Jie Zhu

Jie Zhu, Jiyang Qi, Mingyu Ding et al.

In this paper, we are interested in understanding self-supervised pretraining through studying the capability that self-supervised representation pretraining methods learn part-aware representations. The study is mainly motivated by that random views, used in contrastive learning, and random masked (visible) patches, used in masked image modeling, are often about object parts. We explain that contrastive learning is a part-to-whole task: the projection layer hallucinates the whole object representation from the object part representation learned from the encoder, and that masked image modeling is a part-to-part task: the masked patches of the object are hallucinated from the visible patches. The explanation suggests that the self-supervised pretrained encoder is required to understand the object part. We empirically compare the off-the-shelf encoders pretrained with several representative methods on object-level recognition and part-level recognition. The results show that the fully-supervised model outperforms self-supervised models for object-level recognition, and most self-supervised contrastive learning and masked image modeling methods outperform the fully-supervised method for part-level recognition. It is observed that the combination of contrastive learning and masked image modeling further improves the performance.

Xiaoqing Lian, Jie Zhu, Tianxu Lv et al.

Significant differences in protein structures hinder the generalization of existing drug-target interaction (DTI) models, which often rely heavily on pre-learned binding principles or detailed annotations. In contrast, BioBridge designs an Inductive-Associative pipeline inspired by the workflow of scientists who base their accumulated expertise on drawing insights into novel drug-target pairs from weakly related references. BioBridge predicts novel drug-target interactions using limited sequence data, incorporating multi-level encoders with adversarial training to accumulate transferable binding principles. On these principles basis, BioBridge employs a dynamic prototype meta-learning framework to associate insights from weakly related annotations, enabling robust predictions for previously unseen drug-target pairs. Extensive experiments demonstrate that BioBridge surpasses existing models, especially for unseen proteins. Notably, when only homologous protein binding data is available, BioBridge proves effective for virtual screening of the epidermal growth factor receptor and adenosine receptor, underscoring its potential in drug discovery.

Jie Zhu, Huabin Huang, Banghuai Li et al.

Modern semantic segmentation methods devote much effect to adjusting image feature representations to improve the segmentation performance in various ways, such as architecture design, attention mechnism, etc. However, almost all those methods neglect the particularity of class weights (in the classification layer) in segmentation models. In this paper, we notice that the class weights of categories that tend to share many adjacent boundary pixels lack discrimination, thereby limiting the performance. We call this issue Boundary-caused Class Weights Confusion (BCWC). We try to focus on this problem and propose a novel method named Embedded Conditional Random Field (E-CRF) to alleviate it. E-CRF innovatively fuses the CRF into the CNN network as an organic whole for more effective end-to-end optimization. The reasons are two folds. It utilizes CRF to guide the message passing between pixels in high-level features to purify the feature representation of boundary pixels, with the help of inner pixels belonging to the same object. More importantly, it enables optimizing class weights from both scale and direction during backpropagation. We make detailed theoretical analysis to prove it. Besides, superpixel is integrated into E-CRF and served as an auxiliary to exploit the local object prior for more reliable message passing. Finally, our proposed method yields impressive results on ADE20K, Cityscapes, and Pascal Context datasets.

Guangshun Wei, Zhiming Cui, Jie Zhu et al.

Artificial intelligence (AI) technology is increasingly used for digital orthodontics, but one of the challenges is to automatically and accurately detect tooth landmarks and axes. This is partly because of sophisticated geometric definitions of them, and partly due to large variations among individual tooth and across different types of tooth. As such, we propose a deep learning approach with a labeled dataset by professional dentists to the tooth landmark/axis detection on tooth model that are crucial for orthodontic treatments. Our method can extract not only tooth landmarks in the form of point (e.g. cusps), but also axes that measure the tooth angulation and inclination. The proposed network takes as input a 3D tooth model and predicts various types of the tooth landmarks and axes. Specifically, we encode the landmarks and axes as dense fields defined on the surface of the tooth model. This design choice and a set of added components make the proposed network more suitable for extracting sparse landmarks from a given 3D tooth model. Extensive evaluation of the proposed method was conducted on a set of dental models prepared by experienced dentists. Results show that our method can produce tooth landmarks with high accuracy. Our method was examined and justified via comparison with the state-of-the-art methods as well as the ablation studies.

Jie Zhu, Blanca Gallego

We propose a general formulation for continuous treatment recommendation problems in settings with clinical survival data, which we call the Deep Survival Dose Response Function (DeepSDRF). That is, we consider the problem of learning the conditional average dose response (CADR) function solely from historical data in which observed factors (confounders) affect both observed treatment and time-to-event outcomes. The estimated treatment effect from DeepSDRF enables us to develop recommender algorithms with the correction for selection bias. We compared two recommender approaches based on random search and reinforcement learning and found similar performance in terms of patient outcome. We tested the DeepSDRF and the corresponding recommender on extensive simulation studies and the eICU Research Institute (eRI) database. To the best of our knowledge, this is the first time that causal models are used to address the continuous treatment effect with observational data in a medical context.