arXiv subjects

Chen Li

Publications and source records attributed to Chen Li.

At least 487 records · Page 27Linked to original sources

arXiv2020

Gastric histopathology image segmentation using a hierarchical conditional random field

For the Convolutional Neural Networks (CNNs) applied in the intelligent diagnosis of gastric cancer, existing methods mostly focus on individual characteristics or network frameworks without a policy to depict the integral information. Mainly, Conditional Random Field (CRF), an efficient and stable algorithm for analyzing images containing complicated contents, can characterize spatial relation in images. In this paper, a novel Hierarchical Conditional Random Field (HCRF) based Gastric Histopathology Image Segmentation (GHIS) method is proposed, which can automatically localize abnormal (cancer) regions in gastric histopathology images obtained by an optical microscope to assist histopathologists in medical work. This HCRF model is built up with higher order potentials, including pixel-level and patch-level potentials, and graph-based post-processing is applied to further improve its segmentation performance. Especially, a CNN is trained to build up the pixel-level potentials and another three CNNs are fine-tuned to build up the patch-level potentials for sufficient spatial segmentation information. In the experiment, a hematoxylin and eosin (H&E) stained gastric histopathological dataset with 560 abnormal images are divided into training, validation and test sets with a ratio of 1 : 1 : 2. Finally, segmentation accuracy, recall and specificity of 78.91%, 65.59%, and 81.33% are achieved on the test set. Our HCRF model demonstrates high segmentation performance and shows its effectiveness and future potential in the GHIS field.

cs.CV↗

arXiv2020

Observation of magnon-polarons in a uniaxial antiferromagnetic insulator

Magnon-polarons, a type of hybridized excitations between magnons and phonons, were first reported in yttrium iron garnet as anomalies in the spin Seebeck effect responses. Here we report an observation of antiferromagnetic (AFM) magnon-polarons in a uniaxial AFM insulator Cr2O3. Despite the relatively higher energy of magnon than that of the acoustic phonons, near the spin-flop transition of ~ 6 T, the left-handed magnon spectrum shifts downward to hybridize with the acoustic phonons to form AFM magnon-polarons, which can also be probed by the spin Seebeck effect. The spin Seebeck signal is founded to be enhanced due to the magnon-polarons at low temperatures.

cond-mat.mtrl-sci↗

arXiv2020

Heuristic Semi-Supervised Learning for Graph Generation Inspired by Electoral College

Recently, graph-based algorithms have drawn much attention because of their impressive success in semi-supervised setups. For better model performance, previous studies learn to transform the topology of the input graph. However, these works only focus on optimizing the original nodes and edges, leaving the direction of augmenting existing data unexplored. In this paper, by simulating the generation process of graph signals, we propose a novel heuristic pre-processing technique, namely ELectoral COllege (ELCO), which automatically expands new nodes and edges to refine the label similarity within a dense subgraph. Substantially enlarging the original training set with high-quality generated labeled data, our framework can effectively benefit downstream models. To justify the generality and practicality of ELCO, we couple it with the popular Graph Convolution Network and Graph Attention Network to perform extensive evaluations on three standard datasets. In all setups tested, our method boosts the average score of base models by a large margin of 4.7 points, as well as consistently outperforms the state-of-the-art. We release our code and data on https://github.com/RingBDStack/ELCO to guarantee reproducibility.

cs.SI↗

arXiv2020

A Nanoscale Room-Temperature Multilayer Skyrmionic Synapse for Deep Spiking Neural Networks

Magnetic skyrmions have attracted considerable interest, especially after their recent experimental demonstration at room temperature in multilayers. The robustness, nanoscale size and non-volatility of skyrmions have triggered a substantial amount of research on skyrmion-based low-power, ultra-dense nanocomputing and neuromorphic systems such as artificial synapses. Room-temperature operation is required to integrate skyrmionic synapses in practical future devices. Here, we numerically propose a nanoscale skyrmionic synapse composed of magnetic multilayers that enables room-temperature device operation tailored for optimal synaptic resolution. We demonstrate that when embedding such multilayer skyrmionic synapses in a simple spiking neural network (SNN) with unsupervised learning via the spike-timing-dependent plasticity rule, we can achieve only a 78% classification accuracy in the MNIST handwritten data set under realistic conditions. We propose that this performance can be significantly improved to about 98.61% by using a deep SNN with supervised learning. Our results illustrate that the proposed skyrmionic synapse can be a potential candidate for future energy-efficient neuromorphic edge computing.

physics.app-ph↗

arXiv2020

Tempura: A General Cost Based Optimizer Framework for Incremental Data Processing (Extended Version)

Incremental processing is widely-adopted in many applications, ranging from incremental view maintenance, stream computing, to recently emerging progressive data warehouse and intermittent query processing. Despite many algorithms developed on this topic, none of them can produce an incremental plan that always achieves the best performance, since the optimal plan is data dependent. In this paper, we develop a novel cost-based optimizer framework, called Tempura, for optimizing incremental data processing. We propose an incremental query planning model called TIP based on the concept of time-varying relations, which can formally model incremental processing in its most general form. We give a full specification of Tempura, which can not only unify various existing techniques to generate an optimal incremental plan, but also allow the developer to add their rewrite rules. We study how to explore the plan space and search for an optimal incremental plan. We conduct a thorough experimental evaluation of Tempura in various incremental processing scenarios to show its effectiveness and efficiency.

cs.DB↗

arXiv2020

Towards Chirality Control of Graphene Nanoribbons Embedded in Hexagonal Boron Nitride

The integrated inplane growth of two dimensional materials with similar lattices, but distinct electrical properties, could provide a promising route to achieve integrated circuitry of atomic thickness. However, fabrication of edge specific GNR in the lattice of hBN still remains an enormous challenge for present approaches. Here we developed a two step growth method and successfully achieved sub 5 nm wide zigzag and armchair GNRs embedded in hBN, respectively. Further transport measurements reveal that the sub 7 nm wide zigzag GNRs exhibit openings of the band gap inversely proportional to their width, while narrow armchair GNRs exhibit some fluctuation in the bandgap width relationship.This integrated lateral growth of edge specific GNRs in hBN brings semiconducting building blocks to atomically thin layer, and will provide a promising route to achieve intricate nanoscale electrical circuits on high quality insulating hBN substrates.

cond-mat.mes-hall↗

arXiv2020

Weakly Supervised Generative Network for Multiple 3D Human Pose Hypotheses

3D human pose estimation from a single image is an inverse problem due to the inherent ambiguity of the missing depth. Several previous works addressed the inverse problem by generating multiple hypotheses. However, these works are strongly supervised and require ground truth 2D-to-3D correspondences which can be difficult to obtain. In this paper, we propose a weakly supervised deep generative network to address the inverse problem and circumvent the need for ground truth 2D-to-3D correspondences. To this end, we design our network to model a proposal distribution which we use to approximate the unknown multi-modal target posterior distribution. We achieve the approximation by minimizing the KL divergence between the proposal and target distributions, and this leads to a 2D reprojection error and a prior loss term that can be weakly supervised. Furthermore, we determine the most probable solution as the conditional mode of the samples using the mean-shift algorithm. We evaluate our method on three benchmark datasets -- Human3.6M, MPII and MPI-INF-3DHP. Experimental results show that our approach is capable of generating multiple feasible hypotheses and achieves state-of-the-art results compared to existing weakly supervised approaches. Our source code is available at the project website.

cs.CV↗

arXiv2020

Renal Cell Carcinoma Detection and Subtyping with Minimal Point-Based Annotation in Whole-Slide Images

Obtaining a large amount of labeled data in medical imaging is laborious and time-consuming, especially for histopathology. However, it is much easier and cheaper to get unlabeled data from whole-slide images (WSIs). Semi-supervised learning (SSL) is an effective way to utilize unlabeled data and alleviate the need for labeled data. For this reason, we proposed a framework that employs an SSL method to accurately detect cancerous regions with a novel annotation method called Minimal Point-Based annotation, and then utilize the predicted results with an innovative hybrid loss to train a classification model for subtyping. The annotator only needs to mark a few points and label them are cancer or not in each WSI. Experiments on three significant subtypes of renal cell carcinoma (RCC) proved that the performance of the classifier trained with the Min-Point annotated dataset is comparable to a classifier trained with the segmentation annotated dataset for cancer region detection. And the subtyping model outperforms a model trained with only diagnostic labels by 12% in terms of f1-score for testing WSIs.

eess.IV↗

arXiv2020

A Multi-scale CNN-CRF Framework for Environmental Microorganism Image Segmentation

To assist researchers to identify Environmental Microorganisms (EMs) effectively, a Multiscale CNN-CRF (MSCC) framework for the EM image segmentation is proposed in this paper. There are two parts in this framework: The first is a novel pixel-level segmentation approach, using a newly introduced Convolutional Neural Network (CNN), namely, "mU-Net-B3", with a dense Conditional Random Field (CRF) postprocessing. The second is a VGG-16 based patch-level segmentation method with a novel "buffer" strategy, which further improves the segmentation quality of the details of the EMs. In the experiment, compared with the state-of-the-art methods on 420 EM images, the proposed MSCC method reduces the memory requirement from 355 MB to 103 MB, improves the overall evaluation indexes (Dice, Jaccard, Recall, Accuracy) from 85.24%, 77.42%, 82.27%, and 96.76% to 87.13%, 79.74%, 87.12%, and 96.91%, respectively, and reduces the volume overlap error from 22.58% to 20.26%. Therefore, the MSCC method shows great potential in the EM segmentation field.

cs.CV↗

arXiv2020

A Comprehensive Review for Breast Histopathology Image Analysis Using Classical and Deep Neural Networks

Breast cancer is one of the most common and deadliest cancers among women. Since histopathological images contain sufficient phenotypic information, they play an indispensable role in the diagnosis and treatment of breast cancers. To improve the accuracy and objectivity of Breast Histopathological Image Analysis (BHIA), Artificial Neural Network (ANN) approaches are widely used in the segmentation and classification tasks of breast histopathological images. In this review, we present a comprehensive overview of the BHIA techniques based on ANNs. First of all, we categorize the BHIA systems into classical and deep neural networks for in-depth investigation. Then, the relevant studies based on BHIA systems are presented. After that, we analyze the existing models to discover the most suitable algorithms. Finally, publicly accessible datasets, along with their download links, are provided for the convenience of future researchers.

eess.IV↗

arXiv2020

Scalable Partial Explainability in Neural Networks via Flexible Activation Functions

Achieving transparency in black-box deep learning algorithms is still an open challenge. High dimensional features and decisions given by deep neural networks (NN) require new algorithms and methods to expose its mechanisms. Current state-of-the-art NN interpretation methods (e.g. Saliency maps, DeepLIFT, LIME, etc.) focus more on the direct relationship between NN outputs and inputs rather than the NN structure and operations itself. In current deep NN operations, there is uncertainty over the exact role played by neurons with fixed activation functions. In this paper, we achieve partially explainable learning model by symbolically explaining the role of activation functions (AF) under a scalable topology. This is carried out by modeling the AFs as adaptive Gaussian Processes (GP), which sit within a novel scalable NN topology, based on the Kolmogorov-Arnold Superposition Theorem (KST). In this scalable NN architecture, the AFs are generated by GP interpolation between control points and can thus be tuned during the back-propagation procedure via gradient descent. The control points act as the core enabler to both local and global adjustability of AF, where the GP interpolation constrains the intrinsic autocorrelation to avoid over-fitting. We show that there exists a trade-off between the NN's expressive power and interpretation complexity, under linear KST topology scaling. To demonstrate this, we perform a case study on a binary classification dataset of banknote authentication. By quantitatively and qualitatively investigating the mapping relationship between inputs and output, our explainable model can provide interpretation over each of the one-dimensional attributes. These early results suggest that our model has the potential to act as the final interpretation layer for deep neural networks.

cs.LG↗

arXiv2020

Riemannian Proximal Policy Optimization

In this paper, We propose a general Riemannian proximal optimization algorithm with guaranteed convergence to solve Markov decision process (MDP) problems. To model policy functions in MDP, we employ Gaussian mixture model (GMM) and formulate it as a nonconvex optimization problem in the Riemannian space of positive semidefinite matrices. For two given policy functions, we also provide its lower bound on policy improvement by using bounds derived from the Wasserstein distance of GMMs. Preliminary experiments show the efficacy of our proposed Riemannian proximal policy optimization algorithm.

cs.LG↗

arXiv2020

Modeling relation paths for knowledge base completion via joint adversarial training

Knowledge Base Completion (KBC), which aims at determining the missing relations between entity pairs, has received increasing attention in recent years. Most existing KBC methods focus on either embedding the Knowledge Base (KB) into a specific semantic space or leveraging the joint probability of Random Walks (RWs) on multi-hop paths. Only a few unified models take both semantic and path-related features into consideration with adequacy. In this paper, we propose a novel method to explore the intrinsic relationship between the single relation (i.e. 1-hop path) and multi-hop paths between paired entities. We use Hierarchical Attention Networks (HANs) to select important relations in multi-hop paths and encode them into low-dimensional vectors. By treating relations and multi-hop paths as two different input sources, we use a feature extractor, which is shared by two downstream components (i.e. relation classifier and source discriminator), to capture shared/similar information between them. By joint adversarial training, we encourage our model to extract features from the multi-hop paths which are representative for relation completion. We apply the trained model (except for the source discriminator) to several large-scale KBs for relation completion. Experimental results show that our method outperforms existing path information-based approaches. Since each sub-module of our model can be well interpreted, our model can be applied to a large number of relation learning tasks.

cs.AI↗

arXiv2020

Flexible all-PM NALM Yb:fiber laser design for frequency comb applications: operation regimes and their noise properties

We present a flexible all-polarization-maintaining (PM) mode-locked ytterbium (Yb):fiber laser based on a nonlinear amplifying loop mirror (NALM). In addition to providing detailed design considerations, we discuss the different operation regimes accessible by this versatile laser architecture and experimentally analyze five representative mode-locking states. These five states were obtained in a 78-MHz configuration at different intracavity group delay dispersion (GDD) values ranging from anomalous (-0.035 ps$^2$) to normal (+0.015 ps$^2$). We put a particular focus on the characterization of the intensity noise as well as the free-running linewidth of the carrier-envelope-offset (CEO) frequency as a function of the different operation regimes. We observe that operation points far from the spontaneous emission peak of Yb (~1030 nm) and close to zero intracavity dispersion can be found, where the influence of pump noise is strongly suppressed. For such an operation point, we show that a CEO linewidth of less than 10-kHz at 1 s integration can be obtained without any active stabilization.

physics.optics↗

arXiv2020

Foldover Features for Dynamic Object Behavior Description in Microscopic Videos

Behavior description is conducive to the analysis of tiny objects, similar objects, objects with weak visual information and objects with similar visual information, playing a fundamental role in the identification and classification of dynamic objects in microscopic videos. To this end, we propose foldover features to describe the behavior of dynamic objects. First, we generate foldover for each object in microscopic videos in X, Y and Z directions, respectively. Then, we extract foldover features from the X, Y and Z directions with statistical methods, respectively. Finally, we use four different classifiers to test the effectiveness of the proposed foldover features. In the experiment, we use a sperm microscopic video dataset to evaluate the proposed foldover features, including three types of 1374 sperms, and obtain the highest classification accuracy of 96.5%.

cs.CV↗

arXiv2020

A Study of Selectively Digital Etching Silicon-Germanium with Nitric and Hydrofluoric Acids

A digital etching method was proposed to achieve excellent control of etching depth. The digital etching characteristics of p+ Si and Si0.7Ge0.3 using the combinations of HNO3 oxidation and BOE oxide removal processes were studied. Experiments showed that oxidation saturates with time due to low activation energy. A physical model was presented to describe the wet oxidation process with nitric acid. The model was calibrated with experimental data and the oxidation saturation time, final oxide thickness, and selectivity between Si0.7Ge0.3 and p+ Si were obtained. The digital etch of laminated Si0.7Ge0.3/p+ Si was also investigated. The depth of the tunnels formed by etching SiGe layers between two Si layers was found in proportion to digital etching cycles. And oxidation would also saturate and the saturated relative etched amount per cycle (REPC) was 0.5 nm (4 monolayers). A corrected selectivity calculation formula was presented. The oxidation model was also calibrated with Si0.7Ge0.3/p+ Si stacks, and selectivity from model was the same with the corrected formula. The model can also be used to analyze process variations and repeatability. And it could act as a guidance for experiment design. Selectivity and repeatability should make a trade-off.

physics.app-ph↗

arXiv2020

A hybrid text normalization system using multi-head self-attention for mandarin

In this paper, we propose a hybrid text normalization system using multi-head self-attention. The system combines the advantages of a rule-based model and a neural model for text preprocessing tasks. Previous studies in Mandarin text normalization usually use a set of hand-written rules, which are hard to improve on general cases. The idea of our proposed system is motivated by the neural models from recent studies and has a better performance on our internal news corpus. This paper also includes different attempts to deal with imbalanced pattern distribution of the dataset. Overall, the performance of the system is improved by over 1.5% on sentence-level and it has a potential to improve further.

cs.CL↗

arXiv2020

OpenHI2 -- Open source histopathological image platform

Transition from conventional to digital pathology requires a new category of biomedical informatic infrastructure which could facilitate delicate pathological routine. Pathological diagnoses are sensitive to many external factors and is known to be subjective. Only systems that can meet strict requirements in pathology would be able to run along pathological routines and eventually digitized the study area, and the developed platform should comply with existing pathological routines and international standards. Currently, there are a number of available software tools which can perform histopathological tasks including virtual slide viewing, annotating, and basic image analysis, however, none of them can serve as a digital platform for pathology. Here we describe OpenHI2, an enhanced version Open Histopathological Image platform which is capable of supporting all basic pathological tasks and file formats; ready to be deployed in medical institutions on a standard server environment or cloud computing infrastructure. In this paper, we also describe the development decisions for the platform and propose solutions to overcome technical challenges so that OpenHI2 could be used as a platform for histopathological images. Further addition can be made to the platform since each component is modularized and fully documented. OpenHI2 is free, open-source, and available at https://gitlab.com/BioAI/OpenHI.

q-bio.QM↗