenes effectively and efficiently. It also enjoys the benefit of coordinate boosting in which the whole network outperforms each expert trained without coordination. Extensive experiments demonstrate that the presented manner outperforms the state-of-the-art single-task methods on image quality and has better inference efficiency. Furthermore, we have collected the first real-world winter scenes dataset to evaluate winter image restoration methods, which contains various hazy and snowy images snapped in winter. Both the dataset and source code will be publicly available.

preprint2022arXiv

Towards Real-time High-Definition Image Snow Removal: Efficient Pyramid Network with Asymmetrical Encoder-decoder Architecture

In winter scenes, the degradation of images taken under snow can be pretty complex, where the spatial distribution of snowy degradation is varied from image to image. Recent methods adopt deep neural networks to directly recover clean scenes from snowy images. However, due to the paradox caused by the variation of complex snowy degradation, achieving reliable High-Definition image desnowing performance in real time is a considerable challenge. We develop a novel Efficient Pyramid Network with asymmetrical encoder-decoder architecture for real-time HD image desnowing. The general idea of our proposed network is to utilize the multi-scale feature flow fully and implicitly mine clean cues from features. Compared with previous state-of-the-art desnowing methods, our approach achieves a better complexity-performance trade-off and effectively handles the processing difficulties of HD and Ultra-HD images. The extensive experiments on three large-scale image desnowing datasets demonstrate that our method surpasses all state-of-the-art approaches by a large margin both quantitatively and qualitatively, boosting the PSNR metric from 31.76 dB to 34.10 dB on the CSD test dataset and from 28.29 dB to 30.87 dB on the SRRS test dataset.

preprint2022arXiv

Towards Reliable and Explainable AI Model for Solid Pulmonary Nodule Diagnosis

Lung cancer has the highest mortality rate of deadly cancers in the world. Early detection is essential to treatment of lung cancer. However, detection and accurate diagnosis of pulmonary nodules depend heavily on the experiences of radiologists and can be a heavy workload for them. Computer-aided diagnosis (CAD) systems have been developed to assist radiologists in nodule detection and diagnosis, greatly easing the workload while increasing diagnosis accuracy. Recent development of deep learning, greatly improved the performance of CAD systems. However, lack of model reliability and interpretability remains a major obstacle for its large-scale clinical application. In this work, we proposed a multi-task explainable deep-learning model for pulmonary nodule diagnosis. Our neural model can not only predict lesion malignancy but also identify relevant manifestations. Further, the location of each manifestation can also be visualized for visual interpretability. Our proposed neural model achieved a test AUC of 0.992 on LIDC public dataset and a test AUC of 0.923 on our in-house dataset. Moreover, our experimental results proved that by incorporating manifestation identification tasks into the multi-task model, the accuracy of the malignancy classification can also be improved. This multi-task explainable model may provide a scheme for better interaction with the radiologists in a clinical environment.

preprint2022arXiv

Uformer: A Unet based dilated complex & real dual-path conformer network for simultaneous speech enhancement and dereverberation

Complex spectrum and magnitude are considered as two major features of speech enhancement and dereverberation. Traditional approaches always treat these two features separately, ignoring their underlying relationship. In this paper, we propose Uformer, a Unet based dilated complex & real dual-path conformer network in both complex and magnitude domain for simultaneous speech enhancement and dereverberation. We exploit time attention (TA) and dilated convolution (DC) to leverage local and global contextual information and frequency attention (FA) to model dimensional information. These three sub-modules contained in the proposed dilated complex & real dual-path conformer module effectively improve the speech enhancement and dereverberation performance. Furthermore, hybrid encoder and decoder are adopted to simultaneously model the complex spectrum and magnitude and promote the information interaction between two domains. Encoder decoder attention is also applied to enhance the interaction between encoder and decoder. Our experimental results outperform all SOTA time and complex domain models objectively and subjectively. Specifically, Uformer reaches 3.6032 DNSMOS on the blind test set of Interspeech 2021 DNS Challenge, which outperforms all top-performed models. We also carry out ablation experiments to tease apart all proposed sub-modules that are most important.

preprint2022arXiv

Underwater Light Field Retention : Neural Rendering for Underwater Imaging

Underwater Image Rendering aims to generate a true-tolife underwater image from a given clean one, which could be applied to various practical applications such as underwater image enhancement, camera filter, and virtual gaming. We explore two less-touched but challenging problems in underwater image rendering, namely, i) how to render diverse underwater scenes by a single neural network? ii) how to adaptively learn the underwater light fields from natural exemplars, i,e., realistic underwater images? To this end, we propose a neural rendering method for underwater imaging, dubbed UWNR (Underwater Neural Rendering). Specifically, UWNR is a data-driven neural network that implicitly learns the natural degenerated model from authentic underwater images, avoiding introducing erroneous biases by hand-craft imaging models. Compared with existing underwater image generation methods, UWNR utilizes the natural light field to simulate the main characteristics ofthe underwater scene. Thus, it is able to synthesize a wide variety ofunderwater images from one clean image with various realistic underwater images. Extensive experiments demonstrate that our approach achieves better visual effects and quantitative metrics over previous methods. Moreover, we adopt UWNR to build an open Large Neural Rendering Underwater Dataset containing various types of water quality, dubbed LNRUD. The source code and LNRUD are available at https: //github.com/Ephemeral182/UWNR.

preprint2022arXiv

Zero Pixel Directional Boundary by Vector Transform

Boundaries are among the primary visual cues used by human and computer vision systems. One of the key problems in boundary detection is the label representation, which typically leads to class imbalance and, as a consequence, to thick boundaries that require non-differential post-processing steps to be thinned. In this paper, we re-interpret boundaries as 1-D surfaces and formulate a one-to-one vector transform function that allows for training of boundary prediction completely avoiding the class imbalance issue. Specifically, we define the boundary representation at any point as the unit vector pointing to the closest boundary surface. Our problem formulation leads to the estimation of direction as well as richer contextual information of the boundary, and, if desired, the availability of zero-pixel thin boundaries also at training time. Our method uses no hyper-parameter in the training loss and a fixed stable hyper-parameter at inference. We provide theoretical justification/discussions of the vector transform representation. We evaluate the proposed loss method using a standard architecture and show the excellent performance over other losses and representations on several datasets. Code is available at https://github.com/edomel/BoundaryVT.

preprint2021arXiv

Coarse-grained decomposition and fine-grained interaction for multi-hop question answering

Recent advances regarding question answering and reading comprehension have resulted in models that surpass human performance when the answer is contained in a single, continuous passage of text, requiring only single-hop reasoning. However, in actual scenarios, lots of complex queries require multi-hop reasoning. The key to the Question Answering task is semantic feature interaction between documents and questions, which is widely processed by Bi-directional Attention Flow (Bi-DAF), but Bi-DAF generally captures only the surface semantics of words in complex questions and fails to capture implied semantic feature of intermediate answers. As a result, Bi-DAF partially ignores part of the contexts related to the question and cannot extract the most important parts of multiple documents. In this paper we propose a new model architecture for multi-hop question answering, by applying two completion strategies: (1) Coarse-Grain complex question Decomposition (CGDe) strategy are introduced to decompose complex question into simple ones under the condition of without any additional annotations (2) Fine-Grained Interaction (FGIn) strategy are introduced to better represent each word in the document and extract more comprehensive and accurate sentences related to the inference path. The above two strategies are combined and tested on the SQuAD and HotpotQA datasets, and the experimental results show that our method outperforms state-of-the-art baselines.

preprint2021arXiv

Deep Learning for Distinguishing Normal versus Abnormal Chest Radiographs and Generalization to Unseen Diseases

Chest radiography (CXR) is the most widely-used thoracic clinical imaging modality and is crucial for guiding the management of cardiothoracic conditions. The detection of specific CXR findings has been the main focus of several artificial intelligence (AI) systems. However, the wide range of possible CXR abnormalities makes it impractical to build specific systems to detect every possible condition. In this work, we developed and evaluated an AI system to classify CXRs as normal or abnormal. For development, we used a de-identified dataset of 248,445 patients from a multi-city hospital network in India. To assess generalizability, we evaluated our system using 6 international datasets from India, China, and the United States. Of these datasets, 4 focused on diseases that the AI was not trained to detect: 2 datasets with tuberculosis and 2 datasets with coronavirus disease 2019. Our results suggest that the AI system generalizes to new patient populations and abnormalities. In a simulated workflow where the AI system prioritized abnormal cases, the turnaround time for abnormal cases reduced by 7-28%. These results represent an important step towards evaluating whether AI can be safely used to flag cases in a general setting where previously unseen abnormalities exist.

preprint2021arXiv

DNA: Deeply-supervised Nonlinear Aggregation for Salient Object Detection

Recent progress on salient object detection mainly aims at exploiting how to effectively integrate multi-scale convolutional features in convolutional neural networks (CNNs). Many popular methods impose deep supervision to perform side-output predictions that are linearly aggregated for final saliency prediction. In this paper, we theoretically and experimentally demonstrate that linear aggregation of side-output predictions is suboptimal, and it only makes limited use of the side-output information obtained by deep supervision. To solve this problem, we propose Deeply-supervised Nonlinear Aggregation (DNA) for better leveraging the complementary information of various side-outputs. Compared with existing methods, it i) aggregates side-output features rather than predictions, and ii) adopts nonlinear instead of linear transformations. Experiments demonstrate that DNA can successfully break through the bottleneck of current linear approaches. Specifically, the proposed saliency detector, a modified U-Net architecture with DNA, performs favorably against state-of-the-art methods on various datasets and evaluation metrics without bells and whistles.

preprint2021arXiv

Does Your Dermatology Classifier Know What It Doesn&#39;t Know? Detecting the Long-Tail of Unseen Conditions

We develop and rigorously evaluate a deep learning based system that can accurately classify skin conditions while detecting rare conditions for which there is not enough data available for training a confident classifier. We frame this task as an out-of-distribution (OOD) detection problem. Our novel approach, hierarchical outlier detection (HOD) assigns multiple abstention classes for each training outlier class and jointly performs a coarse classification of inliers vs. outliers, along with fine-grained classification of the individual classes. We demonstrate the effectiveness of the HOD loss in conjunction with modern representation learning approaches (BiT, SimCLR, MICLe) and explore different ensembling strategies for further improving the results. We perform an extensive subgroup analysis over conditions of varying risk levels and different skin types to investigate how the OOD detection performance changes over each subgroup and demonstrate the gains of our framework in comparison to baselines. Finally, we introduce a cost metric to approximate downstream clinical impact. We use this cost metric to compare the proposed method against a baseline system, thereby making a stronger case for the overall system effectiveness in a real-world deployment scenario.

preprint2021arXiv

Optical and electronic properties of colloidal CdSe Quantum Rings

Luminescent colloidal CdSe nanorings are a new type of semiconductor structure that have attracted interest due to the potential for unique physics arising from their non-trivial toroidal shape. However, the exciton properties and dynamics of these materials with complex topology are not yet well understood. Here, we use a combination of femtosecond vibrational spectroscopy, temperature-resolved photoluminescence (PL), and single particle measurements to study these materials. We find that on transformation of CdSe nanoplatelets to nanorings, by perforating the center of platelets, the emission lifetime decreases and the emission spectrum broadens due to ensemble variations in the ring size and thickness. The reduced PL quantum yield of nanorings (~10%) compared to platelets (~30%) is attributed to an enhanced coupling between: (i) excitons and CdSe LO-phonons at 200 cm-1 and (ii) negatively charged selenium-rich traps which give nanorings a high surface charge (~-50 mV). Population of these weakly emissive trap sites dominates the emission properties with an increased trap emission at low temperatures relative to excitonic emission. Our results provide a detailed picture of the nature of excitons in nanorings and the influence of phonons and surface charge in explaining the broad shape of the PL spectrum and the origin of PL quantum yield losses. Furthermore, they suggest that the excitonic properties of nanorings are not solely a consequence of the toroidal shape but are also a result of traps introduced by puncturing the platelet center.

preprint2021arXiv

Revealing Cluster Structures Based on Mixed Sampling Frequencies

This paper proposes a new linearized mixed data sampling (MIDAS) model and develops a framework to infer clusters in a panel regression with mixed frequency data. The linearized MIDAS estimation method is more flexible and substantially simpler to implement than competing approaches. We show that the proposed clustering algorithm successfully recovers true membership in the cross-section, both in theory and in simulations, without requiring prior knowledge of the number of clusters. This methodology is applied to a mixed-frequency Okun&#39;s law model for state-level data in the U.S. and uncovers four meaningful clusters based on the dynamic features of state-level labor markets.

preprint2020arXiv

Deep Learning for Strong Lensing Search: Tests of the Convolutional Neural Networks and New Candidates from KiDS DR3

Convolutional Neutral Networks have been successfully applied in searching for strong lensing systems, leading to discoveries of new candidates from large surveys. On the other hand, systematic investigations about their robustness are still lacking. In this paper, we first construct a neutral network, and apply it to $r$-band images of Luminous Red Galaxies (LRGs) of the Kilo Degree Survey (KiDS) Data Release 3 to search for strong lensing systems. We build two sets of training samples, one fully from simulations, and the other one using the LRG stamps from KiDS observations as the foreground lens images. With the former training sample, we find 48 high probability candidates after human-inspection, and among them, 27 are newly identified. Using the latter training set, about 67\% of the aforementioned 48 candidates are also found, and there are 11 more new strong lensing candidates identified. We then carry out tests on the robustness of the network performance with respect to the variation of PSF. With the testing samples constructed using PSF in the range of 0.4 to 2 times of the median PSF of the training sample, we find that our network performs rather stable, and the degradation is small. We also investigate how the volume of the training set can affect our network performance by varying it from 0.1 millions to 0.8 millions. The output results are rather stable showing that within the considered range, our network performance is not very sensitive to the volume size.

preprint2020arXiv

Detecting hidden signs of diabetes in external eye photographs

Diabetes-related retinal conditions can be detected by examining the posterior of the eye. By contrast, examining the anterior of the eye can reveal conditions affecting the front of the eye, such as changes to the eyelids, cornea, or crystalline lens. In this work, we studied whether external photographs of the front of the eye can reveal insights into both diabetic retinal diseases and blood glucose control. We developed a deep learning system (DLS) using external eye photographs of 145,832 patients with diabetes from 301 diabetic retinopathy (DR) screening sites in one US state, and evaluated the DLS on three validation sets containing images from 198 sites in 18 other US states. In validation set A (n=27,415 patients, all undilated), the DLS detected poor blood glucose control (HbA1c > 9%) with an area under receiver operating characteristic curve (AUC) of 70.2; moderate-or-worse DR with an AUC of 75.3; diabetic macular edema with an AUC of 78.0; and vision-threatening DR with an AUC of 79.4. For all 4 prediction tasks, the DLS&#39;s AUC was higher (p<0.001) than using available self-reported baseline characteristics (age, sex, race/ethnicity, years with diabetes). In terms of positive predictive value, the predicted top 5% of patients had a 67% chance of having HbA1c > 9%, and a 20% chance of having vision threatening diabetic retinopathy. The results generalized to dilated pupils (validation set B, 5,058 patients) and to a different screening service (validation set C, 10,402 patients). Our results indicate that external eye photographs contain information useful for healthcare providers managing patients with diabetes, and may help prioritize patients for in-person screening. Further work is needed to validate these findings on different devices and patient populations (those without diabetes) to evaluate its utility for remote diagnosis and management.

preprint2020arXiv

Generalized Zero-Shot Learning via VAE-Conditioned Generative Flow

Generalized zero-shot learning (GZSL) aims to recognize both seen and unseen classes by transferring knowledge from semantic descriptions to visual representations. Recent generative methods formulate GZSL as a missing data problem, which mainly adopts GANs or VAEs to generate visual features for unseen classes. However, GANs often suffer from instability, and VAEs can only optimize the lower bound on the log-likelihood of observed data. To overcome the above limitations, we resort to generative flows, a family of generative models with the advantage of accurate likelihood estimation. More specifically, we propose a conditional version of generative flows for GZSL, i.e., VAE-Conditioned Generative Flow (VAE-cFlow). By using VAE, the semantic descriptions are firstly encoded into tractable latent distributions, conditioned on that the generative flow optimizes the exact log-likelihood of the observed visual features. We ensure the conditional latent distribution to be both semantic meaningful and inter-class discriminative by i) adopting the VAE reconstruction objective, ii) releasing the zero-mean constraint in VAE posterior regularization, and iii) adding a classification regularization on the latent variables. Our method achieves state-of-the-art GZSL results on five well-known benchmark datasets, especially for the significant improvement in the large-scale setting. Code is released at https://github.com/guyuchao/VAE-cFlow-ZSL.

preprint2020arXiv

Interpretable Survival Prediction for Colorectal Cancer using Deep Learning

Deriving interpretable prognostic features from deep-learning-based prognostic histopathology models remains a challenge. In this study, we developed a deep learning system (DLS) for predicting disease specific survival for stage II and III colorectal cancer using 3,652 cases (27,300 slides). When evaluated on two validation datasets containing 1,239 cases (9,340 slides) and 738 cases (7,140 slides) respectively, the DLS achieved a 5-year disease-specific survival AUC of 0.70 (95%CI 0.66-0.73) and 0.69 (95%CI 0.64-0.72), and added significant predictive value to a set of 9 clinicopathologic features. To interpret the DLS, we explored the ability of different human-interpretable features to explain the variance in DLS scores. We observed that clinicopathologic features such as T-category, N-category, and grade explained a small fraction of the variance in DLS scores (R2=18% in both validation sets). Next, we generated human-interpretable histologic features by clustering embeddings from a deep-learning based image-similarity model and showed that they explain the majority of the variance (R2 of 73% to 80%). Furthermore, the clustering-derived feature most strongly associated with high DLS scores was also highly prognostic in isolation. With a distinct visual appearance (poorly differentiated tumor cell clusters adjacent to adipose tissue), this feature was identified by annotators with 87.0-95.5% accuracy. Our approach can be used to explain predictions from a prognostic deep learning model and uncover potentially-novel prognostic features that can be reliably identified by people for future validation studies.

preprint2020arXiv

Laser-assisted high-energy proton pulse extraction for feasibility study of co-located muon source at the SNS

We have experimentally demonstrated the first non-intrusive 1-GeV proton beam extraction for the generation of muons with a temporal structure optimized for Muon Spin Relaxation/Rotation/Resonance (MuSR) applications. The proton pulses are extracted based on the laser neutralization of 1 GeV hydrogen ion (H-) beam in the high energy beam transport of the Spallation Neutron Source (SNS) accelerator. The maximum flux of the extracted proton beam accounts for only 0.2% of the total proton beam used for neutron production, a marked difference from the 20% reduction at other co-located muon and neutron facilities, and thus the proposed method will result in negligible impact on the SNS operation. This paper describes the development of a fiber/solid-state hybrid laser system that has high flexibility of pulse structure and output power, initial experiments on laser neutralization of H- beam and separation of H0 beam from the existing SNS accelerator beam line, conversion of H0 to proton at the SNS linac dump, and measurement results of 30 ns/50 kHz proton pulses. This system conclusively demonstrates the feasibility of laser-based proton beam extraction to power a world-leading MuSR facility at the SNS.

preprint2020arXiv

Magnetic ordering and spin dynamics in $S=5/2$ staggered triangular lattice antiferromagnet Ba$_2$MnTeO$_6$

We report studies of the magnetic properties of a staggered stacked triangular lattice Ba$_2$MnTeO$_6$ using magnetic susceptibility, specific heat, neutron powder diffraction and inelastic neutron scattering measurements, as well as first principles density functional theory calculations. Neutron diffraction measurements reveal an antiferromagnetic order with a propagated vector $\textbf{\emph{k}}=(0.5, 0.5, 0)$ and N{é}el transition temperature of $T_\text{N}\approx20$ K. The dominant interaction derived from the Curie-Weiss fitting to the inverse DC susceptibility is antiferromagnetic. Through modelling the INS spectrum with the linear spin wave theory, the magnetic exchange interactions for the nearest intralayer, nearest interlayer, and next nearest interlayer are determined to be $J_1=0.27(3),J_2=0.27(3),$ and $J_3=-0.05(1)$ meV, respectively, and a small value of easy-axis anisotropy of $D_{zz}=-0.01$ meV is introduced. We derive a magnetic phase diagram that reveals that it is the competition between $J_1, J_2$, and $J_3$ that stabilizes the collinear stripe-type antiferromagnetic order.

preprint2020arXiv

MS-TCN++: Multi-Stage Temporal Convolutional Network for Action Segmentation

With the success of deep learning in classifying short trimmed videos, more attention has been focused on temporally segmenting and classifying activities in long untrimmed videos. State-of-the-art approaches for action segmentation utilize several layers of temporal convolution and temporal pooling. Despite the capabilities of these approaches in capturing temporal dependencies, their predictions suffer from over-segmentation errors. In this paper, we propose a multi-stage architecture for the temporal action segmentation task that overcomes the limitations of the previous approaches. The first stage generates an initial prediction that is refined by the next ones. In each stage we stack several layers of dilated temporal convolutions covering a large receptive field with few parameters. While this architecture already performs well, lower layers still suffer from a small receptive field. To address this limitation, we propose a dual dilated layer that combines both large and small receptive fields. We further decouple the design of the first stage from the refining stages to address the different requirements of these stages. Extensive evaluation shows the effectiveness of the proposed model in capturing long-range dependencies and recognizing action segments. Our models achieve state-of-the-art results on three datasets: 50Salads, Georgia Tech Egocentric Activities (GTEA), and the Breakfast dataset.

preprint2020arXiv

Predicting Prostate Cancer-Specific Mortality with A.I.-based Gleason Grading

Gleason grading of prostate cancer is an important prognostic factor but suffers from poor reproducibility, particularly among non-subspecialist pathologists. Although artificial intelligence (A.I.) tools have demonstrated Gleason grading on-par with expert pathologists, it remains an open question whether A.I. grading translates to better prognostication. In this study, we developed a system to predict prostate-cancer specific mortality via A.I.-based Gleason grading and subsequently evaluated its ability to risk-stratify patients on an independent retrospective cohort of 2,807 prostatectomy cases from a single European center with 5-25 years of follow-up (median: 13, interquartile range 9-17). The A.I.&#39;s risk scores produced a C-index of 0.84 (95%CI 0.80-0.87) for prostate cancer-specific mortality. Upon discretizing these risk scores into risk groups analogous to pathologist Grade Groups (GG), the A.I. had a C-index of 0.82 (95%CI 0.78-0.85). On the subset of cases with a GG in the original pathology report (n=1,517), the A.I.&#39;s C-indices were 0.87 and 0.85 for continuous and discrete grading, respectively, compared to 0.79 (95%CI 0.71-0.86) for GG obtained from the reports. These represent improvements of 0.08 (95%CI 0.01-0.15) and 0.07 (95%CI 0.00-0.14) respectively. Our results suggest that A.I.-based Gleason grading can lead to effective risk-stratification and warrants further evaluation for improving disease management.

preprint2020arXiv

Predicting Risk of Developing Diabetic Retinopathy using Deep Learning

Diabetic retinopathy (DR) screening is instrumental in preventing blindness, but faces a scaling challenge as the number of diabetic patients rises. Risk stratification for the development of DR may help optimize screening intervals to reduce costs while improving vision-related outcomes. We created and validated two versions of a deep learning system (DLS) to predict the development of mild-or-worse (&#34;Mild+&#34;) DR in diabetic patients undergoing DR screening. The two versions used either three-fields or a single field of color fundus photographs (CFPs) as input. The training set was derived from 575,431 eyes, of which 28,899 had known 2-year outcome, and the remaining were used to augment the training process via multi-task learning. Validation was performed on both an internal validation set (set A; 7,976 eyes; 3,678 with known outcome) and an external validation set (set B; 4,762 eyes; 2,345 with known outcome). For predicting 2-year development of DR, the 3-field DLS had an area under the receiver operating characteristic curve (AUC) of 0.79 (95%CI, 0.78-0.81) on validation set A. On validation set B (which contained only a single field), the 1-field DLS&#39;s AUC was 0.70 (95%CI, 0.67-0.74). The DLS was prognostic even after adjusting for available risk factors (p<0.001). When added to the risk factors, the 3-field DLS improved the AUC from 0.72 (95%CI, 0.68-0.76) to 0.81 (95%CI, 0.77-0.84) in validation set A, and the 1-field DLS improved the AUC from 0.62 (95%CI, 0.58-0.66) to 0.71 (95%CI, 0.68-0.75) in validation set B. The DLSs in this study identified prognostic information for DR development from CFPs. This information is independent of and more informative than the available risk factors.

preprint2020arXiv

Tunable Optoelectronic Properties of WS$_2$ by Local Strain Engineering and Folding

Local strain engineering is an exciting approach to tune the optoelectronic properties of materials. Two dimensional (2D) materials such as 2D transition metal dichalcogenides (TMDs) are particularly well suited for this purpose because they have high flexibility and they can withstand high deformations before rupture. Local strain engineering in 2D TMDs is achieved via strained wrinkles. Wrinkles on thick layers of TMDs are reported to show interesting photoluminescence enhancement due to bandgap modulation and funneling effect. However, the wrinkles in ultrathin TMDs have not been investigated because they can easily fall down to form folds in these ultrathin layers of TMDCs. Here, we have achieved both wrinkles and folds simultaneously in 1-3L WS2 using a new fabrication technique. A layer dependent reduction in surface potential is found for both folded layers and perfect pack layers due to the dominant interlayer screening effect. Strain dependent modulation in semi conductive junction properties is observed for strain induced wrinkles through current scanning. Thermo-ionic modelling suggests that the strained (1.6%) wrinkles can lower the Schottky barrier height (SBH) by 20%. Upon illumination, SBH reduces significantly due to photo-generated carriers. Our results present an important advance towards controlling the optoelectronic properties of atomically thin WS2 via strain engineering, with applications in optoelectronics, quantum optics and nanophotonics device fabrication.

preprint2019arXiv

A deep learning system for differential diagnosis of skin diseases

Skin conditions affect an estimated 1.9 billion people worldwide. A shortage of dermatologists causes long wait times and leads patients to seek dermatologic care from general practitioners. However, the diagnostic accuracy of general practitioners has been reported to be only 0.24-0.70 (compared to 0.77-0.96 for dermatologists), resulting in referral errors, delays in care, and errors in diagnosis and treatment. In this paper, we developed a deep learning system (DLS) to provide a differential diagnosis of skin conditions for clinical cases (skin photographs and associated medical histories). The DLS distinguishes between 26 skin conditions that represent roughly 80% of the volume of skin conditions seen in primary care. The DLS was developed and validated using de-identified cases from a teledermatology practice serving 17 clinical sites via a temporal split: the first 14,021 cases for development and the last 3,756 cases for validation. On the validation set, where a panel of three board-certified dermatologists defined the reference standard for every case, the DLS achieved 0.71 and 0.93 top-1 and top-3 accuracies respectively. For a random subset of the validation set (n=963 cases), 18 clinicians reviewed the cases for comparison. On this subset, the DLS achieved a 0.67 top-1 accuracy, non-inferior to board-certified dermatologists (0.63, p<0.001), and higher than primary care physicians (PCPs, 0.45) and nurse practitioners (NPs, 0.41). The top-3 accuracy showed a similar trend: 0.90 DLS, 0.75 dermatologists, 0.60 PCPs, and 0.55 NPs. These results highlight the potential of the DLS to augment general practitioners to accurately diagnose skin conditions by suggesting differential diagnoses that may not have been considered. Future work will be needed to prospectively assess the clinical impact of using this tool in actual clinical workflows.

preprint2019arXiv

Deep Learning and Glaucoma Specialists: The Relative Importance of Optic Disc Features to Predict Glaucoma Referral in Fundus Photos

Glaucoma is the leading cause of preventable, irreversible blindness world-wide. The disease can remain asymptomatic until severe, and an estimated 50%-90% of people with glaucoma remain undiagnosed. Glaucoma screening is recommended for early detection and treatment. A cost-effective tool to detect glaucoma could expand screening access to a much larger patient population, but such a tool is currently unavailable. We trained a deep learning algorithm using a retrospective dataset of 86,618 images, assessed for glaucomatous optic nerve head features and referable glaucomatous optic neuropathy (GON). The algorithm was validated using 3 datasets. For referable GON, the algorithm had an AUC of 0.945 (95% CI, 0.929-0.960) in dataset A (1205 images, 1 image/patient; 18.1% referable), images adjudicated by panels of Glaucoma Specialists (GSs); 0.855 (95% CI, 0.841-0.870) in dataset B (9642 images, 1 image/patient; 9.2% referable), images from Atlanta Veterans Affairs Eye Clinic diabetic teleretinal screening program; and 0.881 (95% CI, 0.838-0.918) in dataset C (346 images, 1 image/patient; 81.7% referable), images from Dr. Shroff&#39;s Charity Eye Hospital&#39;s glaucoma clinic. The algorithm showed significantly higher sensitivity than 7 of 10 graders not involved in determining the reference standard, including 2 of 3 GSs, and showed higher specificity than 3 graders, while remaining comparable to others. For both GSs and the algorithm, the most crucial features related to referable GON were: presence of vertical cup-to-disc ratio of 0.7 or more, neuroretinal rim notching, retinal nerve fiber layer defect, and bared circumlinear vessels. An algorithm trained on fundus images alone can detect referable GON with higher sensitivity than and comparable specificity to eye care providers. The algorithm maintained good performance on an independent dataset with diagnoses based on a full glaucoma workup.

preprint2019arXiv

Deep learning-based survival prediction for multiple cancer types using histopathology images

Prognostic information at diagnosis has important implications for cancer treatment and monitoring. Although cancer staging, histopathological assessment, molecular features, and clinical variables can provide useful prognostic insights, improving risk stratification remains an active research area. We developed a deep learning system (DLS) to predict disease specific survival across 10 cancer types from The Cancer Genome Atlas (TCGA). We used a weakly-supervised approach without pixel-level annotations, and tested three different survival loss functions. The DLS was developed using 9,086 slides from 3,664 cases and evaluated using 3,009 slides from 1,216 cases. In multivariable Cox regression analysis of the combined cohort including all 10 cancers, the DLS was significantly associated with disease specific survival (hazard ratio of 1.58, 95% CI 1.28-1.70, p<0.0001) after adjusting for cancer type, stage, age, and sex. In a per-cancer adjusted subanalysis, the DLS remained a significant predictor of survival in 5 of 10 cancer types. Compared to a baseline model including stage, age, and sex, the c-index of the model demonstrated an absolute 3.7% improvement (95% CI 1.0-6.5) in the combined cohort. Additionally, our models stratified patients within individual cancer stages, particularly stage II (p=0.025) and stage III (p<0.001). By developing and evaluating prognostic models across multiple cancer types, this work represents one of the most comprehensive studies exploring the direct prediction of clinical outcomes using deep learning and histopathology images. Our analysis demonstrates the potential for this approach to provide prognostic information in multiple cancer types, and even within specific pathologic stages. However, given the relatively small number of clinical events, we observed wide confidence intervals, suggesting that future work will benefit from larger datasets.

preprint2019arXiv

Detecting Anemia from Retinal Fundus Images

Despite its high prevalence, anemia is often undetected due to the invasiveness and cost of screening and diagnostic tests. Though some non-invasive approaches have been developed, they are less accurate than invasive methods, resulting in an unmet need for more accurate non-invasive methods. Here, we show that deep learning-based algorithms can detect anemia and quantify several related blood measurements using retinal fundus images both in isolation and in combination with basic metadata such as patient demographics. On a validation dataset of 11,388 patients from the UK Biobank, our algorithms achieved a mean absolute error of 0.63 g/dL (95% confidence interval (CI) 0.62-0.64) in quantifying hemoglobin concentration and an area under receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.86-0.89) in detecting anemia. This work shows the potential of automated non-invasive anemia screening based on fundus images, particularly in diabetic patients, who may have regular retinal imaging and are at increased risk of further morbidity and mortality from anemia.

preprint2019arXiv

Similar Image Search for Histopathology: SMILY

The increasing availability of large institutional and public histopathology image datasets is enabling the searching of these datasets for diagnosis, research, and education. Though these datasets typically have associated metadata such as diagnosis or clinical notes, even carefully curated datasets rarely contain annotations of the location of regions of interest on each image. Because pathology images are extremely large (up to 100,000 pixels in each dimension), further laborious visual search of each image may be needed to find the feature of interest. In this paper, we introduce a deep learning based reverse image search tool for histopathology images: Similar Medical Images Like Yours (SMILY). We assessed SMILY&#39;s ability to retrieve search results in two ways: using pathologist-provided annotations, and via prospective studies where pathologists evaluated the quality of SMILY search results. As a negative control in the second evaluation, pathologists were blinded to whether search results were retrieved by SMILY or randomly. In both types of assessments, SMILY was able to retrieve search results with similar histologic features, organ site, and prostate cancer Gleason grade compared with the original query. SMILY may be a useful general-purpose tool in the pathologist&#39;s arsenal, to improve the efficiency of searching large archives of histopathology images, without the need to develop and implement specific tools for each application.

preprint2019arXiv

Whole-Slide Image Focus Quality: Automatic Assessment and Impact on AI Cancer Detection

Digital pathology enables remote access or consults and powerful image analysis algorithms. However, the slide digitization process can create artifacts such as out-of-focus (OOF). OOF is often only detected upon careful review, potentially causing rescanning and workflow delays. Although scan-time operator screening for whole-slide OOF is feasible, manual screening for OOF affecting only parts of a slide is impractical. We developed a convolutional neural network (ConvFocus) to exhaustively localize and quantify the severity of OOF regions on digitized slides. ConvFocus was developed using our refined semi-synthetic OOF data generation process, and evaluated using real whole-slide images spanning 3 different tissue types and 3 different stain types that were digitized by two different scanners. ConvFocus&#39;s predictions were compared with pathologist-annotated focus quality grades across 514 distinct regions representing 37,700 35x35 $μ$m image patches, and 21 digitized &#34;z-stack&#34; whole-slide images that contain known OOF patterns. When compared to pathologist-graded focus quality, ConvFocus achieved Spearman rank coefficients of 0.81 and 0.94 on two scanners, and reproduced the expected OOF patterns from z-stack scanning. We also evaluated the impact of OOF on the accuracy of a state-of-the-art metastatic breast cancer detector and saw a consistent decrease in performance with increasing OOF. Comprehensive whole-slide OOF categorization could enable rescans prior to pathologist review, potentially reducing the impact of digitization focus issues on the clinical workflow. We show that the algorithm trained on our semi-synthetic OOF data generalizes well to real OOF regions across tissue types, stains, and scanners. Finally, quantitative OOF maps can flag regions that might otherwise be misclassified by image analysis algorithms, preventing OOF-induced errors.

preprint2018arXiv

Development and Validation of a Deep Learning Algorithm for Improving Gleason Scoring of Prostate Cancer

For prostate cancer patients, the Gleason score is one of the most important prognostic factors, potentially determining treatment independent of the stage. However, Gleason scoring is based on subjective microscopic examination of tumor morphology and suffers from poor reproducibility. Here we present a deep learning system (DLS) for Gleason scoring whole-slide images of prostatectomies. Our system was developed using 112 million pathologist-annotated image patches from 1,226 slides, and evaluated on an independent validation dataset of 331 slides, where the reference standard was established by genitourinary specialist pathologists. On the validation dataset, the mean accuracy among 29 general pathologists was 0.61. The DLS achieved a significantly higher diagnostic accuracy of 0.70 (p=0.002) and trended towards better patient risk stratification in correlations to clinical follow-up data. Our approach could improve the accuracy of Gleason scoring and subsequent therapy decisions, particularly where specialist expertise is unavailable. The DLS also goes beyond the current Gleason system to more finely characterize and quantitate tumor morphology, providing opportunities for refinement of the Gleason system itself.

preprint2018arXiv

Microscope 2.0: An Augmented Reality Microscope with Real-time Artificial Intelligence Integration

The brightfield microscope is instrumental in the visual examination of both biological and physical samples at sub-millimeter scales. One key clinical application has been in cancer histopathology, where the microscopic assessment of the tissue samples is used for the diagnosis and staging of cancer and thus guides clinical therapy. However, the interpretation of these samples is inherently subjective, resulting in significant diagnostic variability. Moreover, in many regions of the world, access to pathologists is severely limited due to lack of trained personnel. In this regard, Artificial Intelligence (AI) based tools promise to improve the access and quality of healthcare. However, despite significant advances in AI research, integration of these tools into real-world cancer diagnosis workflows remains challenging because of the costs of image digitization and difficulties in deploying AI solutions. Here we propose a cost-effective solution to the integration of AI: the Augmented Reality Microscope (ARM). The ARM overlays AI-based information onto the current view of the sample through the optical pathway in real-time, enabling seamless integration of AI into the regular microscopy workflow. We demonstrate the utility of ARM in the detection of lymph node metastases in breast cancer and the identification of prostate cancer with a latency that supports real-time workflows. We anticipate that ARM will remove barriers towards the use of AI in microscopic analysis and thus improve the accuracy and efficiency of cancer diagnosis. This approach is applicable to other microscopy tasks and AI algorithms in the life sciences and beyond.

preprint2017arXiv

Detecting Cancer Metastases on Gigapixel Pathology Images

Each year, the treatment decisions for more than 230,000 breast cancer patients in the U.S. hinge on whether the cancer has metastasized away from the breast. Metastasis detection is currently performed by pathologists reviewing large expanses of biological tissues. This process is labor intensive and error-prone. We present a framework to automatically detect and localize tumors as small as 100 x 100 pixels in gigapixel microscopy images sized 100,000 x 100,000 pixels. Our method leverages a convolutional neural network (CNN) architecture and obtains state-of-the-art results on the Camelyon16 dataset in the challenging lesion-level tumor detection task. At 8 false positives per image, we detect 92.4% of the tumors, relative to 82.7% by the previous best automated approach. For comparison, a human pathologist attempting exhaustive search achieved 73.2% sensitivity. We achieve image-level AUC scores above 97% on both the Camelyon16 test set and an independent set of 110 slides. In addition, we discover that two slides in the Camelyon16 training set were erroneously labeled normal. Our approach could considerably reduce false negative rates in metastasis detection.

preprint2017arXiv

Predicting Cardiovascular Risk Factors from Retinal Fundus Photographs using Deep Learning

Traditionally, medical discoveries are made by observing associations and then designing experiments to test these hypotheses. However, observing and quantifying associations in images can be difficult because of the wide variety of features, patterns, colors, values, shapes in real data. In this paper, we use deep learning, a machine learning technique that learns its own features, to discover new knowledge from retinal fundus images. Using models trained on data from 284,335 patients, and validated on two independent datasets of 12,026 and 999 patients, we predict cardiovascular risk factors not previously thought to be present or quantifiable in retinal images, such as such as age (within 3.26 years), gender (0.97 AUC), smoking status (0.71 AUC), HbA1c (within 1.39%), systolic blood pressure (within 11.23mmHg) as well as major adverse cardiac events (0.70 AUC). We further show that our models used distinct aspects of the anatomy to generate each prediction, such as the optic disc or blood vessels, opening avenues of further research.

preprint2016arXiv

Soft Phonon Modes and Diffuse Scattering in Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 Relaxor Ferroelectrics

Single crystals of a ternary relaxor ferroelectric system, 0.29Pb(In1/2Nb1/2)O3-0.45Pb(Mg1/3Nb2/3)O3-0.26PbTiO3, have been studied using triple-axis based elastic and inelastic neutron scattering. Elastic diffuse scattering confirms the presence of polar nano-regions (PNRs) in this system. The PNRs emerge at the Burns temperature, TB = 630 K and then grow continuously in population and correlation size as the crystal cools down to 100 K. At 300 K, characteristic &#39;butterfly&#39; and ellipsoid shaped diffuse scattering patterns are observed on the HK0 reciprocal space plane. Electrical poling along the [110] direction produces a marked asymmetry in the diffuse scattering patterns, with the parallel-to-the-field components enhanced while the perpendicular-to-the-field components suppressed. Several low energy phonon branches along the [001] and [111] directions were studied. Most significantly, the PNR-acoustic phonon coupling is confirmed for the [110] transverse acoustic (TA) phonons polarized along the [1-10] real space direction and the [100] TA phonons. This coupling appears to be anisotropic and correlated with the distribution of PNRs, and also affected by the relative length scales of the PNRs and phonon wave vectors. The well-known &#39;waterfall&#39; phenomenon is observed on the [001] and [110] transverse optical (TO) branches, near the zone center. The optical phonon measurements also reveal a lowest-energy, zone center soft TO mode, whose squared phonon energy increase linearly with decreasing temperature below the TB.

preprint2016arXiv

Transferring Knowledge from Text to Predict Disease Onset

In many domains such as medicine, training data is in short supply. In such cases, external knowledge is often helpful in building predictive models. We propose a novel method to incorporate publicly available domain expertise to build accurate models. Specifically, we use word2vec models trained on a domain-specific corpus to estimate the relevance of each feature&#39;s text description to the prediction problem. We use these relevance estimates to rescale the features, causing more important features to experience weaker regularization. We apply our method to predict the onset of five chronic diseases in the next five years in two genders and two age groups. Our rescaling approach improves the accuracy of the model, particularly when there are few positive examples. Furthermore, our method selects 60% fewer features, easing interpretation by physicians. Our method is applicable to other domains where feature and outcome descriptions are available.