Xin Gao

Juexiao Zhou, Longxi Zhou, Di Wang et al. · tsinghua

Heterogeneous data is endemic due to the use of diverse models and settings of devices by hospitals in the field of medical imaging. However, there are few open-source frameworks for federated heterogeneous medical image analysis with personalization and privacy protection simultaneously without the demand to modify the existing model structures or to share any private data. In this paper, we proposed PPPML-HMI, an open-source learning paradigm for personalized and privacy-preserving federated heterogeneous medical image analysis. To our best knowledge, personalization and privacy protection were achieved simultaneously for the first time under the federated scenario by integrating the PerFedAvg algorithm and designing our novel cyclic secure aggregation with the homomorphic encryption algorithm. To show the utility of PPPML-HMI, we applied it to a simulated classification task namely the classification of healthy people and patients from the RAD-ChestCT Dataset, and one real-world segmentation task namely the segmentation of lung infections from COVID-19 CT scans. For the real-world task, PPPML-HMI achieved $\sim$5\% higher Dice score on average compared to conventional FL under the heterogeneous scenario. Meanwhile, we applied the improved deep leakage from gradients to simulate adversarial attacks and showed the solid privacy-preserving capability of PPPML-HMI. By applying PPPML-HMI to both tasks with different neural networks, a varied number of users, and sample sizes, we further demonstrated the strong robustness of PPPML-HMI.

Juexiao Zhou, Haoyang Li, Xingyu Liao et al. · tsinghua

Revoking personal private data is one of the basic human rights, which has already been sheltered by several privacy-preserving laws in many countries. However, with the development of data science, machine learning and deep learning techniques, this right is usually neglected or violated as more and more patients' data are being collected and used for model training, especially in intelligent healthcare, thus making intelligent healthcare a sector where technology must meet the law, regulations, and privacy principles to ensure that the innovation is for the common good. In order to secure patients' right to be forgotten, we proposed a novel solution by using auditing to guide the forgetting process, where auditing means determining whether a dataset has been used to train the model and forgetting requires the information of a query dataset to be forgotten from the target model. We unified these two tasks by introducing a new approach called knowledge purification. To implement our solution, we developed AFS, a unified open-source software, which is able to evaluate and revoke patients' private data from pre-trained deep learning models. We demonstrated the generality of AFS by applying it to four tasks on different datasets with various data sizes and architectures of deep learning networks. The software is publicly available at \url{https://github.com/JoshuaChou2018/AFS}.

Shubo Tian, Qiao Jin, Lana Yeganova et al. · tsinghua

ChatGPT has drawn considerable attention from both the general public and domain experts with its remarkable text generation capabilities. This has subsequently led to the emergence of diverse applications in the field of biomedicine and health. In this work, we examine the diverse applications of large language models (LLMs), such as ChatGPT, in biomedicine and health. Specifically we explore the areas of biomedical information retrieval, question answering, medical text summarization, information extraction, and medical education, and investigate whether LLMs possess the transformative power to revolutionize these tasks or whether the distinct complexities of biomedical domain presents unique challenges. Following an extensive literature survey, we find that significant advances have been made in the field of text generation tasks, surpassing the previous state-of-the-art methods. For other applications, the advances have been modest. Overall, LLMs have not yet revolutionized biomedicine, but recent rapid progress indicates that such methods hold great potential to provide valuable means for accelerating discovery and improving health. We also find that the use of LLMs, like ChatGPT, in the fields of biomedicine and health entails various risks and challenges, including fabricated information in its generated responses, as well as legal and privacy concerns associated with sensitive patient data. We believe this survey can provide a comprehensive and timely overview to biomedical researchers and healthcare practitioners on the opportunities and challenges associated with using ChatGPT and other LLMs for transforming biomedicine and health.

Xiuying Chen, Hind Alamro, Mingzhe Li et al. · pku

The related work section is an important component of a scientific paper, which highlights the contribution of the target paper in the context of the reference papers. Authors can save their time and effort by using the automatically generated related work section as a draft to complete the final related work. Most of the existing related work section generation methods rely on extracting off-the-shelf sentences to make a comparative discussion about the target work and the reference papers. However, such sentences need to be written in advance and are hard to obtain in practice. Hence, in this paper, we propose an abstractive target-aware related work generator (TAG), which can generate related work sections consisting of new sentences. Concretely, we first propose a target-aware graph encoder, which models the relationships between reference papers and the target paper with target-centered attention mechanisms. In the decoding process, we propose a hierarchical decoder that attends to the nodes of different levels in the graph with keyphrases as semantic indicators. Finally, to generate a more informative related work, we propose multi-level contrastive optimization objectives, which aim to maximize the mutual information between the generated related work with the references and minimize that with non-references. Extensive experiments on two public scholar datasets show that the proposed model brings substantial improvements over several strong baselines in terms of automatic and tailored human evaluations.

Junbo Yin, Jianbing Shen, Xin Gao et al.

Previous works for LiDAR-based 3D object detection mainly focus on the single-frame paradigm. In this paper, we propose to detect 3D objects by exploiting temporal information in multiple frames, i.e., the point cloud videos. We empirically categorize the temporal information into short-term and long-term patterns. To encode the short-term data, we present a Grid Message Passing Network (GMPNet), which considers each grid (i.e., the grouped points) as a node and constructs a k-NN graph with the neighbor grids. To update features for a grid, GMPNet iteratively collects information from its neighbors, thus mining the motion cues in grids from nearby frames. To further aggregate the long-term frames, we propose an Attentive Spatiotemporal Transformer GRU (AST-GRU), which contains a Spatial Transformer Attention (STA) module and a Temporal Transformer Attention (TTA) module. STA and TTA enhance the vanilla GRU to focus on small objects and better align the moving objects. Our overall framework supports both online and offline video object detection in point clouds. We implement our algorithm based on prevalent anchor-based and anchor-free detectors. The evaluation results on the challenging nuScenes benchmark show the superior performance of our method, achieving the 1st on the leaderboard without any bells and whistles, by the time the paper is submitted.

Juexiao Zhou, Xiuying Chen, Xin Gao

Medical artificial general intelligence (AGI) is an emerging field that aims to develop systems specifically designed for medical applications that possess the ability to understand, learn, and apply knowledge across a wide range of tasks and domains. Large language models (LLMs) represent a significant step towards AGI. However, training cross-domain LLMs in the medical field poses significant challenges primarily attributed to the requirement of collecting data from diverse domains. This task becomes particularly difficult due to privacy restrictions and the scarcity of publicly available medical datasets. Here, we propose Medical AGI (MedAGI), a paradigm to unify domain-specific medical LLMs with the lowest cost, and suggest a possible path to achieve medical AGI. With an increasing number of domain-specific professional multimodal LLMs in the medical field being developed, MedAGI is designed to automatically select appropriate medical models by analyzing users' questions with our novel adaptive expert selection algorithm. It offers a unified approach to existing LLMs in the medical field, eliminating the need for retraining regardless of the introduction of new models. This characteristic renders it a future-proof solution in the dynamically advancing medical domain. To showcase the resilience of MedAGI, we conducted an evaluation across three distinct medical domains: dermatology diagnosis, X-ray diagnosis, and analysis of pathology pictures. The results demonstrated that MedAGI exhibited remarkable versatility and scalability, delivering exceptional performance across diverse domains. Our code is publicly available to facilitate further research at https://github.com/JoshuaChou2018/MedAGI.

Xiuying Chen, Mingzhe Li, Shen Gao et al. · pku

Nowadays, time-stamped web documents related to a general news query floods spread throughout the Internet, and timeline summarization targets concisely summarizing the evolution trajectory of events along the timeline. Unlike traditional document summarization, timeline summarization needs to model the time series information of the input events and summarize important events in chronological order. To tackle this challenge, in this paper, we propose a Unified Timeline Summarizer (UTS) that can generate abstractive and extractive timeline summaries in time order. Concretely, in the encoder part, we propose a graph-based event encoder that relates multiple events according to their content dependency and learns a global representation of each event. In the decoder part, to ensure the chronological order of the abstractive summary, we propose to extract the feature of event-level attention in its generation process with sequential information remained and use it to simulate the evolutionary attention of the ground truth summary. The event-level attention can also be used to assist in extracting summary, where the extracted summary also comes in time sequence. We augment the previous Chinese large-scale timeline summarization dataset and collect a new English timeline dataset. Extensive experiments conducted on these datasets and on the out-of-domain Timeline 17 dataset show that UTS achieves state-of-the-art performance in terms of both automatic and human evaluations.

Xiuying Chen, Mingzhe Li, Xin Gao et al.

Despite the success achieved in neural abstractive summarization based on pre-trained language models, one unresolved issue is that the generated summaries are not always faithful to the input document. There are two possible causes of the unfaithfulness problem: (1) the summarization model fails to understand or capture the gist of the input text, and (2) the model over-relies on the language model to generate fluent but inadequate words. In this work, we propose a Faithfulness Enhanced Summarization model (FES), which is designed for addressing these two problems and improving faithfulness in abstractive summarization. For the first problem, we propose to use question-answering (QA) to examine whether the encoder fully grasps the input document and can answer the questions on the key information in the input. The QA attention on the proper input words can also be used to stipulate how the decoder should attend to the source. For the second problem, we introduce a max-margin loss defined on the difference between the language and the summarization model, aiming to prevent the overconfidence of the language model. Extensive experiments on two benchmark summarization datasets, CNN/DM and XSum, demonstrate that our model significantly outperforms strong baselines. The evaluation of factual consistency also shows that our model generates more faithful summaries than baselines.

Gongning Luo, Kuanquan Wang, Jun Liu et al.

Efficient automatic segmentation of multi-level (i.e. main and branch) pulmonary arteries (PA) in CTPA images plays a significant role in clinical applications. However, most existing methods concentrate only on main PA or branch PA segmentation separately and ignore segmentation efficiency. Besides, there is no public large-scale dataset focused on PA segmentation, which makes it highly challenging to compare the different methods. To benchmark multi-level PA segmentation algorithms, we organized the first \textbf{P}ulmonary \textbf{AR}tery \textbf{SE}gmentation (PARSE) challenge. On the one hand, we focus on both the main PA and the branch PA segmentation. On the other hand, for better clinical application, we assign the same score weight to segmentation efficiency (mainly running time and GPU memory consumption during inference) while ensuring PA segmentation accuracy. We present a summary of the top algorithms and offer some suggestions for efficient and accurate multi-level PA automatic segmentation. We provide the PARSE challenge as open-access for the community to benchmark future algorithm developments at \url{https://parse2022.grand-challenge.org/Parse2022/}.

Xiuying Chen, Guodong Long, Chongyang Tao et al.

A robust summarization system should be able to capture the gist of the document, regardless of the specific word choices or noise in the input. In this work, we first explore the summarization models' robustness against perturbations including word-level synonym substitution and noise. To create semantic-consistent substitutes, we propose a SummAttacker, which is an efficient approach to generating adversarial samples based on language models. Experimental results show that state-of-the-art summarization models have a significant decrease in performance on adversarial and noisy test sets. Next, we analyze the vulnerability of the summarization systems and explore improving the robustness by data augmentation. Specifically, the first brittleness factor we found is the poor understanding of infrequent words in the input. Correspondingly, we feed the encoder with more diverse cases created by SummAttacker in the input space. The other factor is in the latent space, where the attacked inputs bring more variations to the hidden states. Hence, we construct adversarial decoder input and devise manifold softmixing operation in hidden space to introduce more diversity. Experimental results on Gigaword and CNN/DM datasets demonstrate that our approach achieves significant improvements over strong baselines and exhibits higher robustness on noisy, attacked, and clean datasets.

Xiuying Chen, Mingzhe Li, Shen Gao et al.

In a citation graph, adjacent paper nodes share related scientific terms and topics. The graph thus conveys unique structure information of document-level relatedness that can be utilized in the paper summarization task, for exploring beyond the intra-document information. In this work, we focus on leveraging citation graphs to improve scientific paper extractive summarization under different settings. We first propose a Multi-granularity Unsupervised Summarization model (MUS) as a simple and low-cost solution to the task. MUS finetunes a pre-trained encoder model on the citation graph by link prediction tasks. Then, the abstract sentences are extracted from the corresponding paper considering multi-granularity information. Preliminary results demonstrate that citation graph is helpful even in a simple unsupervised framework. Motivated by this, we next propose a Graph-based Supervised Summarization model (GSS) to achieve more accurate results on the task when large-scale labeled data are available. Apart from employing the link prediction as an auxiliary task, GSS introduces a gated sentence encoder and a graph information fusion module to take advantage of the graph information to polish the sentence representation. Experiments on a public benchmark dataset show that MUS and GSS bring substantial improvements over the prior state-of-the-art model.

Xinyu Zhang, Zhiwei Li, Zhenhong Zou et al. · tsinghua

Noise has always been nonnegligible trouble in object detection by creating confusion in model reasoning, thereby reducing the informativeness of the data. It can lead to inaccurate recognition due to the shift in the observed pattern, that requires a robust generalization of the models. To implement a general vision model, we need to develop deep learning models that can adaptively select valid information from multi-modal data. This is mainly based on two reasons. Multi-modal learning can break through the inherent defects of single-modal data, and adaptive information selection can reduce chaos in multi-modal data. To tackle this problem, we propose a universal uncertainty-aware multi-modal fusion model. It adopts a multi-pipeline loosely coupled architecture to combine the features and results from point clouds and images. To quantify the correlation in multi-modal information, we model the uncertainty, as the inverse of data information, in different modalities and embed it in the bounding box generation. In this way, our model reduces the randomness in fusion and generates reliable output. Moreover, we conducted a completed investigation on the KITTI 2D object detection dataset and its derived dirty data. Our fusion model is proven to resist severe noise interference like Gaussian, motion blur, and frost, with only slight degradation. The experiment results demonstrate the benefits of our adaptive fusion. Our analysis on the robustness of multi-modal fusion will provide further insights for future research.

Xiuying Chen, Mingzhe Li, Jiayi Zhang et al.

As it is cumbersome and expensive to acquire a huge amount of data for training neural dialog models, data augmentation is proposed to effectively utilize existing training samples. However, current data augmentation techniques on the dialog generation task mostly augment all cases in the training dataset without considering the intrinsic attributes between different cases. We argue that not all cases are beneficial for augmentation task, and the cases suitable for augmentation should obey the following two attributes: (1) low-quality (the dialog model cannot generate a high-quality response for the case), (2) representative (the case should represent the property of the whole dataset). Herein, we explore this idea by proposing a Selective Data Augmentation framework (SDA) for the response generation task. SDA employs a dual adversarial network to select the lowest quality and most representative data points for augmentation in one stage. Extensive experiments conducted on two publicly available datasets, i.e., DailyDialog and OpenSubtitles, show that our framework can improve the response generation performance with respect to various metrics.

Hongyan Bao, Yufei Han, Yujun Zhou et al.

Our work targets at searching feasible adversarial perturbation to attack a classifier with high-dimensional categorical inputs in a domain-agnostic setting. This is intrinsically an NP-hard knapsack problem where the exploration space becomes explosively larger as the feature dimension increases. Without the help of domain knowledge, solving this problem via heuristic method, such as Branch-and-Bound, suffers from exponential complexity, yet can bring arbitrarily bad attack results. We address the challenge via the lens of multi-armed bandit based combinatorial search. Our proposed method, namely FEAT, treats modifying each categorical feature as pulling an arm in multi-armed bandit programming. Our objective is to achieve highly efficient and effective attack using an Orthogonal Matching Pursuit (OMP)-enhanced Upper Confidence Bound (UCB) exploration strategy. Our theoretical analysis bounding the regret gap of FEAT guarantees its practical attack performance. In empirical analysis, we compare FEAT with other state-of-the-art domain-agnostic attack methods over various real-world categorical data sets of different applications. Substantial experimental observations confirm the expected efficiency and attack effectiveness of FEAT applied in different application scenarios. Our work further hints the applicability of FEAT for assessing the adversarial vulnerability of classification systems with high-dimensional categorical inputs.

Kaiwen Wan, Lei Li, Dengqiang Jia et al.

Medical images are generally acquired with limited field-of-view (FOV), which could lead to incomplete regions of interest (ROI), and thus impose a great challenge on medical image analysis. This is particularly evident for the learning-based multi-target landmark detection, where algorithms could be misleading to learn primarily the variation of background due to the varying FOV, failing the detection of targets. Based on learning a navigation policy, instead of predicting targets directly, reinforcement learning (RL)-based methods have the potential totackle this challenge in an efficient manner. Inspired by this, in this work we propose a multi-agent RL framework for simultaneous multi-target landmark detection. This framework is aimed to learn from incomplete or (and) complete images to form an implicit knowledge of global structure, which is consolidated during the training stage for the detection of targets from either complete or incomplete test images. To further explicitly exploit the global structural information from incomplete images, we propose to embed a shape model into the RL process. With this prior knowledge, the proposed RL model can not only localize dozens of targetssimultaneously, but also work effectively and robustly in the presence of incomplete images. We validated the applicability and efficacy of the proposed method on various multi-target detection tasks with incomplete images from practical clinics, using body dual-energy X-ray absorptiometry (DXA), cardiac MRI and head CT datasets. Results showed that our method could predict whole set of landmarks with incomplete training images up to 80% missing proportion (average distance error 2.29 cm on body DXA), and could detect unseen landmarks in regions with missing image information outside FOV of target images (average distance error 6.84 mm on 3D half-head CT).

Helene Orsini, Hongyan Bao, Yujun Zhou et al.

Machine Learning-as-a-Service systems (MLaaS) have been largely developed for cybersecurity-critical applications, such as detecting network intrusions and fake news campaigns. Despite effectiveness, their robustness against adversarial attacks is one of the key trust concerns for MLaaS deployment. We are thus motivated to assess the adversarial robustness of the Machine Learning models residing at the core of these security-critical applications with categorical inputs. Previous research efforts on accessing model robustness against manipulation of categorical inputs are specific to use cases and heavily depend on domain knowledge, or require white-box access to the target ML model. Such limitations prevent the robustness assessment from being as a domain-agnostic service provided to various real-world applications. We propose a provably optimal yet computationally highly efficient adversarial robustness assessment protocol for a wide band of ML-driven cybersecurity-critical applications. We demonstrate the use of the domain-agnostic robustness assessment method with substantial experimental study on fake news detection and intrusion detection problems.

Xiong Zhou, Xianming Liu, Deming Zhai et al.

One of the main challenges for feature representation in deep learning-based classification is the design of appropriate loss functions that exhibit strong discriminative power. The classical softmax loss does not explicitly encourage discriminative learning of features. A popular direction of research is to incorporate margins in well-established losses in order to enforce extra intra-class compactness and inter-class separability, which, however, were developed through heuristic means, as opposed to rigorous mathematical principles. In this work, we attempt to address this limitation by formulating the principled optimization objective as learning towards the largest margins. Specifically, we firstly define the class margin as the measure of inter-class separability, and the sample margin as the measure of intra-class compactness. Accordingly, to encourage discriminative representation of features, the loss function should promote the largest possible margins for both classes and samples. Furthermore, we derive a generalized margin softmax loss to draw general conclusions for the existing margin-based losses. Not only does this principled framework offer new perspectives to understand and interpret existing margin-based losses, but it also provides new insights that can guide the design of new tools, including sample margin regularization and largest margin softmax loss for the class-balanced case, and zero-centroid regularization for the class-imbalanced case. Experimental results demonstrate the effectiveness of our strategy on a variety of tasks, including visual classification, imbalanced classification, person re-identification, and face verification.

Zhihang Hu, Qinze Yu, Yucheng Guo et al.

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the vast combinatorial search space. Recently, computational approaches, specifically deep learning models have emerged as an efficient way to discover synergistic combinations. While previous methods reported fair performance, their models usually do not take advantage of multi-modal data and they are unable to handle new drugs or cell lines. In this study, we collected data from various datasets covering various drug-related aspects. Then, we take advantage of large-scale pre-training models to generate informative representations and features for drugs, proteins, and diseases. Based on that, a message-passing graph is built on top to propagate information together with graph structure learning flexibility. This is first introduced in the biological networks and enables us to generate pseudo-relations in the graph. Our framework achieves state-of-the-art results in comparison with other deep learning-based methods on synergistic prediction benchmark datasets. We are also capable of inferencing new drug combination data in a test on an independent set released by AstraZeneca, where 10% of improvement over previous methods is observed. In addition, we're robust against unseen drugs and surpass almost 15% AU ROC compared to the second-best model. We believe our framework contributes to both the future wet-lab discovery of novel drugs and the building of promising guidance for precise combination medicine.

Xin Gao

In the field of medical image, deep convolutional neural networks(ConvNets) have achieved great success in the classification, segmentation, and registration tasks thanks to their unparalleled capacity to learn image features. However, these tasks often require large amounts of manually annotated data and are labor-intensive. Therefore, it is of significant importance for us to study unsupervised semantic feature learning tasks. In our work, we propose to learn features in medical images by training ConvNets to recognize the geometric transformation applied to images and present a simple self-supervised task that can easily predict the geometric transformation. We precisely define a set of geometric transformations in mathematical terms and generalize this model to 3D, taking into account the distinction between spatial and time dimensions. We evaluated our self-supervised method on CMR images of different modalities (bSSFP, T2, LGE) and achieved accuracies of 96.4%, 97.5%, and 96.4%, respectively. The code and models of our paper will be published on: https://github.com/gaoxin492/Geometric_Transformation_CMR

Ruochi Zhang, Haoran Wu, Yuting Xiu et al.

In recent years, the scientific community has become increasingly interested on peptides with non-canonical amino acids due to their superior stability and resistance to proteolytic degradation. These peptides present promising modifications to biological, pharmacological, and physiochemical attributes in both endogenous and engineered peptides. Notwithstanding their considerable advantages, the scientific community exhibits a conspicuous absence of an effective pre-trained model adept at distilling feature representations from such complex peptide sequences. We herein propose PepLand, a novel pre-training architecture for representation and property analysis of peptides spanning both canonical and non-canonical amino acids. In essence, PepLand leverages a comprehensive multi-view heterogeneous graph neural network tailored to unveil the subtle structural representations of peptides. Empirical validations underscore PepLand's effectiveness across an array of peptide property predictions, encompassing protein-protein interactions, permeability, solubility, and synthesizability. The rigorous evaluation confirms PepLand's unparalleled capability in capturing salient synthetic peptide features, thereby laying a robust foundation for transformative advances in peptide-centric research domains. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/pepland

Xiong Zhou, Xianming Liu, Deming Zhai et al.

The success of deep neural networks greatly relies on the availability of large amounts of high-quality annotated data, which however are difficult or expensive to obtain. The resulting labels may be class imbalanced, noisy or human biased. It is challenging to learn unbiased classification models from imperfectly annotated datasets, on which we usually suffer from overfitting or underfitting. In this work, we thoroughly investigate the popular softmax loss and margin-based loss, and offer a feasible approach to tighten the generalization error bound by maximizing the minimal sample margin. We further derive the optimality condition for this purpose, which indicates how the class prototypes should be anchored. Motivated by theoretical analysis, we propose a simple yet effective method, namely prototype-anchored learning (PAL), which can be easily incorporated into various learning-based classification schemes to handle imperfect annotation. We verify the effectiveness of PAL on class-imbalanced learning and noise-tolerant learning by extensive experiments on synthetic and real-world datasets.

Juexiao Zhou, Bin Zhang, Xiuying Chen et al.

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the analytical process by requiring minimal user input while delivering detailed step-by-step plans for various bioinformatics tasks. Through rigorous validation by expert bioinformaticians, AutoBA's robustness and adaptability are affirmed across a diverse range of omics analysis cases, including whole genome sequencing (WGS), RNA sequencing (RNA-seq), single-cell RNA-seq, ChIP-seq, and spatial transcriptomics. AutoBA's unique capacity to self-design analysis processes based on input data variations further underscores its versatility. Compared with online bioinformatic services, AutoBA deploys the analysis locally, preserving data privacy. Moreover, different from the predefined pipeline, AutoBA has adaptability in sync with emerging bioinformatics tools. Overall, AutoBA represents a convenient tool, offering robustness and adaptability for complex omics data analysis.

Zixuan Huang, Yunfeng Wang, Zhiwen Chen et al.

Skeleton extraction is a task focused on providing a simple representation of an object by extracting the skeleton from the given binary or RGB image. In recent years many attractive works in skeleton extraction have been made. But as far as we know, there is little research on how to utilize the context information in the binary shape of objects. In this paper, we propose an attention-based model called Context Attention Network (CANet), which integrates the context extraction module in a UNet architecture and can effectively improve the ability of network to extract the skeleton pixels. Meanwhile, we also use some novel techniques including distance transform, weight focal loss to achieve good results on the given dataset. Finally, without model ensemble and with only 80% of the training images, our method achieves 0.822 F1 score during the development phase and 0.8507 F1 score during the final phase of the Pixel SkelNetOn Competition, ranking 1st place on the leaderboard.

Changyu Chen, Xiting Wang, Ting-En Lin et al.

In reasoning tasks, even a minor error can cascade into inaccurate results, leading to suboptimal performance of large language models in such domains. Earlier fine-tuning approaches sought to mitigate this by leveraging more precise supervisory signals from human labeling, larger models, or self-sampling, although at a high cost. Conversely, we develop a method that avoids external resources, relying instead on introducing perturbations to the input. Our training approach randomly masks certain tokens within the chain of thought, a technique we found to be particularly effective for reasoning tasks. When applied to fine-tuning with GSM8K on Llama-2-7B, this method achieved a 5\% improvement in GSM8K accuracy and a 10\% improvement in GSM-IC accuracy over standard supervised fine-tuning with a few codes modified. Furthermore, it is complementary to existing methods. When integrated with related explicit data augmentation methods, it leads to improvements across five datasets of various augmentation methods, as well as two different base models. We further investigate the mechanisms behind this improvement through case studies and quantitative analysis, suggesting that our approach may provide superior support for the model in capturing long-distance dependencies, especially those related to questions. This enhancement could deepen understanding of the premises in questions and prior steps. Our code is available at Github.

Bintao He, Fa Zhang, Chenjie Feng et al.

Advances on cryo-electron imaging technologies have led to a rapidly increasing number of density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational heterogeneity analysis using global alignment and atomic model assembly through local alignment. Here, we propose a fast and accurate global and local cryo-electron microscopy density map alignment method CryoAlign, which leverages local density feature descriptors to capture spatial structure similarities. CryoAlign is the first feature-based EM map alignment tool, in which the employment of feature-based architecture enables the rapid establishment of point pair correspondences and robust estimation of alignment parameters. Extensive experimental evaluations demonstrate the superiority of CryoAlign over the existing methods in both alignment accuracy and speed.

Junbo Yin, Chao Zha, Wenjia He et al.

Existing PLMs generate protein sequences based on a single-condition constraint from a specific modality, struggling to simultaneously satisfy multiple constraints across different modalities. In this work, we introduce CFP-Gen, a novel diffusion language model for Combinatorial Functional Protein GENeration. CFP-Gen facilitates the de novo protein design by integrating multimodal conditions with functional, sequence, and structural constraints. Specifically, an Annotation-Guided Feature Modulation (AGFM) module is introduced to dynamically adjust the protein feature distribution based on composable functional annotations, e.g., GO terms, IPR domains and EC numbers. Meanwhile, the Residue-Controlled Functional Encoding (RCFE) module captures residue-wise interaction to ensure more precise control. Additionally, off-the-shelf 3D structure encoders can be seamlessly integrated to impose geometric constraints. We demonstrate that CFP-Gen enables high-throughput generation of novel proteins with functionality comparable to natural proteins, while achieving a high success rate in designing multifunctional proteins. Code and data available at https://github.com/yinjunbo/cfpgen.

Xiuying Chen, Tairan Wang, Juexiao Zhou et al.

Artificial intelligence (AI) systems, particularly those based on deep learning models, have increasingly achieved expert-level performance in medical applications. However, there is growing concern that such AI systems may reflect and amplify human bias, and reduce the quality of their performance in historically under-served populations. The fairness issue has attracted considerable research interest in the medical imaging classification field, yet it remains understudied in the text generation domain. In this study, we investigate the fairness problem in text generation within the medical field and observe significant performance discrepancies across different races, sexes, and age groups, including intersectional groups, various model scales, and different evaluation metrics. To mitigate this fairness issue, we propose an algorithm that selectively optimizes those underperformed groups to reduce bias. The selection rules take into account not only word-level accuracy but also the pathology accuracy to the target reference, while ensuring that the entire process remains fully differentiable for effective model training. Our evaluations across multiple backbones, datasets, and modalities demonstrate that our proposed algorithm enhances fairness in text generation without compromising overall performance. Specifically, the disparities among various groups across different metrics were diminished by more than 30% with our algorithm, while the relative change in text generation accuracy was typically within 2%. By reducing the bias generated by deep learning models, our proposed approach can potentially alleviate concerns about the fairness and reliability of text generation diagnosis in medical domain. Our code is publicly available to facilitate further research at https://github.com/iriscxy/GenFair.

Yilan Zhang, Li Nanbo, Changchun Yang et al.

The integration of histology images and gene profiles has shown great promise for improving survival prediction in cancer. However, current approaches often struggle to model intra- and inter-modal interactions efficiently and effectively due to the high dimensionality and complexity of the inputs. A major challenge is capturing critical prognostic events that, though few, underlie the complexity of the observed inputs and largely determine patient outcomes. These events, manifested as high-level structural signals such as spatial histologic patterns or pathway co-activations, are typically sparse, patient-specific, and unannotated, making them inherently difficult to uncover. To address this, we propose SlotSPE, a slot-based framework for structural prognostic event modeling. Specifically, inspired by the principle of factorial coding, we compress each patient's multimodal inputs into compact, modality-specific sets of mutually distinctive slots using slot attention. By leveraging these slot representations as encodings for prognostic events, our framework enables both efficient and effective modeling of complex intra- and inter-modal interactions, while also facilitating seamless incorporation of biological priors that enhance prognostic relevance. Extensive experiments on ten cancer benchmarks show that SlotSPE outperforms existing methods in 8 out of 10 cohorts, achieving an overall improvement of 2.9%. It remains robust under missing genomic data and delivers markedly improved interpretability through structured event decomposition.

Qiang Yang, Xiuying Chen, Changsheng Ma et al.

The global impact of the COVID-19 pandemic has highlighted the need for a comprehensive understanding of public sentiment and reactions. Despite the availability of numerous public datasets on COVID-19, some reaching volumes of up to 100 billion data points, challenges persist regarding the availability of labeled data and the presence of coarse-grained or inappropriate sentiment labels. In this paper, we introduce SenWave, a novel fine-grained multi-language sentiment analysis dataset specifically designed for analyzing COVID-19 tweets, featuring ten sentiment categories across five languages. The dataset comprises 10,000 annotated tweets each in English and Arabic, along with 30,000 translated tweets in Spanish, French, and Italian, derived from English tweets. Additionally, it includes over 105 million unlabeled tweets collected during various COVID-19 waves. To enable accurate fine-grained sentiment classification, we fine-tuned pre-trained transformer-based language models using the labeled tweets. Our study provides an in-depth analysis of the evolving emotional landscape across languages, countries, and topics, revealing significant insights over time. Furthermore, we assess the compatibility of our dataset with ChatGPT, demonstrating its robustness and versatility in various applications. Our dataset and accompanying code are publicly accessible on the repository\footnote{https://github.com/gitdevqiang/SenWave}. We anticipate that this work will foster further exploration into fine-grained sentiment analysis for complex events within the NLP community, promoting more nuanced understanding and research innovations.

Zinan Tang, Xin Gao, Qizhi Pei et al.

Supervised Fine-Tuning (SFT) Large Language Models (LLM) fundamentally rely on high-quality training data. While data selection and data synthesis are two common strategies to improve data quality, existing approaches often face limitations in static dataset curation that fail to adapt to evolving model capabilities. In this paper, we introduce Middo, a self-evolving Model-informed dynamic data optimization framework that uses model-aware data selection and context-preserving data refinement. Unlike conventional one-off filtering/synthesis methods, our framework establishes a closed-loop optimization system: (1) A self-referential diagnostic module proactively identifies suboptimal samples through tri-axial model signals - loss patterns (complexity), embedding cluster dynamics (diversity), and self-alignment scores (quality); (2) An adaptive optimization engine then transforms suboptimal samples into pedagogically valuable training points while preserving semantic integrity; (3) This optimization process continuously evolves with model capability through dynamic learning principles. Experiments on multiple benchmarks demonstrate that our Middo consistently enhances the quality of seed data and boosts LLM's performance with improving accuracy by 7.15% on average while maintaining the original dataset scale. This work establishes a new paradigm for sustainable LLM training through dynamic human-AI co-evolution of data and models. Our datasets, models, and code are publicly available at https://github.com/Word2VecT/Middo.

Yibo Gao, Zheyao Gao, Xin Gao et al.

Due to the high stakes in medical decision-making, there is a compelling demand for interpretable deep learning methods in medical image analysis. Concept Bottleneck Models (CBM) have emerged as an active interpretable framework incorporating human-interpretable concepts into decision-making. However, their concept predictions may lack reliability when applied to clinical diagnosis, impeding concept explanations' quality. To address this, we propose an evidential Concept Embedding Model (evi-CEM), which employs evidential learning to model the concept uncertainty. Additionally, we offer to leverage the concept uncertainty to rectify concept misalignments that arise when training CBMs using vision-language models without complete concept supervision. With the proposed methods, we can enhance concept explanations' reliability for both supervised and label-efficient settings. Furthermore, we introduce concept uncertainty for effective test-time intervention. Our evaluation demonstrates that evi-CEM achieves superior performance in terms of concept prediction, and the proposed concept rectification effectively mitigates concept misalignments for label-efficient training. Our code is available at https://github.com/obiyoag/evi-CEM.

Xiuying Chen, Mingzhe Li, Shen Gao et al.

A proficient summarization model should exhibit both flexibility -- the capacity to handle a range of in-domain summarization tasks, and adaptability -- the competence to acquire new knowledge and adjust to unseen out-of-domain tasks. Unlike large language models (LLMs) that achieve this through parameter scaling, we propose a more parameter-efficient approach in this study. Our motivation rests on the principle that the general summarization ability to capture salient information can be shared across different tasks, while the domain-specific summarization abilities need to be distinct and tailored. Concretely, we propose MoeSumm, a Mixture-of-Expert Summarization architecture, which utilizes a main expert for gaining the general summarization capability and deputy experts that selectively collaborate to meet specific summarization task requirements. We further propose a max-margin loss to stimulate the separation of these abilities. Our model's distinct separation of general and domain-specific summarization abilities grants it with notable flexibility and adaptability, all while maintaining parameter efficiency. MoeSumm achieves flexibility by managing summarization across multiple domains with a single model, utilizing a shared main expert and selected deputy experts. It exhibits adaptability by tailoring deputy experts to cater to out-of-domain few-shot and zero-shot scenarios. Experimental results on 11 datasets show the superiority of our model compared with recent baselines and LLMs. We also provide statistical and visual evidence of the distinct separation of the two abilities in MoeSumm (https://github.com/iriscxy/MoE_Summ).

Ruochi Zhang, Haoran Wu, Chang Liu et al.

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/PepHarmony or http://www.healthinformaticslab.org/supp/.

Xiong Zhou, Xianming Liu, Junjun Jiang et al.

Robust loss functions are essential for training deep neural networks with better generalization power in the presence of noisy labels. Symmetric loss functions are confirmed to be robust to label noise. However, the symmetric condition is overly restrictive. In this work, we propose a new class of loss functions, namely \textit{asymmetric loss functions}, which are robust to learning with noisy labels for various types of noise. We investigate general theoretical properties of asymmetric loss functions, including classification calibration, excess risk bound, and noise tolerance. Meanwhile, we introduce the asymmetry ratio to measure the asymmetry of a loss function. The empirical results show that a higher ratio would provide better noise tolerance. Moreover, we modify several commonly-used loss functions and establish the necessary and sufficient conditions for them to be asymmetric. Experimental results on benchmark datasets demonstrate that asymmetric loss functions can outperform state-of-the-art methods. The code is available at \href{https://github.com/hitcszx/ALFs}{https://github.com/hitcszx/ALFs}

Zhengzhong Liu, Guanxiong Ding, Avinash Bukkittu et al.

Empirical natural language processing (NLP) systems in application domains (e.g., healthcare, finance, education) involve interoperation among multiple components, ranging from data ingestion, human annotation, to text retrieval, analysis, generation, and visualization. We establish a unified open-source framework to support fast development of such sophisticated NLP workflows in a composable manner. The framework introduces a uniform data representation to encode heterogeneous results by a wide range of NLP tasks. It offers a large repository of processors for NLP tasks, visualization, and annotation, which can be easily assembled with full interoperability under the unified representation. The highly extensible framework allows plugging in custom processors from external off-the-shelf NLP and deep learning libraries. The whole framework is delivered through two modularized yet integratable open-source projects, namely Forte (for workflow infrastructure and NLP function processors) and Stave (for user interaction, visualization, and annotation).

Yu Li, Chao Huang, Lizhong Ding et al.

Deep learning, which is especially formidable in handling big data, has achieved great success in various fields, including bioinformatics. With the advances of the big data era in biology, it is foreseeable that deep learning will become increasingly important in the field and will be incorporated in vast majorities of analysis pipelines. In this review, we provide both the exoteric introduction of deep learning, and concrete examples and implementations of its representative applications in bioinformatics. We start from the recent achievements of deep learning in the bioinformatics field, pointing out the problems which are suitable to use deep learning. After that, we introduce deep learning in an easy-to-understand fashion, from shallow neural networks to legendary convolutional neural networks, legendary recurrent neural networks, graph neural networks, generative adversarial networks, variational autoencoder, and the most recent state-of-the-art architectures. After that, we provide eight examples, covering five bioinformatics research directions and all the four kinds of data type, with the implementation written in Tensorflow and Keras. Finally, we discuss the common issues, such as overfitting and interpretability, that users will encounter when adopting deep learning methods and provide corresponding suggestions. The implementations are freely available at \url{https://github.com/lykaust15/Deep_learning_examples}.

Yu Li, Lizhong Ding, Xin Gao

While deep learning models and techniques have achieved great empirical success, our understanding of the source of success in many aspects remains very limited. In an attempt to bridge the gap, we investigate the decision boundary of a production deep learning architecture with weak assumptions on both the training data and the model. We demonstrate, both theoretically and empirically, that the last weight layer of a neural network converges to a linear SVM trained on the output of the last hidden layer, for both the binary case and the multi-class case with the commonly used cross-entropy loss. Furthermore, we show empirically that training a neural network as a whole, instead of only fine-tuning the last weight layer, may result in better bias constant for the last weight layer, which is important for generalization. In addition to facilitating the understanding of deep learning, our result can be helpful for solving a broad range of practical problems of deep learning, such as catastrophic forgetting and adversarial attacking. The experiment codes are available at https://github.com/lykaust15/NN_decision_boundary

Yu Li, Zhongxiao Li, Lizhong Ding et al.

A plain well-trained deep learning model often does not have the ability to learn new knowledge without forgetting the previously learned knowledge, which is known as catastrophic forgetting. Here we propose a novel method, SupportNet, to efficiently and effectively solve the catastrophic forgetting problem in the class incremental learning scenario. SupportNet combines the strength of deep learning and support vector machine (SVM), where SVM is used to identify the support data from the old data, which are fed to the deep learning model together with the new data for further training so that the model can review the essential information of the old data when learning the new information. Two powerful consolidation regularizers are applied to stabilize the learned representation and ensure the robustness of the learned model. We validate our method with comprehensive experiments on various tasks, which show that SupportNet drastically outperforms the state-of-the-art incremental learning methods and even reaches similar performance as the deep learning model trained from scratch on both old and new data. Our program is accessible at: https://github.com/lykaust15/SupportNet

Yu Li, Fan Xu, Fa Zhang et al.

Super-resolution fluorescence microscopy, with a resolution beyond the diffraction limit of light, has become an indispensable tool to directly visualize biological structures in living cells at a nanometer-scale resolution. Despite advances in high-density super-resolution fluorescent techniques, existing methods still have bottlenecks, including extremely long execution time, artificial thinning and thickening of structures, and lack of ability to capture latent structures. Here we propose a novel deep learning guided Bayesian inference approach, DLBI, for the time-series analysis of high-density fluorescent images. Our method combines the strength of deep learning and statistical inference, where deep learning captures the underlying distribution of the fluorophores that are consistent with the observed time-series fluorescent images by exploring local features and correlation along time-axis, and statistical inference further refines the ultrastructure extracted by deep learning and endues physical meaning to the final image. Comprehensive experimental results on both real and simulated datasets demonstrate that our method provides more accurate and realistic local patch and large-field reconstruction than the state-of-the-art method, the 3B analysis, while our method is more than two orders of magnitude faster. The main program is available at https://github.com/lykaust15/DLBI

Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf

Motivation: Ontologies are widely used in biology for data annotation, integration, and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of information that characterize ontology classes. Annotations commonly used in ontologies include class labels, descriptions, or synonyms. Despite being a rich source of semantic information, the ontology meta-data are generally unexploited by ontology-based analysis methods such as semantic similarity measures. Results: We propose a novel method, OPA2Vec, to generate vector representations of biological entities in ontologies by combining formal ontology axioms and annotation axioms from the ontology meta-data. We apply a Word2Vec model that has been pre-trained on PubMed abstracts to produce feature vectors from our collected data. We validate our method in two different ways: first, we use the obtained vector representations of proteins as a similarity measure to predict protein-protein interaction (PPI) on two different datasets. Second, we evaluate our method on predicting gene-disease associations based on phenotype similarity by generating vector representations of genes and diseases using a phenotype ontology, and applying the obtained vectors to predict gene-disease associations. These two experiments are just an illustration of the possible applications of our method. OPA2Vec can be used to produce vector representations of any biomedical entity given any type of biomedical ontology. Availability: https://github.com/bio-ontology-research-group/opa2vec Contact: robert.hoehndorf@kaust.edu.sa and xin.gao@kaust.edu.sa.

Xin Yang, Hao Yu, Xin Gao et al.

Data privacy and silos are nontrivial and greatly challenging in many real-world applications. Federated learning is a decentralized approach to training models across multiple local clients without the exchange of raw data from client devices to global servers. However, existing works focus on a static data environment and ignore continual learning from streaming data with incremental tasks. Federated Continual Learning (FCL) is an emerging paradigm to address model learning in both federated and continual learning environments. The key objective of FCL is to fuse heterogeneous knowledge from different clients and retain knowledge of previous tasks while learning on new ones. In this work, we delineate federated learning and continual learning first and then discuss their integration, i.e., FCL, and particular FCL via knowledge fusion. In summary, our motivations are four-fold: we (1) raise a fundamental problem called ''spatial-temporal catastrophic forgetting'' and evaluate its impact on the performance using a well-known method called federated averaging (FedAvg), (2) integrate most of the existing FCL methods into two generic frameworks, namely synchronous FCL and asynchronous FCL, (3) categorize a large number of methods according to the mechanism involved in knowledge fusion, and finally (4) showcase an outlook on the future work of FCL.

Xin Gao, Tianheng Qiu, Xinyu Zhang et al.

Coarse-to-fine schemes are widely used in traditional single-image motion deblur; however, in the context of deep learning, existing multi-scale algorithms not only require the use of complex modules for feature fusion of low-scale RGB images and deep semantics, but also manually generate low-resolution pairs of images that do not have sufficient confidence. In this work, we propose a multi-scale network based on single-input and multiple-outputs(SIMO) for motion deblurring. This simplifies the complexity of algorithms based on a coarse-to-fine scheme. To alleviate restoration defects impacting detail information brought about by using a multi-scale architecture, we combine the characteristics of real-world blurring trajectories with a learnable wavelet transform module to focus on the directional continuity and frequency features of the step-by-step transitions between blurred images to sharp images. In conclusion, we propose a multi-scale network with a learnable discrete wavelet transform (MLWNet), which exhibits state-of-the-art performance on multiple real-world deblurred datasets, in terms of both subjective and objective quality as well as computational efficiency.

Qingqing Zhu, Xiuying Chen, Qiao Jin et al.

In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging. Current metrics, such as Conventional Natural Language Generation (NLG) and Clinical Efficacy (CE), often fall short in capturing the semantic intricacies of clinical contexts or overemphasize clinical details, undermining report clarity. To overcome these issues, our proposed method synergizes the expertise of professional radiologists with Large Language Models (LLMs), like GPT-3.5 and GPT-4 1. Utilizing In-Context Instruction Learning (ICIL) and Chain of Thought (CoT) reasoning, our approach aligns LLM evaluations with radiologist standards, enabling detailed comparisons between human and AI generated reports. This is further enhanced by a Regression model that aggregates sentence evaluation scores. Experimental results show that our "Detailed GPT-4 (5-shot)" model achieves a 0.48 score, outperforming the METEOR metric by 0.19, while our "Regressed GPT-4" model shows even greater alignment with expert evaluations, exceeding the best existing metric by a 0.35 margin. Moreover, the robustness of our explanations has been validated through a thorough iterative strategy. We plan to publicly release annotations from radiology experts, setting a new standard for accuracy in future assessments. This underscores the potential of our approach in enhancing the quality assessment of AI-driven medical reports.

Yuetan Chu, Gongning Luo, Longxi Zhou et al.

Pulmonary artery-vein segmentation is crucial for disease diagnosis and surgical planning and is traditionally achieved by Computed Tomography Pulmonary Angiography (CTPA). However, concerns regarding adverse health effects from contrast agents used in CTPA have constrained its clinical utility. In contrast, identifying arteries and veins using non-contrast CT, a conventional and low-cost clinical examination routine, has long been considered impossible. Here we propose a High-abundant Pulmonary Artery-vein Segmentation (HiPaS) framework achieving accurate artery-vein segmentation on both non-contrast CT and CTPA across various spatial resolutions. HiPaS first performs spatial normalization on raw CT volumes via a super-resolution module, and then iteratively achieves segmentation results at different branch levels by utilizing the lower-level vessel segmentation as a prior for higher-level vessel segmentation. We trained and validated HiPaS on our established multi-centric dataset comprising 1,073 CT volumes with meticulous manual annotations. Both quantitative experiments and clinical evaluation demonstrated the superior performance of HiPaS, achieving an average dice score of 91.8% and a sensitivity of 98.0%. Further experiments showed the non-inferiority of HiPaS segmentation on non-contrast CT compared to segmentation on CTPA. Employing HiPaS, we have conducted an anatomical study of pulmonary vasculature on 11,784 participants in China (six sites), discovering a new association of pulmonary vessel anatomy with sex, age, and disease states: vessel abundance suggests a significantly higher association with females than males with slightly decreasing with age, and is also influenced by certain diseases, under the controlling of lung volumes.

Xiuying Chen, Tairan Wang, Qingqing Zhu et al.

The summarization capabilities of pretrained and large language models (LLMs) have been widely validated in general areas, but their use in scientific corpus, which involves complex sentences and specialized knowledge, has been less assessed. This paper presents conceptual and experimental analyses of scientific summarization, highlighting the inadequacies of traditional evaluation methods, such as $n$-gram, embedding comparison, and QA, particularly in providing explanations, grasping scientific concepts, or identifying key content. Subsequently, we introduce the Facet-aware Metric (FM), employing LLMs for advanced semantic matching to evaluate summaries based on different aspects. This facet-aware approach offers a thorough evaluation of abstracts by decomposing the evaluation task into simpler subtasks.Recognizing the absence of an evaluation benchmark in this domain, we curate a Facet-based scientific summarization Dataset (FD) with facet-level annotations. Our findings confirm that FM offers a more logical approach to evaluating scientific summaries. In addition, fine-tuned smaller models can compete with LLMs in scientific contexts, while LLMs have limitations in learning from in-context information in scientific domains. This suggests an area for future enhancement of LLMs.

Xiaoqing Zhang, Xiuying Chen, Shen Gao et al.

Information-seeking dialogue systems are widely used in e-commerce systems, with answers that must be tailored to fit the specific settings of the online system. Given the user query, the information-seeking dialogue systems first retrieve a subset of response candidates, then further select the best response from the candidate set through re-ranking. Current methods mainly retrieve response candidates based solely on the current query, however, incorporating similar questions could introduce more diverse content, potentially refining the representation and improving the matching process. Hence, in this paper, we proposed a Query-bag based Pseudo Relevance Feedback framework (QB-PRF), which constructs a query-bag with related queries to serve as pseudo signals to guide information-seeking conversations. Concretely, we first propose a Query-bag Selection module (QBS), which utilizes contrastive learning to train the selection of synonymous queries in an unsupervised manner by leveraging the representations learned from pre-trained VAE. Secondly, we come up with a Query-bag Fusion module (QBF) that fuses synonymous queries to enhance the semantic representation of the original query through multidimensional attention computation. We verify the effectiveness of the QB-PRF framework on two competitive pretrained backbone models, including BERT and GPT-2. Experimental results on two benchmark datasets show that our framework achieves superior performance over strong baselines.

Juexiao Zhou, Zhongyi Han, Mankun Xin et al.

Global population aging presents increasing challenges to healthcare systems, with coronary artery disease (CAD) responsible for approximately 17.8 million deaths annually, making it a leading cause of global mortality. As CAD is largely preventable, early detection and proactive management are essential. In this work, we introduce DigitalShadow, an advanced early warning system for CAD, powered by a fine-tuned facial foundation model. The system is pre-trained on 21 million facial images and subsequently fine-tuned into LiveCAD, a specialized CAD risk assessment model trained on 7,004 facial images from 1,751 subjects across four hospitals in China. DigitalShadow functions passively and contactlessly, extracting facial features from live video streams without requiring active user engagement. Integrated with a personalized database, it generates natural language risk reports and individualized health recommendations. With privacy as a core design principle, DigitalShadow supports local deployment to ensure secure handling of user data.

Xiuying Chen, Shen Gao, Mingzhe Li et al.

Nowadays, neural text generation has made tremendous progress in abstractive summarization tasks. However, most of the existing summarization models take in the whole document all at once, which sometimes cannot meet the needs in practice. Practically, social text streams such as news events and tweets keep growing from time to time, and can only be fed to the summarization system step by step. Hence, in this paper, we propose the task of Stepwise Summarization, which aims to generate a new appended summary each time a new document is proposed. The appended summary should not only summarize the newly added content but also be coherent with the previous summary, to form an up-to-date complete summary. To tackle this challenge, we design an adversarial learning model, named Stepwise Summary Generator (SSG). First, SSG selectively processes the new document under the guidance of the previous summary, obtaining polished document representation. Next, SSG generates the summary considering both the previous summary and the document. Finally, a convolutional-based discriminator is employed to determine whether the newly generated summary is coherent with the previous summary. For the experiment, we extend the traditional two-step update summarization setting to a multi-step stepwise setting, and re-propose a large-scale stepwise summarization dataset based on a public story generation dataset. Extensive experiments on this dataset show that SSG achieves state-of-the-art performance in terms of both automatic metrics and human evaluations. Ablation studies demonstrate the effectiveness of each module in our framework. We also discuss the benefits and limitations of recent large language models on this task.

Xiuying Chen, Mingzhe Li, Shen Gao et al.

Automatic summarization plays an important role in the exponential document growth on the Web. On content websites such as CNN.com and WikiHow.com, there often exist various kinds of side information along with the main document for attention attraction and easier understanding, such as videos, images, and queries. Such information can be used for better summarization, as they often explicitly or implicitly mention the essence of the article. However, most of the existing side-aware summarization methods are designed to incorporate either single-modal or multi-modal side information, and cannot effectively adapt to each other. In this paper, we propose a general summarization framework, which can flexibly incorporate various modalities of side information. The main challenges in designing a flexible summarization model with side information include: (1) the side information can be in textual or visual format, and the model needs to align and unify it with the document into the same semantic space, (2) the side inputs can contain information from various aspects, and the model should recognize the aspects useful for summarization. To address these two challenges, we first propose a unified topic encoder, which jointly discovers latent topics from the document and various kinds of side information. The learned topics flexibly bridge and guide the information flow between multiple inputs in a graph encoder through a topic-aware interaction. We secondly propose a triplet contrastive learning mechanism to align the single-modal or multi-modal information into a unified semantic space, where the summary quality is enhanced by better understanding the document and side information. Results show that our model significantly surpasses strong baselines on three public single-modal or multi-modal benchmark summarization datasets.

Nanyi Fei, Zhiwu Lu, Yizhao Gao et al.

The fundamental goal of artificial intelligence (AI) is to mimic the core cognitive activities of human. Despite tremendous success in the AI research, most of existing methods have only single-cognitive ability. To overcome this limitation and take a solid step towards artificial general intelligence (AGI), we develop a foundation model pre-trained with huge multimodal data, which can be quickly adapted for various downstream cognitive tasks. To achieve this goal, we propose to pre-train our foundation model by self-supervised learning with weak semantic correlation data crawled from the Internet and show that promising results can be obtained on a wide range of downstream tasks. Particularly, with the developed model-interpretability tools, we demonstrate that strong imagination ability is now possessed by our foundation model. We believe that our work makes a transformative stride towards AGI, from our common practice of "weak or narrow AI" to that of "strong or generalized AI".