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Wu, Jian


A Comprehensive Review of Computer-aided Whole-slide Image Analysis: from Datasets to Feature Extraction, Segmentation, Classification, and Detection Approaches

arXiv.org Artificial Intelligence

With the development of computer-aided diagnosis (CAD) and image scanning technology, Whole-slide Image (WSI) scanners are widely used in the field of pathological diagnosis. Therefore, WSI analysis has become the key to modern digital pathology. Since 2004, WSI has been used more and more in CAD. Since machine vision methods are usually based on semi-automatic or fully automatic computers, they are highly efficient and labor-saving. The combination of WSI and CAD technologies for segmentation, classification, and detection helps histopathologists obtain more stable and quantitative analysis results, save labor costs and improve diagnosis objectivity. This paper reviews the methods of WSI analysis based on machine learning. Firstly, the development status of WSI and CAD methods are introduced. Secondly, we discuss publicly available WSI datasets and evaluation metrics for segmentation, classification, and detection tasks. Then, the latest development of machine learning in WSI segmentation, classification, and detection are reviewed continuously. Finally, the existing methods are studied, the applicabilities of the analysis methods are analyzed, and the application prospects of the analysis methods in this field are forecasted.


Doctor Imitator: A Graph-based Bone Age Assessment Framework Using Hand Radiographs

arXiv.org Artificial Intelligence

Bone age assessment is challenging in clinical practice due to the complicated bone age assessment process. Current automatic bone age assessment methods were designed with rare consideration of the diagnostic logistics and thus may yield certain uninterpretable hidden states and outputs. Consequently, doctors can find it hard to cooperate with such models harmoniously because it is difficult to check the correctness of the model predictions. In this work, we propose a new graph-based deep learning framework for bone age assessment with hand radiographs, called Doctor Imitator (DI). The architecture of DI is designed to learn the diagnostic logistics of doctors using the scoring methods (e.g., the Tanner-Whitehouse method) for bone age assessment. Specifically, the convolutions of DI capture the local features of the anatomical regions of interest (ROIs) on hand radiographs and predict the ROI scores by our proposed Anatomy-based Group Convolution, summing up for bone age prediction. Besides, we develop a novel Dual Graph-based Attention module to compute patient-specific attention for ROI features and context attention for ROI scores. As far as we know, DI is the first automatic bone age assessment framework following the scoring methods without fully supervised hand radiographs. Experiments on hand radiographs with only bone age supervision verify that DI can achieve excellent performance with sparse parameters and provide more interpretability.


Speaker diarization with session-level speaker embedding refinement using graph neural networks

arXiv.org Machine Learning

Deep speaker embedding models have been commonly used as a building block for speaker diarization systems; however, the speaker embedding model is usually trained according to a global loss defined on the training data, which could be sub-optimal for distinguishing speakers locally in a specific meeting session. In this work we present the first use of graph neural networks (GNNs) for the speaker diarization problem, utilizing a GNN to refine speaker embeddings locally using the structural information between speech segments inside each session. The speaker embeddings extracted by a pre-trained model are remapped into a new embedding space, in which the different speakers within a single session are better separated. The model is trained for linkage prediction in a supervised manner by minimizing the difference between the affinity matrix constructed by the refined embeddings and the ground-truth adjacency matrix. Spectral clustering is then applied on top of the refined embeddings. We show that the clustering performance of the refined speaker embeddings outperforms the original embeddings significantly on both simulated and real meeting data, and our system achieves the state-of-the-art result on the NIST SRE 2000 CALLHOME database.


Practical Two-Step Lookahead Bayesian Optimization

Neural Information Processing Systems

Expected improvement and other acquisition functions widely used in Bayesian optimization use a "one-step" assumption: they value objective function evaluations assuming no future evaluations will be performed. Because we usually evaluate over multiple steps, this assumption may leave substantial room for improvement. Existing theory gives acquisition functions looking multiple steps in the future but calculating them requires solving a high-dimensional continuous-state continuous-action Markov decision process (MDP). Fast exact solutions of this MDP remain out of reach of today's methods. As a result, previous two- and multi-step lookahead Bayesian optimization algorithms are either too expensive to implement in most practical settings or resort to heuristics that may fail to fully realize the promise of two-step lookahead.


Bayesian Optimization with Gradients

Neural Information Processing Systems

Bayesian optimization has shown success in global optimization of expensive-to-evaluate multimodal objective functions. However, unlike most optimization methods, Bayesian optimization typically does not use derivative information. In this paper we show how Bayesian optimization can exploit derivative information to find good solutions with fewer objective function evaluations. In particular, we develop a novel Bayesian optimization algorithm, the derivative-enabled knowledge-gradient (dKG), which is one-step Bayes-optimal, asymptotically consistent, and provides greater one-step value of information than in the derivative-free setting. We also compute the dKG acquisition function and its gradient using a novel fast discretization-free technique.


The Parallel Knowledge Gradient Method for Batch Bayesian Optimization

Neural Information Processing Systems

In many applications of black-box optimization, one can evaluate multiple points simultaneously, e.g. when evaluating the performances of several different neural network architectures in a parallel computing environment. In this paper, we develop a novel batch Bayesian optimization algorithm --- the parallel knowledge gradient method. By construction, this method provides the one-step Bayes optimal batch of points to sample. We provide an efficient strategy for computing this Bayes-optimal batch of points, and we demonstrate that the parallel knowledge gradient method finds global optima significantly faster than previous batch Bayesian optimization algorithms on both synthetic test functions and when tuning hyperparameters of practical machine learning algorithms, especially when function evaluations are noisy. Papers published at the Neural Information Processing Systems Conference.


Method and Dataset Mining in Scientific Papers

arXiv.org Machine Learning

Literature analysis facilitates researchers better understanding the development of science and technology. The conventional literature analysis focuses on the topics, authors, abstracts, keywords, references, etc., and rarely pays attention to the content of papers. In the field of machine learning, the involved methods (M) and datasets (D) are key information in papers. The extraction and mining of M and D are useful for discipline analysis and algorithm recommendation. In this paper, we propose a novel entity recognition model, called MDER, and constructe datasets from the papers of the PAKDD conferences (2009-2019). Some preliminary experiments are conducted to assess the extraction performance and the mining results are visualized.


Personalized Context-aware Re-ranking for E-commerce Recommender Systems

arXiv.org Artificial Intelligence

Ranking is a core task in E-commerce recommender systems, which aims at providing an ordered list of items to users. Typically, a ranking function is learned from the labeled dataset to optimize the global performance, which produces a ranking score for each individual item. However, it may be sub-optimal because the scoring function applies to each item individually and does not explicitly consider the mutual influence between items, as well as the differences of users' preferences or intents. Therefore, we propose a personalized context-aware re-ranking model for E-commerce recommender systems. The proposed re-ranking model can be easily deployed as a follow-up modular after ranking by directly using the existing feature vectors of ranking. It directly optimizes the whole recommendation list by employing a transformer structure to efficiently encode the information of all items in the list. Specifically, the Transformer applies a self-attention mechanism that directly models the global relationships between any pair of items in the whole list. Besides, we introduce the personalized embedding to model the differences between feature distributions for different users. Experimental results on both offline benchmarks and real-world online E-commerce systems demonstrate the significant improvements of the proposed re-ranking model.


Practical Multi-fidelity Bayesian Optimization for Hyperparameter Tuning

arXiv.org Machine Learning

Bayesian optimization is popular for optimizing time-consuming black-box objectives. Nonetheless, for hyperparameter tuning in deep neural networks, the time required to evaluate the validation error for even a few hyperparameter settings remains a bottleneck. Multi-fidelity optimization promises relief using cheaper proxies to such objectives --- for example, validation error for a network trained using a subset of the training points or fewer iterations than required for convergence. We propose a highly flexible and practical approach to multi-fidelity Bayesian optimization, focused on efficiently optimizing hyperparameters for iteratively trained supervised learning models. We introduce a new acquisition function, the trace-aware knowledge-gradient, which efficiently leverages both multiple continuous fidelity controls and trace observations --- values of the objective at a sequence of fidelities, available when varying fidelity using training iterations. We provide a provably convergent method for optimizing our acquisition function and show it outperforms state-of-the-art alternatives for hyperparameter tuning of deep neural networks and large-scale kernel learning.


Bayesian Optimization with Gradients

arXiv.org Artificial Intelligence

Bayesian optimization has been successful at global optimization of expensive-to-evaluate multimodal objective functions. However, unlike most optimization methods, Bayesian optimization typically does not use derivative information. In this paper we show how Bayesian optimization can exploit derivative information to decrease the number of objective function evaluations required for good performance. In particular, we develop a novel Bayesian optimization algorithm, the derivative-enabled knowledge-gradient (dKG), for which we show one-step Bayes-optimality, asymptotic consistency, and greater one-step value of information than is possible in the derivative-free setting. Our procedure accommodates noisy and incomplete derivative information, comes in both sequential and batch forms, and can optionally reduce the computational cost of inference through automatically selected retention of a single directional derivative. We also compute the d-KG acquisition function and its gradient using a novel fast discretization-free technique. We show d-KG provides state-of-the-art performance compared to a wide range of optimization procedures with and without gradients, on benchmarks including logistic regression, deep learning, kernel learning, and k-nearest neighbors.