Jun Bai

Mohammad Mahdi Behzadi, Mohammad Madani, Hanzhang Wang et al.

Prostate cancer is the most common cancer in men worldwide and the second leading cause of cancer death in the United States. One of the prognostic features in prostate cancer is the Gleason grading of histopathology images. The Gleason grade is assigned based on tumor architecture on Hematoxylin and Eosin (H&E) stained whole slide images (WSI) by the pathologists. This process is time-consuming and has known interobserver variability. In the past few years, deep learning algorithms have been used to analyze histopathology images, delivering promising results for grading prostate cancer. However, most of the algorithms rely on the fully annotated datasets which are expensive to generate. In this work, we proposed a novel weakly-supervised algorithm to classify prostate cancer grades. The proposed algorithm consists of three steps: (1) extracting discriminative areas in a histopathology image by employing the Multiple Instance Learning (MIL) algorithm based on Transformers, (2) representing the image by constructing a graph using the discriminative patches, and (3) classifying the image into its Gleason grades by developing a Graph Convolutional Neural Network (GCN) based on the gated attention mechanism. We evaluated our algorithm using publicly available datasets, including TCGAPRAD, PANDA, and Gleason 2019 challenge datasets. We also cross validated the algorithm on an independent dataset. Results show that the proposed model achieved state-of-the-art performance in the Gleason grading task in terms of accuracy, F1 score, and cohen-kappa. The code is available at https://github.com/NabaviLab/Prostate-Cancer.

Jianfei Zhang, Jun Bai, Chenghua Lin et al.

Variational autoencoders (VAEs) are one of the powerful unsupervised learning frameworks in NLP for latent representation learning and latent-directed generation. The classic optimization goal of VAEs is to maximize the Evidence Lower Bound (ELBo), which consists of a conditional likelihood for generation and a negative Kullback-Leibler (KL) divergence for regularization. In practice, optimizing ELBo often leads the posterior distribution of all samples converge to the same degenerated local optimum, namely posterior collapse or KL vanishing. There are effective ways proposed to prevent posterior collapse in VAEs, but we observe that they in essence make trade-offs between posterior collapse and hole problem, i.e., mismatch between the aggregated posterior distribution and the prior distribution. To this end, we introduce new training objectives to tackle both two problems through a novel regularization based on the probabilistic density gap between the aggregated posterior distribution and the prior distribution. Through experiments on language modeling, latent space visualization and interpolation, we show that our proposed method can solve both problems effectively and thus outperforms the existing methods in latent-directed generation. To the best of our knowledge, we are the first to jointly solve the hole problem and the posterior collapse.

Jun Bai, Zhuofan Chen, Zhenzi Li et al.

Text ranking has witnessed significant advancements, attributed to the utilization of dual-encoder enhanced by Pre-trained Language Models (PLMs). Given the proliferation of available PLMs, selecting the most effective one for a given dataset has become a non-trivial challenge. As a promising alternative to human intuition and brute-force fine-tuning, Transferability Estimation (TE) has emerged as an effective approach to model selection. However, current TE methods are primarily designed for classification tasks, and their estimated transferability may not align well with the objectives of text ranking. To address this challenge, we propose to compute the expected rank as transferability, explicitly reflecting the model's ranking capability. Furthermore, to mitigate anisotropy and incorporate training dynamics, we adaptively scale isotropic sentence embeddings to yield an accurate expected rank score. Our resulting method, Adaptive Ranking Transferability (AiRTran), can effectively capture subtle differences between models. On challenging model selection scenarios across various text ranking datasets, it demonstrates significant improvements over previous classification-oriented TE methods, human intuition, and ChatGPT with minor time consumption.

Jun Bai, Xiaofeng Zhang, Chen Li et al.

Transferability estimation has been attached to great attention in the computer vision fields. Researchers try to estimate with low computational cost the performance of a model when transferred from a source task to a given target task. Considering the effectiveness of such estimations, the communities of natural language processing also began to study similar problems for the selection of pre-trained language models. However, there is a lack of a comprehensive comparison between these estimation methods yet. Also, the differences between vision and language scenarios make it doubtful whether previous conclusions can be established across fields. In this paper, we first conduct a thorough survey of existing transferability estimation methods being able to find the most suitable model, then we conduct a detailed empirical study for the surveyed methods based on the GLUE benchmark. From qualitative and quantitative analyses, we demonstrate the strengths and weaknesses of existing methods and show that H-Score generally performs well with superiorities in effectiveness and efficiency. We also outline the difficulties of consideration of training details, applicability to text generation, and consistency to certain metrics which shed light on future directions.