Wei Shao

Yinya Huang, Ruixin Hong, Hongming Zhang et al.

In this study, we delve into the realm of counterfactual reasoning capabilities of large language models (LLMs). Our primary objective is to cultivate the counterfactual thought processes within LLMs and rigorously assess these processes for their validity. Specifically, we introduce a novel task, Counterfactual Logical Modification (CLOMO), and a high-quality human-annotated benchmark. In this task, LLMs must adeptly alter a given argumentative text to uphold a predetermined logical relationship. To effectively evaluate a generation model's counterfactual capabilities, we propose an innovative evaluation metric, the decomposed Self-Evaluation Score (SES) to directly evaluate the natural language output of LLMs instead of modeling the task as a multiple-choice problem. Analysis shows that the proposed automatic metric aligns well with human preference. Our experimental results show that while LLMs demonstrate a notable capacity for logical counterfactual thinking, there remains a discernible gap between their current abilities and human performance. Code and data are available at https://github.com/Eleanor-H/CLOMO.

Haochen Tan, Wei Shao, Han Wu et al.

Contrastive learning has shown great potential in unsupervised sentence embedding tasks, e.g., SimCSE. However, We find that these existing solutions are heavily affected by superficial features like the length of sentences or syntactic structures. In this paper, we propose a semantics-aware contrastive learning framework for sentence embeddings, termed Pseudo-Token BERT (PT-BERT), which is able to exploit the pseudo-token space (i.e., latent semantic space) representation of a sentence while eliminating the impact of superficial features such as sentence length and syntax. Specifically, we introduce an additional pseudo token embedding layer independent of the BERT encoder to map each sentence into a sequence of pseudo tokens in a fixed length. Leveraging these pseudo sequences, we are able to construct same-length positive and negative pairs based on the attention mechanism to perform contrastive learning. In addition, we utilize both the gradient-updating and momentum-updating encoders to encode instances while dynamically maintaining an additional queue to store the representation of sentence embeddings, enhancing the encoder's learning performance for negative examples. Experiments show that our model outperforms the state-of-the-art baselines on six standard semantic textual similarity (STS) tasks. Furthermore, experiments on alignments and uniformity losses, as well as hard examples with different sentence lengths and syntax, consistently verify the effectiveness of our method.

Ahjol Senbi, Tianyu Huang, Fei Lyu et al.

We explore the feasibility and potential of building a ground-truth-free evaluation model to assess the quality of segmentations generated by the Segment Anything Model (SAM) and its variants in medical imaging. This evaluation model estimates segmentation quality scores by analyzing the coherence and consistency between the input images and their corresponding segmentation predictions. Based on prior research, we frame the task of training this model as a regression problem within a supervised learning framework, using Dice scores (and optionally other metrics) along with mean squared error to compute the training loss. The model is trained utilizing a large collection of public datasets of medical images with segmentation predictions from SAM and its variants. We name this model EvanySeg (Evaluation of Any Segmentation in Medical Images). Our exploration of convolution-based models (e.g., ResNet) and transformer-based models (e.g., ViT) suggested that ViT yields better performance for this task. EvanySeg can be employed for various tasks, including: (1) identifying poorly segmented samples by detecting low-percentile segmentation quality scores; (2) benchmarking segmentation models without ground truth by averaging quality scores across test samples; (3) alerting human experts to poor-quality segmentation predictions during human-AI collaboration by applying a threshold within the score space; and (4) selecting the best segmentation prediction for each test sample at test time when multiple segmentation models are available, by choosing the prediction with the highest quality score. Models and code will be made available at https://github.com/ahjolsenbics/EvanySeg.

Jirong Yi, Qiaosheng Zhang, Zhen Chen et al.

As one of the central tasks in machine learning, regression finds lots of applications in different fields. An existing common practice for solving regression problems is the mean square error (MSE) minimization approach or its regularized variants which require prior knowledge about the models. Recently, Yi et al., proposed a mutual information based supervised learning framework where they introduced a label entropy regularization which does not require any prior knowledge. When applied to classification tasks and solved via a stochastic gradient descent (SGD) optimization algorithm, their approach achieved significant improvement over the commonly used cross entropy loss and its variants. However, they did not provide a theoretical convergence analysis of the SGD algorithm for the proposed formulation. Besides, applying the framework to regression tasks is nontrivial due to the potentially infinite support set of the label. In this paper, we investigate the regression under the mutual information based supervised learning framework. We first argue that the MSE minimization approach is equivalent to a conditional entropy learning problem, and then propose a mutual information learning formulation for solving regression problems by using a reparameterization technique. For the proposed formulation, we give the convergence analysis of the SGD algorithm for solving it in practice. Finally, we consider a multi-output regression data model where we derive the generalization performance lower bound in terms of the mutual information associated with the underlying data distribution. The result shows that the high dimensionality can be a bless instead of a curse, which is controlled by a threshold. We hope our work will serve as a good starting point for further research on the mutual information based regression.

Wei Shao, Lei Huang, Shuqi Liu et al.

Embedding-based neural topic models could explicitly represent words and topics by embedding them to a homogeneous feature space, which shows higher interpretability. However, there are no explicit constraints for the training of embeddings, leading to a larger optimization space. Also, a clear description of the changes in embeddings and the impact on model performance is still lacking. In this paper, we propose an embedding regularized neural topic model, which applies the specially designed training constraints on word embedding and topic embedding to reduce the optimization space of parameters. To reveal the changes and roles of embeddings, we introduce \textbf{uniformity} into the embedding-based neural topic model as the evaluation metric of embedding space. On this basis, we describe how embeddings tend to change during training via the changes in the uniformity of embeddings. Furthermore, we demonstrate the impact of changes in embeddings in embedding-based neural topic models through ablation studies. The results of experiments on two mainstream datasets indicate that our model significantly outperforms baseline models in terms of the harmony between topic quality and document modeling. This work is the first attempt to exploit uniformity to explore changes in embeddings of embedding-based neural topic models and their impact on model performance to the best of our knowledge.

Jiahao Xu, Wei Shao, Lihui Chen et al.

This paper proposes the DistillCSE framework, which performs contrastive learning under the self-training paradigm with knowledge distillation. The potential advantage of DistillCSE is its self-enhancing feature: using a base model to provide additional supervision signals, a stronger model may be learned through knowledge distillation. However, the vanilla DistillCSE through the standard implementation of knowledge distillation only achieves marginal improvements due to severe overfitting. The further quantitative analyses demonstrate the reason that the standard knowledge distillation exhibits a relatively large variance of the teacher model's logits due to the essence of contrastive learning. To mitigate the issue induced by high variance, this paper accordingly proposed two simple yet effective solutions for knowledge distillation: a Group-P shuffling strategy as an implicit regularization and the averaging logits from multiple teacher components. Experiments on standard benchmarks demonstrate that the proposed DistillCSE outperforms many strong baseline methods and yields a new state-of-the-art performance.

Muhammad Imran, Jonathan R. Krebs, Vishal Balaji Sivaraman et al.

Multi-class segmentation of the aorta in computed tomography angiography (CTA) scans is essential for diagnosing and planning complex endovascular treatments for patients with aortic dissections. However, existing methods reduce aortic segmentation to a binary problem, limiting their ability to measure diameters across different branches and zones. Furthermore, no open-source dataset is currently available to support the development of multi-class aortic segmentation methods. To address this gap, we organized the AortaSeg24 MICCAI Challenge, introducing the first dataset of 100 CTA volumes annotated for 23 clinically relevant aortic branches and zones. This dataset was designed to facilitate both model development and validation. The challenge attracted 121 teams worldwide, with participants leveraging state-of-the-art frameworks such as nnU-Net and exploring novel techniques, including cascaded models, data augmentation strategies, and custom loss functions. We evaluated the submitted algorithms using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD), highlighting the approaches adopted by the top five performing teams. This paper presents the challenge design, dataset details, evaluation metrics, and an in-depth analysis of the top-performing algorithms. The annotated dataset, evaluation code, and implementations of the leading methods are publicly available to support further research. All resources can be accessed at https://aortaseg24.grand-challenge.org.

Muhammad Imran, Jonathan R Krebs, Veera Rajasekhar Reddy Gopu et al.

Advancements in medical imaging and endovascular grafting have facilitated minimally invasive treatments for aortic diseases. Accurate 3D segmentation of the aorta and its branches is crucial for interventions, as inaccurate segmentation can lead to erroneous surgical planning and endograft construction. Previous methods simplified aortic segmentation as a binary image segmentation problem, overlooking the necessity of distinguishing between individual aortic branches. In this paper, we introduce Context Infused Swin-UNet (CIS-UNet), a deep learning model designed for multi-class segmentation of the aorta and thirteen aortic branches. Combining the strengths of Convolutional Neural Networks (CNNs) and Swin transformers, CIS-UNet adopts a hierarchical encoder-decoder structure comprising a CNN encoder, symmetric decoder, skip connections, and a novel Context-aware Shifted Window Self-Attention (CSW-SA) as the bottleneck block. Notably, CSW-SA introduces a unique utilization of the patch merging layer, distinct from conventional Swin transformers. It efficiently condenses the feature map, providing a global spatial context and enhancing performance when applied at the bottleneck layer, offering superior computational efficiency and segmentation accuracy compared to the Swin transformers. We trained our model on computed tomography (CT) scans from 44 patients and tested it on 15 patients. CIS-UNet outperformed the state-of-the-art SwinUNetR segmentation model, which is solely based on Swin transformers, by achieving a superior mean Dice coefficient of 0.713 compared to 0.697, and a mean surface distance of 2.78 mm compared to 3.39 mm. CIS-UNet's superior 3D aortic segmentation offers improved precision and optimization for planning endovascular treatments. Our dataset and code will be publicly available.

Muhammad Imran, Wayne G. Brisbane, Li-Ming Su et al.

Background and objective: Micro-ultrasound (micro-US) is a novel imaging modality with diagnostic accuracy comparable to MRI for detecting clinically significant prostate cancer (csPCa). We investigated whether artificial intelligence (AI) interpretation of micro-US can outperform clinical screening methods using PSA and digital rectal examination (DRE). Methods: We retrospectively studied 145 men who underwent micro-US guided biopsy (79 with csPCa, 66 without). A self-supervised convolutional autoencoder was used to extract deep image features from 2D micro-US slices. Random forest classifiers were trained using five-fold cross-validation to predict csPCa at the slice level. Patients were classified as csPCa-positive if 88 or more consecutive slices were predicted positive. Model performance was compared with a classifier using PSA, DRE, prostate volume, and age. Key findings and limitations: The AI-based micro-US model and clinical screening model achieved AUROCs of 0.871 and 0.753, respectively. At a fixed threshold, the micro-US model achieved 92.5% sensitivity and 68.1% specificity, while the clinical model showed 96.2% sensitivity but only 27.3% specificity. Limitations include a retrospective single-center design and lack of external validation. Conclusions and clinical implications: AI-interpreted micro-US improves specificity while maintaining high sensitivity for csPCa detection. This method may reduce unnecessary biopsies and serve as a low-cost alternative to PSA-based screening. Patient summary: We developed an AI system to analyze prostate micro-ultrasound images. It outperformed PSA and DRE in detecting aggressive cancer and may help avoid unnecessary biopsies.

Lichun Zhang, Steve Ran Zhou, Moon Hyung Choi et al. · stanford

Prostate cancer is a leading cause of cancer-related deaths among men. The recent development of high frequency, micro-ultrasound imaging offers improved resolution compared to conventional ultrasound and potentially a better ability to differentiate clinically significant cancer from normal tissue. However, the features of prostate cancer remain subtle, with ambiguous borders with normal tissue and large variations in appearance, making it challenging for both machine learning and humans to localize it on micro-ultrasound images. We propose a novel Mask Enhanced Deeply-supervised Micro-US network, termed MedMusNet, to automatically and more accurately segment prostate cancer to be used as potential targets for biopsy procedures. MedMusNet leverages predicted masks of prostate cancer to enforce the learned features layer-wisely within the network, reducing the influence of noise and improving overall consistency across frames. MedMusNet successfully detected 76% of clinically significant cancer with a Dice Similarity Coefficient of 0.365, significantly outperforming the baseline Swin-M2F in specificity and accuracy (Wilcoxon test, Bonferroni correction, p-value<0.05). While the lesion-level and patient-level analyses showed improved performance compared to human experts and different baseline, the improvements did not reach statistical significance, likely on account of the small cohort. We have presented a novel approach to automatically detect and segment clinically significant prostate cancer on B-mode micro-ultrasound images. Our MedMusNet model outperformed other models, surpassing even human experts. These preliminary results suggest the potential for aiding urologists in prostate cancer diagnosis via biopsy and treatment decision-making.

Muhammad Imran, Brianna Nguyen, Jake Pensa et al.

Early diagnosis of prostate cancer significantly improves a patient's 5-year survival rate. Biopsy of small prostate cancers is improved with image-guided biopsy. MRI-ultrasound fusion-guided biopsy is sensitive to smaller tumors but is underutilized due to the high cost of MRI and fusion equipment. Micro-ultrasound (micro-US), a novel high-resolution ultrasound technology, provides a cost-effective alternative to MRI while delivering comparable diagnostic accuracy. However, the interpretation of micro-US is challenging due to subtle gray scale changes indicating cancer vs normal tissue. This challenge can be addressed by training urologists with a large dataset of micro-US images containing the ground truth cancer outlines. Such a dataset can be mapped from surgical specimens (histopathology) onto micro-US images via image registration. In this paper, we present a semi-automated pipeline for registering in vivo micro-US images with ex vivo whole-mount histopathology images. Our pipeline begins with the reconstruction of pseudo-whole-mount histopathology images and a 3-dimensional (3D) micro-US volume. Each pseudo-whole-mount histopathology image is then registered with the corresponding axial micro-US slice using a two-stage approach that estimates an affine transformation followed by a deformable transformation. We evaluated our registration pipeline using micro-US and histopathology images from 18 patients who underwent radical prostatectomy. The results showed a Dice coefficient of 0.94 and a landmark error of 2.7 mm, indicating the accuracy of our registration pipeline. This proof-of-concept study demonstrates the feasibility of accurately aligning micro-US and histopathology images. To promote transparency and collaboration in research, we will make our code and dataset publicly available.

Jiahao Xu, Wei Shao, Lihui Chen et al.

This paper improves contrastive learning for sentence embeddings from two perspectives: handling dropout noise and addressing feature corruption. Specifically, for the first perspective, we identify that the dropout noise from negative pairs affects the model's performance. Therefore, we propose a simple yet effective method to deal with such type of noise. Secondly, we pinpoint the rank bottleneck of current solutions to feature corruption and propose a dimension-wise contrastive learning objective to address this issue. Both proposed methods are generic and can be applied to any contrastive learning based models for sentence embeddings. Experimental results on standard benchmarks demonstrate that combining both proposed methods leads to a gain of 1.8 points compared to the strong baseline SimCSE configured with BERT base. Furthermore, applying the proposed method to DiffCSE, another strong contrastive learning based baseline, results in a gain of 1.4 points.

Haochen Tan, Han Wu, Wei Shao et al.

Meetings typically involve multiple participants and lengthy conversations, resulting in redundant and trivial content. To overcome these challenges, we propose a two-step framework, Reconstruct before Summarize (RbS), for effective and efficient meeting summarization. RbS first leverages a self-supervised paradigm to annotate essential contents by reconstructing the meeting transcripts. Secondly, we propose a relative positional bucketing (RPB) algorithm to equip (conventional) summarization models to generate the summary. Despite the additional reconstruction process, our proposed RPB significantly compressed the input, leading to faster processing and reduced memory consumption compared to traditional summarization methods. We validate the effectiveness and efficiency of our method through extensive evaluations and analysis. On two meeting summarization datasets, AMI and ICSI, our approach outperforms previous state-of-the-art approaches without relying on large-scale pre-training or expert-grade annotating tools.

Wei Li, Wei Shao, Shaoxiong Ji et al.

Sentiment analysis in conversations has gained increasing attention in recent years for the growing amount of applications it can serve, e.g., sentiment analysis, recommender systems, and human-robot interaction. The main difference between conversational sentiment analysis and single sentence sentiment analysis is the existence of context information which may influence the sentiment of an utterance in a dialogue. How to effectively encode contextual information in dialogues, however, remains a challenge. Existing approaches employ complicated deep learning structures to distinguish different parties in a conversation and then model the context information. In this paper, we propose a fast, compact and parameter-efficient party-ignorant framework named bidirectional emotional recurrent unit for conversational sentiment analysis. In our system, a generalized neural tensor block followed by a two-channel classifier is designed to perform context compositionality and sentiment classification, respectively. Extensive experiments on three standard datasets demonstrate that our model outperforms the state of the art in most cases.