Yi Li

Yuming Sun, Jian Kang, Chinmay Haridas et al.

Lung cancer is a leading cause of cancer mortality globally, highlighting the importance of understanding its mortality risks to design effective patient-centered therapies. The National Lung Screening Trial (NLST) employed computed tomography texture analysis, which provides objective measurements of texture patterns on CT scans, to quantify the mortality risks of lung cancer patients. Partially linear Cox models have gained popularity for survival analysis by dissecting the hazard function into parametric and nonparametric components, allowing for the effective incorporation of both well-established risk factors (such as age and clinical variables) and emerging risk factors (e.g., image features) within a unified framework. However, when the dimension of parametric components exceeds the sample size, the task of model fitting becomes formidable, while nonparametric modeling grapples with the curse of dimensionality. We propose a novel Penalized Deep Partially Linear Cox Model (Penalized DPLC), which incorporates the SCAD penalty to select important texture features and employs a deep neural network to estimate the nonparametric component of the model. We prove the convergence and asymptotic properties of the estimator and compare it to other methods through extensive simulation studies, evaluating its performance in risk prediction and feature selection. The proposed method is applied to the NLST study dataset to uncover the effects of key clinical and imaging risk factors on patients' survival. Our findings provide valuable insights into the relationship between these factors and survival outcomes.

Ledan Qian, Xiao Zhou, Yi Li et al.

As an essential prerequisite for developing a medical intelligent assistant system, medical image segmentation has received extensive research and concentration from the neural network community. A series of UNet-like networks with encoder-decoder architecture has achieved extraordinary success, in which UNet2+ and UNet3+ redesign skip connections, respectively proposing dense skip connection and full-scale skip connection and dramatically improving compared with UNet in medical image segmentation. However, UNet2+ lacks sufficient information explored from the full scale, which will affect the learning of organs' location and boundary. Although UNet3+ can obtain the full-scale aggregation feature map, owing to the small number of neurons in the structure, it does not satisfy the segmentation of tiny objects when the number of samples is small. This paper proposes a novel network structure combining dense skip connections and full-scale skip connections, named UNet-sharp (UNet\#) for its shape similar to symbol \#. The proposed UNet\# can aggregate feature maps of different scales in the decoder sub-network and capture fine-grained details and coarse-grained semantics from the full scale, which benefits learning the exact location and accurately segmenting the boundary of organs or lesions. We perform deep supervision for model pruning to speed up testing and make it possible for the model to run on mobile devices; furthermore, designing two classification-guided modules to reduce false positives achieves more accurate segmentation results. Various experiments of semantic segmentation and instance segmentation on different modalities (EM, CT, MRI) and dimensions (2D, 3D) datasets, including the nuclei, brain tumor, liver, and lung, demonstrate that the proposed method outperforms state-of-the-art models.

Stephen Salerno, Yi Li

Prognostication for lung cancer, a leading cause of mortality, remains a complex task, as it needs to quantify the associations of risk factors and health events spanning a patient's entire life. One challenge is that an individual's disease course involves non-terminal (e.g., disease progression) and terminal (e.g., death) events, which form semi-competing relationships. Our motivation comes from the Boston Lung Cancer Study, a large lung cancer survival cohort, which investigates how risk factors influence a patient's disease trajectory. Following developments in the prediction of time-to-event outcomes with neural networks, deep learning has become a focal area for the development of risk prediction methods in survival analysis. However, limited work has been done to predict multi-state or semi-competing risk outcomes, where a patient may experience adverse events such as disease progression prior to death. We propose a novel neural expectation-maximization algorithm to bridge the gap between classical statistical approaches and machine learning. Our algorithm enables estimation of the non-parametric baseline hazards of each state transition, risk functions of predictors, and the degree of dependence among different transitions, via a multi-task deep neural network with transition-specific sub-architectures. We apply our method to the Boston Lung Cancer Study and investigate the impact of clinical and genetic predictors on disease progression and mortality.