Chen Liu

Qiuli Wang, Xin Tan, Chen Liu

Since the pandemic of COVID-19, several deep learning methods were proposed to analyze the chest Computed Tomography (CT) for diagnosis. In the current situation, the disease course classification is significant for medical personnel to decide the treatment. Most previous deep-learning-based methods extract features observed from the lung window. However, it has been proved that some appearances related to diagnosis can be observed better from the mediastinal window rather than the lung window, e.g., the pulmonary consolidation happens more in severe symptoms. In this paper, we propose a novel Dual Window RCNN Network (DWRNet), which mainly learns the distinctive features from the successive mediastinal window. Regarding the features extracted from the lung window, we introduce the Lung Window Attention Block (LWA Block) to pay additional attention to them for enhancing the mediastinal-window features. Moreover, instead of picking up specific slices from the whole CT slices, we use a Recurrent CNN and analyze successive slices as videos. Experimental results show that the fused and representative features improve the predictions of disease course by reaching the accuracy of 90.57%, against the baseline with an accuracy of 84.86%. Ablation studies demonstrate that combined dual window features are more efficient than lung-window features alone, while paying attention to lung-window features can improve the model's stability.

Danqi Liao, Chen Liu, Benjamin W. Christensen et al.

Entropy and mutual information in neural networks provide rich information on the learning process, but they have proven difficult to compute reliably in high dimensions. Indeed, in noisy and high-dimensional data, traditional estimates in ambient dimensions approach a fixed entropy and are prohibitively hard to compute. To address these issues, we leverage data geometry to access the underlying manifold and reliably compute these information-theoretic measures. Specifically, we define diffusion spectral entropy (DSE) in neural representations of a dataset as well as diffusion spectral mutual information (DSMI) between different variables representing data. First, we show that they form noise-resistant measures of intrinsic dimensionality and relationship strength in high-dimensional simulated data that outperform classic Shannon entropy, nonparametric estimation, and mutual information neural estimation (MINE). We then study the evolution of representations in classification networks with supervised learning, self-supervision, or overfitting. We observe that (1) DSE of neural representations increases during training; (2) DSMI with the class label increases during generalizable learning but stays stagnant during overfitting; (3) DSMI with the input signal shows differing trends: on MNIST it increases, while on CIFAR-10 and STL-10 it decreases. Finally, we show that DSE can be used to guide better network initialization and that DSMI can be used to predict downstream classification accuracy across 962 models on ImageNet. The official implementation is available at https://github.com/ChenLiu-1996/DiffusionSpectralEntropy.

Haonan Zhang, Yuhan Zhang, Qing Wu et al.

In this paper, we propose an efficient self-supervised arbitrary-scale super-resolution (SR) framework to reconstruct isotropic magnetic resonance (MR) images from anisotropic MRI inputs without involving external training data. The proposed framework builds a training dataset using in-the-wild anisotropic MR volumes with arbitrary image resolution. We then formulate the 3D volume SR task as a SR problem for 2D image slices. The anisotropic volume's high-resolution (HR) plane is used to build the HR-LR image pairs for model training. We further adapt the implicit neural representation (INR) network to implement the 2D arbitrary-scale image SR model. Finally, we leverage the well-trained proposed model to up-sample the 2D LR plane extracted from the anisotropic MR volumes to their HR views. The isotropic MR volumes thus can be reconstructed by stacking and averaging the generated HR slices. Our proposed framework has two major advantages: (1) It only involves the arbitrary-resolution anisotropic MR volumes, which greatly improves the model practicality in real MR imaging scenarios (e.g., clinical brain image acquisition); (2) The INR-based SR model enables arbitrary-scale image SR from the arbitrary-resolution input image, which significantly improves model training efficiency. We perform experiments on a simulated public adult brain dataset and a real collected 7T brain dataset. The results indicate that our current framework greatly outperforms two well-known self-supervised models for anisotropic MR image SR tasks.

Chen Liu, Mengchao Zhang, Zhibin Fu et al.

In natural language processing (NLP), state-of-the-art (SOTA) semi-supervised learning (SSL) frameworks have shown great performance on deep pre-trained language models such as BERT, and are expected to significantly reduce the demand for manual labeling. However, our empirical studies indicate that these frameworks are not suitable for lightweight models such as TextCNN, LSTM and etc. In this work, we develop a new SSL framework called FLiText, which stands for Faster and Lighter semi-supervised Text classification. FLiText introduces an inspirer network together with the consistency regularization framework, which leverages a generalized regular constraint on the lightweight models for efficient SSL. As a result, FLiText obtains new SOTA performance for lightweight models across multiple SSL benchmarks on text classification. Compared with existing SOTA SSL methods on TextCNN, FLiText improves the accuracy of lightweight model TextCNN from 51.00% to 90.49% on IMDb, 39.8% to 58.06% on Yelp-5, and from 55.3% to 65.08% on Yahoo. In addition, compared with the fully supervised method on the full dataset, FLiText just uses less than 1% of labeled data to improve the accuracy by 6.59%, 3.94%, and 3.22% on the datasets of IMDb, Yelp-5, and Yahoo respectively.

Chen Liu, Su Zhu, Zijian Zhao et al.

Spoken Language Understanding (SLU) converts hypotheses from automatic speech recognizer (ASR) into structured semantic representations. ASR recognition errors can severely degenerate the performance of the subsequent SLU module. To address this issue, word confusion networks (WCNs) have been used to encode the input for SLU, which contain richer information than 1-best or n-best hypotheses list. To further eliminate ambiguity, the last system act of dialogue context is also utilized as additional input. In this paper, a novel BERT based SLU model (WCN-BERT SLU) is proposed to encode WCNs and the dialogue context jointly. It can integrate both structural information and ASR posterior probabilities of WCNs in the BERT architecture. Experiments on DSTC2, a benchmark of SLU, show that the proposed method is effective and can outperform previous state-of-the-art models significantly.

Haoran Sun, Xueqing Liu, Xinyang Feng et al.

Cerebral blood volume (CBV) is a hemodynamic correlate of oxygen metabolism and reflects brain activity and function. High-resolution CBV maps can be generated using the steady-state gadolinium-enhanced MRI technique. Such a technique requires an intravenous injection of exogenous gadolinium based contrast agent (GBCA) and recent studies suggest that the GBCA can accumulate in the brain after frequent use. We hypothesize that endogenous sources of contrast might exist within the most conventional and commonly acquired structural MRI, potentially obviating the need for exogenous contrast. Here, we test this hypothesis by developing and optimizing a deep learning algorithm, which we call DeepContrast, in mice. We find that DeepContrast performs equally well as exogenous GBCA in mapping CBV of the normal brain tissue and enhancing glioblastoma. Together, these studies validate our hypothesis that a deep learning approach can potentially replace the need for GBCAs in brain MRI.

Nanyan Zhu, Chen Liu, Zakary S. Singer et al.

The ability to extrapolate gene expression dynamics in living single cells requires robust cell segmentation, and one of the challenges is the amorphous or irregularly shaped cell boundaries. To address this issue, we modified the U-Net architecture to segment cells in fluorescence widefield microscopy images and quantitatively evaluated its performance. We also proposed a novel loss function approach that emphasizes the segmentation accuracy on cell boundaries and encourages shape feature preservation. With a 97% sensitivity, 93% specificity, 91% Jaccard similarity, and 95% Dice coefficient, our proposed method called Residual Attention U-Net with edge-enhancement surpassed the state-of-the-art U-Net in segmentation performance as evaluated by the traditional metrics. More remarkably, the same proposed candidate also performed the best in terms of the preservation of valuable shape features, namely area, eccentricity, major axis length, solidity and orientation. These improvements on shape feature preservation can serve as useful assets for downstream cell tracking and quantification of changes in cell statistics or features over time.