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Wei Fan

Publications and source records attributed to Wei Fan.

At least 181 records · Page 10Linked to original sources

Partly Supervised Multitask Learning

Semi-supervised learning has recently been attracting attention as an alternative to fully supervised models that require large pools of labeled data. Moreover, optimizing a model for multiple tasks can provide better generalizability than single-task learning. Leveraging self-supervision and adversarial training, we propose a novel general purpose semi-supervised, multiple-task model---namely, self-supervised, semi-supervised, multitask learning (S$^4$MTL)---for accomplishing two important tasks in medical imaging, segmentation and diagnostic classification. Experimental results on chest and spine X-ray datasets suggest that our S$^4$MTL model significantly outperforms semi-supervised single task, semi/fully-supervised multitask, and fully-supervised single task models, even with a 50\% reduction of class and segmentation labels. We hypothesize that our proposed model can be effective in tackling limited annotation problems for joint training, not only in medical imaging domains, but also for general-purpose vision tasks.

cs.CV↗

An Extension of LIME with Improvement of Interpretability and Fidelity

While deep learning makes significant achievements in Artificial Intelligence (AI), the lack of transparency has limited its broad application in various vertical domains. Explainability is not only a gateway between AI and real world, but also a powerful feature to detect flaw of the models and bias of the data. Local Interpretable Model-agnostic Explanation (LIME) is a widely-accepted technique that explains the prediction of any classifier faithfully by learning an interpretable model locally around the predicted instance. As an extension of LIME, this paper proposes an high-interpretability and high-fidelity local explanation method, known as Local Explanation using feature Dependency Sampling and Nonlinear Approximation (LEDSNA). Given an instance being explained, LEDSNA enhances interpretability by feature sampling with intrinsic dependency. Besides, LEDSNA improves the local explanation fidelity by approximating nonlinear boundary of local decision. We evaluate our method with classification tasks in both image domain and text domain. Experiments show that LEDSNA's explanation of the back-box model achieves much better performance than original LIME in terms of interpretability and fidelity.

cs.LG↗

Analysis of Scoliosis From Spinal X-Ray Images

Scoliosis is a congenital disease in which the spine is deformed from its normal shape. Measurement of scoliosis requires labeling and identification of vertebrae in the spine. Spine radiographs are the most cost-effective and accessible modality for imaging the spine. Reliable and accurate vertebrae segmentation in spine radiographs is crucial in image-guided spinal assessment, disease diagnosis, and treatment planning. Conventional assessments rely on tedious and time-consuming manual measurement, which is subject to inter-observer variability. A fully automatic method that can accurately identify and segment the associated vertebrae is unavailable in the literature. Leveraging a carefully-adjusted U-Net model with progressive side outputs, we propose an end-to-end segmentation model that provides a fully automatic and reliable segmentation of the vertebrae associated with scoliosis measurement. Our experimental results from a set of anterior-posterior spine X-Ray images indicate that our model, which achieves an average Dice score of 0.993, promises to be an effective tool in the identification and labeling of spinal vertebrae, eventually helping doctors in the reliable estimation of scoliosis. Moreover, estimation of Cobb angles from the segmented vertebrae further demonstrates the effectiveness of our model.

eess.IV↗

Performance evaluation of on-chip wavelength conversion based on InP/In$_{1-x}$Ga$_x$As$_y$P$_{1-y}$ semiconductor waveguide platforms

We propose and design the high confinement InP/In1-xGaxAsyP1-y semiconductor waveguides and report the results of effective wavelength conversion based on this platform. Efficient confinement and mode field area fluctuation at different wavelength is analyzed to achieve the high nonlinear coefficient. The numerical results show that nearly zero phase-mismatch condition can be satisfied through dispersion tailoring of InP/In1-xGaxAsyP1-y waveguides, and the wavelength conversion ranging over 40 nm with the maximum conversion efficiency -26.3 dB is achieved for fixing pump power 100 mW. Meanwhile, the influences of the doping parameter y and pumping wavelength on the bandwidth and conversion efficiency are also discussed and optimized. It is indicated the excellent optical properties of the InP/In1-xGaxAsyP1-y waveguides and pave the way towards direct integration telecom band devices on stand semiconductor platforms.

physics.optics↗

Estimation of genome size using k-mer frequencies from corrected long reads

The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy, third-generation sequencing data cannot be used for k-mer counting and estimating genomic profile based on k-mer frequencies. Thus, in current genome projects, second-generation data is also necessary for accurately determining genome size and other genomic characteristics. We show that corrected third-generation data can be used to count k-mer frequencies and estimate genome size reliably, in replacement of using second-generation data. Therefore, future genome projects can depend on only one sequencing technology to finish both assembly and k-mer analysis, which will largely decrease sequencing cost in both time and money. Moreover, we present a fast light-weight tool kmerfreq and use it to perform all the k-mer counting tasks in this work. We have demonstrated that corrected third-generation sequencing data can be used to estimate genome size and developed a new open-source C/C++ k-mer counting tool, kmerfreq, which is freely available at https://github.com/fanagislab/kmerfreq.

q-bio.GN↗

Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects

Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often difficult to know the accurate genome size and repeat content. Furthermore, many genomes are highly repetitive or heterozygous, posing problems to current assemblers utilizing short reads. Therefore, it is necessary to develop efficient assembly-independent methods for accurate estimation of these genomic characteristics. Results: Here we present a framework for modeling the distribution of k-mer frequency from sequencing data and estimating the genomic characteristics such as genome size, repeat structure and heterozygous rate. By introducing novel techniques of k-mer individuals, float precision estimation, and proper treatment of sequencing error and coverage bias, the estimation accuracy of our method is significantly improved over existing methods. We also studied how the various genomic and sequencing characteristics affect the estimation accuracy using simulated sequencing data, and discussed the limitations on applying our method to real sequencing data. Conclusion: Based on this research, we show that the k-mer frequency analysis can be used as a general and assembly-independent method for estimating genomic characteristics, which can improve our understanding of a species genome, help design the sequencing strategy of genome projects, and guide the development of assembly algorithms. The programs developed in this research are written using C/C++, and freely accessible at Github URL (https://github.com/fanagislab/GCE) or BGI ftp ( ftp://ftp.genomics.org.cn/pub/gce).

q-bio.GN↗

A Modified Perturbed Sampling Method for Local Interpretable Model-agnostic Explanation

Explainability is a gateway between Artificial Intelligence and society as the current popular deep learning models are generally weak in explaining the reasoning process and prediction results. Local Interpretable Model-agnostic Explanation (LIME) is a recent technique that explains the predictions of any classifier faithfully by learning an interpretable model locally around the prediction. However, the sampling operation in the standard implementation of LIME is defective. Perturbed samples are generated from a uniform distribution, ignoring the complicated correlation between features. This paper proposes a novel Modified Perturbed Sampling operation for LIME (MPS-LIME), which is formalized as the clique set construction problem. In image classification, MPS-LIME converts the superpixel image into an undirected graph. Various experiments show that the MPS-LIME explanation of the black-box model achieves much better performance in terms of understandability, fidelity, and efficiency.

cs.LG↗

Explaining the Predictions of Any Image Classifier via Decision Trees

Despite outstanding contribution to the significant progress of Artificial Intelligence (AI), deep learning models remain mostly black boxes, which are extremely weak in explainability of the reasoning process and prediction results. Explainability is not only a gateway between AI and society but also a powerful tool to detect flaws in the model and biases in the data. Local Interpretable Model-agnostic Explanation (LIME) is a recent approach that uses an interpretable model to form a local explanation for the individual prediction result. The current implementation of LIME adopts the linear regression as its interpretable function. However, being so restricted and usually over-simplifying the relationships, linear models fail in situations where nonlinear associations and interactions exist among features and prediction results. This paper implements a decision Tree-based LIME approach, which uses a decision tree model to form an interpretable representation that is locally faithful to the original model. Tree-LIME approach can capture nonlinear interactions among features in the data and creates plausible explanations. Various experiments show that the Tree-LIME explanation of multiple black-box models can achieve more reliable performance in terms of understandability, fidelity, and efficiency.

cs.LG↗

Nonparametric Structure Regularization Machine for 2D Hand Pose Estimation

Hand pose estimation is more challenging than body pose estimation due to severe articulation, self-occlusion and high dexterity of the hand. Current approaches often rely on a popular body pose algorithm, such as the Convolutional Pose Machine (CPM), to learn 2D keypoint features. These algorithms cannot adequately address the unique challenges of hand pose estimation, because they are trained solely based on keypoint positions without seeking to explicitly model structural relationship between them. We propose a novel Nonparametric Structure Regularization Machine (NSRM) for 2D hand pose estimation, adopting a cascade multi-task architecture to learn hand structure and keypoint representations jointly. The structure learning is guided by synthetic hand mask representations, which are directly computed from keypoint positions, and is further strengthened by a novel probabilistic representation of hand limbs and an anatomically inspired composition strategy of mask synthesis. We conduct extensive studies on two public datasets - OneHand 10k and CMU Panoptic Hand. Experimental results demonstrate that explicitly enforcing structure learning consistently improves pose estimation accuracy of CPM baseline models, by 1.17% on the first dataset and 4.01% on the second one. The implementation and experiment code is freely available online. Our proposal of incorporating structural learning to hand pose estimation requires no additional training information, and can be a generic add-on module to other pose estimation models.

cs.CV↗

Shape-Aware Organ Segmentation by Predicting Signed Distance Maps

In this work, we propose to resolve the issue existing in current deep learning based organ segmentation systems that they often produce results that do not capture the overall shape of the target organ and often lack smoothness. Since there is a rigorous mapping between the Signed Distance Map (SDM) calculated from object boundary contours and the binary segmentation map, we exploit the feasibility of learning the SDM directly from medical scans. By converting the segmentation task into predicting an SDM, we show that our proposed method retains superior segmentation performance and has better smoothness and continuity in shape. To leverage the complementary information in traditional segmentation training, we introduce an approximated Heaviside function to train the model by predicting SDMs and segmentation maps simultaneously. We validate our proposed models by conducting extensive experiments on a hippocampus segmentation dataset and the public MICCAI 2015 Head and Neck Auto Segmentation Challenge dataset with multiple organs. While our carefully designed backbone 3D segmentation network improves the Dice coefficient by more than 5% compared to current state-of-the-arts, the proposed model with SDM learning produces smoother segmentation results with smaller Hausdorff distance and average surface distance, thus proving the effectiveness of our method.

cs.CV↗

On the Generation of Medical Question-Answer Pairs

Question answering (QA) has achieved promising progress recently. However, answering a question in real-world scenarios like the medical domain is still challenging, due to the requirement of external knowledge and the insufficient quantity of high-quality training data. In the light of these challenges, we study the task of generating medical QA pairs in this paper. With the insight that each medical question can be considered as a sample from the latent distribution of questions given answers, we propose an automated medical QA pair generation framework, consisting of an unsupervised key phrase detector that explores unstructured material for validity, and a generator that involves a multi-pass decoder to integrate structural knowledge for diversity. A series of experiments have been conducted on a real-world dataset collected from the National Medical Licensing Examination of China. Both automatic evaluation and human annotation demonstrate the effectiveness of the proposed method. Further investigation shows that, by incorporating the generated QA pairs for training, significant improvement in terms of accuracy can be achieved for the examination QA system.

cs.AI↗

Object-Guided Instance Segmentation for Biological Images

Instance segmentation of biological images is essential for studying object behaviors and properties. The challenges, such as clustering, occlusion, and adhesion problems of the objects, make instance segmentation a non-trivial task. Current box-free instance segmentation methods typically rely on local pixel-level information. Due to a lack of global object view, these methods are prone to over- or under-segmentation. On the contrary, the box-based instance segmentation methods incorporate object detection into the segmentation, performing better in identifying the individual instances. In this paper, we propose a new box-based instance segmentation method. Mainly, we locate the object bounding boxes from their center points. The object features are subsequently reused in the segmentation branch as a guide to separate the clustered instances within an RoI patch. Along with the instance normalization, the model is able to recover the target object distribution and suppress the distribution of neighboring attached objects. Consequently, the proposed model performs excellently in segmenting the clustered objects while retaining the target object details. The proposed method achieves state-of-the-art performances on three biological datasets: cell nuclei, plant phenotyping dataset, and neural cells.

cs.CV↗

MedTruth: A Semi-supervised Approach to Discovering Knowledge Condition Information from Multi-Source Medical Data

Knowledge Graph (KG) contains entities and the relations between entities. Due to its representation ability, KG has been successfully applied to support many medical/healthcare tasks. However, in the medical domain, knowledge holds under certain conditions. For example, symptom \emph{runny nose} highly indicates the existence of disease \emph{whooping cough} when the patient is a baby rather than the people at other ages. Such conditions for medical knowledge are crucial for decision-making in various medical applications, which is missing in existing medical KGs. In this paper, we aim to discovery medical knowledge conditions from texts to enrich KGs. Electronic Medical Records (EMRs) are systematized collection of clinical data and contain detailed information about patients, thus EMRs can be a good resource to discover medical knowledge conditions. Unfortunately, the amount of available EMRs is limited due to reasons such as regularization. Meanwhile, a large amount of medical question answering (QA) data is available, which can greatly help the studied task. However, the quality of medical QA data is quite diverse, which may degrade the quality of the discovered medical knowledge conditions. In the light of these challenges, we propose a new truth discovery method, MedTruth, for medical knowledge condition discovery, which incorporates prior source quality information into the source reliability estimation procedure, and also utilizes the knowledge triple information for trustworthy information computation. We conduct series of experiments on real-world medical datasets to demonstrate that the proposed method can discover meaningful and accurate conditions for medical knowledge by leveraging both EMR and QA data. Further, the proposed method is tested on synthetic datasets to validate its effectiveness under various scenarios.

cs.DB↗

Joint Slot Filling and Intent Detection via Capsule Neural Networks

Being able to recognize words as slots and detect the intent of an utterance has been a keen issue in natural language understanding. The existing works either treat slot filling and intent detection separately in a pipeline manner, or adopt joint models which sequentially label slots while summarizing the utterance-level intent without explicitly preserving the hierarchical relationship among words, slots, and intents. To exploit the semantic hierarchy for effective modeling, we propose a capsule-based neural network model which accomplishes slot filling and intent detection via a dynamic routing-by-agreement schema. A re-routing schema is proposed to further synergize the slot filling performance using the inferred intent representation. Experiments on two real-world datasets show the effectiveness of our model when compared with other alternative model architectures, as well as existing natural language understanding services.

cs.CL↗

Multi-Grained Named Entity Recognition

This paper presents a novel framework, MGNER, for Multi-Grained Named Entity Recognition where multiple entities or entity mentions in a sentence could be non-overlapping or totally nested. Different from traditional approaches regarding NER as a sequential labeling task and annotate entities consecutively, MGNER detects and recognizes entities on multiple granularities: it is able to recognize named entities without explicitly assuming non-overlapping or totally nested structures. MGNER consists of a Detector that examines all possible word segments and a Classifier that categorizes entities. In addition, contextual information and a self-attention mechanism are utilized throughout the framework to improve the NER performance. Experimental results show that MGNER outperforms current state-of-the-art baselines up to 4.4% in terms of the F1 score among nested/non-overlapping NER tasks.

cs.CL↗

Neural Multi-Scale Self-Supervised Registration for Echocardiogram Dense Tracking

Echocardiography has become routinely used in the diagnosis of cardiomyopathy and abnormal cardiac blood flow. However, manually measuring myocardial motion and cardiac blood flow from echocardiogram is time-consuming and error-prone. Computer algorithms that can automatically track and quantify myocardial motion and cardiac blood flow are highly sought after, but have not been very successful due to noise and high variability of echocardiography. In this work, we propose a neural multi-scale self-supervised registration (NMSR) method for automated myocardial and cardiac blood flow dense tracking. NMSR incorporates two novel components: 1) utilizing a deep neural net to parameterize the velocity field between two image frames, and 2) optimizing the parameters of the neural net in a sequential multi-scale fashion to account for large variations within the velocity field. Experiments demonstrate that NMSR yields significantly better registration accuracy than state-of-the-art methods, such as advanced normalization tools (ANTs) and VoxelMorph, for both myocardial and cardiac blood flow dense tracking. Our approach promises to provide a fully automated method for fast and accurate analyses of echocardiograms.

cs.CV↗

Soft Limits of Yang-Mills Amplitudes and Conformal Correlators

We study tree-level celestial amplitudes in Yang-Mills theory -- Mellin transforms of multi-gluon scattering amplitudes that convert them into the correlators of conformal primary fields on two-dimensional celestial sphere. By using purely field-theoretical methods, we show that the soft conformal limit of celestial amplitudes, in which one of the primary field operators associated to gauge bosons becomes a dimension one current, is dominated by the contributions of low-energy soft particles. This result confirms conclusions reached by using Yang-Mills theory formulated in curvilinear coordinates, as pioneered by Strominger. By using well-known collinear limits of Yang-Mills amplitudes, we derive the OPE rules for the primary fields and the holomorphic currents arising in the conformally soft limit. The Ward identities following from OPE have the same form as the identities derived by using soft theorems.

hep-th↗

A Complexity-Efficient High Resolution Propagation Parameter Estimation Algorithm for Ultra-Wideband Large-Scale Uniform Circular Array

Millimeter wave (mm-wave) communication with large-scale antenna array configuration is seen as the key enabler of the next generation communication systems. Accurate knowledge of the mm-wave propagation channels is fundamental and essential. In this contribution, a novel complexity-efficient high resolution parameter estimation (HRPE) algorithm is proposed for the mm-wave channel with large-scale uniform circular array (UCA) applied. The proposed algorithm is able to obtain the high-resolution estimation results of the spherical channel propagation parameters. The prior channel information in the delay domain, i.e., the delay trajectories of individual propagation paths observed across the array elements, is exploited, by combining the high-resolution estimation principle and the phase mode excitation technique. Fast initializations, effective interference cancellations and reduced searching spaces achieved by the proposed schemes significantly decrease the algorithm complexity. Furthermore, the channel spatial non-stationarity in path gain across the array elements is considered for the first time in the literature for propagation parameter estimation, which is beneficial to obtain more realistic results as well as to decrease the complexity. A mm-wave measurement campaign at the frequency band of 28-30 GHz using a large-scale UCA is exploited to demonstrate and validate the proposed HRPE algorithm.

eess.SP↗