Yang Nan

IV
h-index69
42papers
1,330citations
Novelty46%
AI Score56

42 Papers

IVSep 5, 2022
Fuzzy Attention Neural Network to Tackle Discontinuity in Airway Segmentation

Yang Nan, Javier Del Ser, Zeyu Tang et al.

Airway segmentation is crucial for the examination, diagnosis, and prognosis of lung diseases, while its manual delineation is unduly burdensome. To alleviate this time-consuming and potentially subjective manual procedure, researchers have proposed methods to automatically segment airways from computerized tomography (CT) images. However, some small-sized airway branches (e.g., bronchus and terminal bronchioles) significantly aggravate the difficulty of automatic segmentation by machine learning models. In particular, the variance of voxel values and the severe data imbalance in airway branches make the computational module prone to discontinuous and false-negative predictions. especially for cohorts with different lung diseases. Attention mechanism has shown the capacity to segment complex structures, while fuzzy logic can reduce the uncertainty in feature representations. Therefore, the integration of deep attention networks and fuzzy theory, given by the fuzzy attention layer, should be an escalated solution for better generalization and robustness. This paper presents an efficient method for airway segmentation, comprising a novel fuzzy attention neural network and a comprehensive loss function to enhance the spatial continuity of airway segmentation. The deep fuzzy set is formulated by a set of voxels in the feature map and a learnable Gaussian membership function. Different from the existing attention mechanism, the proposed channel-specific fuzzy attention addresses the issue of heterogeneous features in different channels. Furthermore, a novel evaluation metric is proposed to assess both the continuity and completeness of airway structures. The efficiency, generalization and robustness of the proposed method have been proved by training on normal lung disease while testing on datasets of lung cancer, COVID-19 and pulmonary fibrosis.

IVMar 10, 2023
Multi-site, Multi-domain Airway Tree Modeling (ATM'22): A Public Benchmark for Pulmonary Airway Segmentation

Minghui Zhang, Yangqian Wu, Hanxiao Zhang et al. · harvard

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.

IVAug 11, 2022
Region-Based Evidential Deep Learning to Quantify Uncertainty and Improve Robustness of Brain Tumor Segmentation

Hao Li, Yang Nan, Javier Del Ser et al.

Despite recent advances in the accuracy of brain tumor segmentation, the results still suffer from low reliability and robustness. Uncertainty estimation is an efficient solution to this problem, as it provides a measure of confidence in the segmentation results. The current uncertainty estimation methods based on quantile regression, Bayesian neural network, ensemble, and Monte Carlo dropout are limited by their high computational cost and inconsistency. In order to overcome these challenges, Evidential Deep Learning (EDL) was developed in recent work but primarily for natural image classification. In this paper, we proposed a region-based EDL segmentation framework that can generate reliable uncertainty maps and robust segmentation results. We used the Theory of Evidence to interpret the output of a neural network as evidence values gathered from input features. Following Subjective Logic, evidence was parameterized as a Dirichlet distribution, and predicted probabilities were treated as subjective opinions. To evaluate the performance of our model on segmentation and uncertainty estimation, we conducted quantitative and qualitative experiments on the BraTS 2020 dataset. The results demonstrated the top performance of the proposed method in quantifying segmentation uncertainty and robustly segmenting tumors. Furthermore, our proposed new framework maintained the advantages of low computational cost and easy implementation and showed the potential for clinical application.

IVJul 19, 2022
Large-Kernel Attention for 3D Medical Image Segmentation

Hao Li, Yang Nan, Javier Del Ser et al.

Automatic segmentation of multiple organs and tumors from 3D medical images such as magnetic resonance imaging (MRI) and computed tomography (CT) scans using deep learning methods can aid in diagnosing and treating cancer. However, organs often overlap and are complexly connected, characterized by extensive anatomical variation and low contrast. In addition, the diversity of tumor shape, location, and appearance, coupled with the dominance of background voxels, makes accurate 3D medical image segmentation difficult. In this paper, a novel large-kernel (LK) attention module is proposed to address these problems to achieve accurate multi-organ segmentation and tumor segmentation. The advantages of convolution and self-attention are combined in the proposed LK attention module, including local contextual information, long-range dependence, and channel adaptation. The module also decomposes the LK convolution to optimize the computational cost and can be easily incorporated into FCNs such as U-Net. Comprehensive ablation experiments demonstrated the feasibility of convolutional decomposition and explored the most efficient and effective network design. Among them, the best Mid-type LK attention-based U-Net network was evaluated on CT-ORG and BraTS 2020 datasets, achieving state-of-the-art segmentation performance. The performance improvement due to the proposed LK attention module was also statistically validated.

IVJul 12, 2022
Human Treelike Tubular Structure Segmentation: A Comprehensive Review and Future Perspectives

Hao Li, Zeyu Tang, Yang Nan et al.

Various structures in human physiology follow a treelike morphology, which often expresses complexity at very fine scales. Examples of such structures are intrathoracic airways, retinal blood vessels, and hepatic blood vessels. Large collections of 2D and 3D images have been made available by medical imaging modalities such as magnetic resonance imaging (MRI), computed tomography (CT), Optical coherence tomography (OCT) and ultrasound in which the spatial arrangement can be observed. Segmentation of these structures in medical imaging is of great importance since the analysis of the structure provides insights into disease diagnosis, treatment planning, and prognosis. Manually labelling extensive data by radiologists is often time-consuming and error-prone. As a result, automated or semi-automated computational models have become a popular research field of medical imaging in the past two decades, and many have been developed to date. In this survey, we aim to provide a comprehensive review of currently publicly available datasets, segmentation algorithms, and evaluation metrics. In addition, current challenges and future research directions are discussed.

IVApr 1, 2022
Data and Physics Driven Learning Models for Fast MRI -- Fundamentals and Methodologies from CNN, GAN to Attention and Transformers

Jiahao Huang, Yingying Fang, Yang Nan et al.

Research studies have shown no qualms about using data driven deep learning models for downstream tasks in medical image analysis, e.g., anatomy segmentation and lesion detection, disease diagnosis and prognosis, and treatment planning. However, deep learning models are not the sovereign remedy for medical image analysis when the upstream imaging is not being conducted properly (with artefacts). This has been manifested in MRI studies, where the scanning is typically slow, prone to motion artefacts, with a relatively low signal to noise ratio, and poor spatial and/or temporal resolution. Recent studies have witnessed substantial growth in the development of deep learning techniques for propelling fast MRI. This article aims to (1) introduce the deep learning based data driven techniques for fast MRI including convolutional neural network and generative adversarial network based methods, (2) survey the attention and transformer based models for speeding up MRI reconstruction, and (3) detail the research in coupling physics and data driven models for MRI acceleration. Finally, we will demonstrate through a few clinical applications, explain the importance of data harmonisation and explainable models for such fast MRI techniques in multicentre and multi-scanner studies, and discuss common pitfalls in current research and recommendations for future research directions.

IVMar 11, 2022
Automatic Fine-grained Glomerular Lesion Recognition in Kidney Pathology

Yang Nan, Fengyi Li, Peng Tang et al.

Recognition of glomeruli lesions is the key for diagnosis and treatment planning in kidney pathology; however, the coexisting glomerular structures such as mesangial regions exacerbate the difficulties of this task. In this paper, we introduce a scheme to recognize fine-grained glomeruli lesions from whole slide images. First, a focal instance structural similarity loss is proposed to drive the model to locate all types of glomeruli precisely. Then an Uncertainty Aided Apportionment Network is designed to carry out the fine-grained visual classification without bounding-box annotations. This double branch-shaped structure extracts common features of the child class from the parent class and produces the uncertainty factor for reconstituting the training dataset. Results of slide-wise evaluation illustrate the effectiveness of the entire scheme, with an 8-22% improvement of the mean Average Precision compared with remarkable detection methods. The comprehensive results clearly demonstrate the effectiveness of the proposed method.

IVAug 4, 2022
Unsupervised Tissue Segmentation via Deep Constrained Gaussian Network

Yang Nan, Peng Tang, Guyue Zhang et al.

Tissue segmentation is the mainstay of pathological examination, whereas the manual delineation is unduly burdensome. To assist this time-consuming and subjective manual step, researchers have devised methods to automatically segment structures in pathological images. Recently, automated machine and deep learning based methods dominate tissue segmentation research studies. However, most machine and deep learning based approaches are supervised and developed using a large number of training samples, in which the pixelwise annotations are expensive and sometimes can be impossible to obtain. This paper introduces a novel unsupervised learning paradigm by integrating an end-to-end deep mixture model with a constrained indicator to acquire accurate semantic tissue segmentation. This constraint aims to centralise the components of deep mixture models during the calculation of the optimisation function. In so doing, the redundant or empty class issues, which are common in current unsupervised learning methods, can be greatly reduced. By validation on both public and in-house datasets, the proposed deep constrained Gaussian network achieves significantly (Wilcoxon signed-rank test) better performance (with the average Dice scores of 0.737 and 0.735, respectively) on tissue segmentation with improved stability and robustness, compared to other existing unsupervised segmentation approaches. Furthermore, the proposed method presents a similar performance (p-value > 0.05) compared to the fully supervised U-Net.

CVAug 16, 2024Code
Beyond the Hype: A dispassionate look at vision-language models in medical scenario

Yang Nan, Huichi Zhou, Xiaodan Xing et al.

Recent advancements in Large Vision-Language Models (LVLMs) have demonstrated remarkable capabilities across diverse tasks, garnering significant attention in AI communities. However, their performance and reliability in specialized domains such as medicine remain insufficiently assessed. In particular, most assessments over-concentrate on evaluating VLMs based on simple Visual Question Answering (VQA) on multi-modality data, while ignoring the in-depth characteristics of LVLMs. In this study, we introduce RadVUQA, a novel Radiological Visual Understanding and Question Answering benchmark, to comprehensively evaluate existing LVLMs. RadVUQA mainly validates LVLMs across five dimensions: 1) Anatomical understanding, assessing the models' ability to visually identify biological structures; 2) Multimodal comprehension, which involves the capability of interpreting linguistic and visual instructions to produce desired outcomes; 3) Quantitative and spatial reasoning, evaluating the models' spatial awareness and proficiency in combining quantitative analysis with visual and linguistic information; 4) Physiological knowledge, measuring the models' capability to comprehend functions and mechanisms of organs and systems; and 5) Robustness, which assesses the models' capabilities against unharmonized and synthetic data. The results indicate that both generalized LVLMs and medical-specific LVLMs have critical deficiencies with weak multimodal comprehension and quantitative reasoning capabilities. Our findings reveal the large gap between existing LVLMs and clinicians, highlighting the urgent need for more robust and intelligent LVLMs. The code is available at https://github.com/Nandayang/RadVUQA

IVJul 3, 2024
Probing Perfection: The Relentless Art of Meddling for Pulmonary Airway Segmentation from HRCT via a Human-AI Collaboration Based Active Learning Method

Shiyi Wang, Yang Nan, Sheng Zhang et al.

In pulmonary tracheal segmentation, the scarcity of annotated data is a prevalent issue in medical segmentation. Additionally, Deep Learning (DL) methods face challenges: the opacity of 'black box' models and the need for performance enhancement. Our Human-Computer Interaction (HCI) based models (RS_UNet, LC_UNet, UUNet, and WD_UNet) address these challenges by combining diverse query strategies with various DL models. We train four HCI models and repeat these steps: (1) Query Strategy: The HCI models select samples that provide the most additional representative information when labeled in each iteration and identify unlabeled samples with the greatest predictive disparity using Wasserstein Distance, Least Confidence, Entropy Sampling, and Random Sampling. (2) Central line correction: Selected samples are used for expert correction of system-generated tracheal central lines in each training round. (3) Update training dataset: Experts update the training dataset after each DL model's training epoch, enhancing the trustworthiness and performance of the models. (4) Model training: The HCI model is trained using the updated dataset and an enhanced UNet version. Experimental results confirm the effectiveness of these HCI-based approaches, showing that WD-UNet, LC-UNet, UUNet, and RS-UNet achieve comparable or superior performance to state-of-the-art DL models. Notably, WD-UNet achieves this with only 15%-35% of the training data, reducing physician annotation time by 65%-85%.

IVJun 20, 2022
CS$^2$: A Controllable and Simultaneous Synthesizer of Images and Annotations with Minimal Human Intervention

Xiaodan Xing, Jiahao Huang, Yang Nan et al.

The destitution of image data and corresponding expert annotations limit the training capacities of AI diagnostic models and potentially inhibit their performance. To address such a problem of data and label scarcity, generative models have been developed to augment the training datasets. Previously proposed generative models usually require manually adjusted annotations (e.g., segmentation masks) or need pre-labeling. However, studies have found that these pre-labeling based methods can induce hallucinating artifacts, which might mislead the downstream clinical tasks, while manual adjustment could be onerous and subjective. To avoid manual adjustment and pre-labeling, we propose a novel controllable and simultaneous synthesizer (dubbed CS$^2$) in this study to generate both realistic images and corresponding annotations at the same time. Our CS$^2$ model is trained and validated using high resolution CT (HRCT) data collected from COVID-19 patients to realize an efficient infections segmentation with minimal human intervention. Our contributions include 1) a conditional image synthesis network that receives both style information from reference CT images and structural information from unsupervised segmentation masks, and 2) a corresponding segmentation mask synthesis network to automatically segment these synthesized images simultaneously. Our experimental studies on HRCT scans collected from COVID-19 patients demonstrate that our CS$^2$ model can lead to realistic synthesized datasets and promising segmentation results of COVID infections compared to the state-of-the-art nnUNet trained and fine-tuned in a fully supervised manner.

CVJul 4, 2023
Graph-Ensemble Learning Model for Multi-label Skin Lesion Classification using Dermoscopy and Clinical Images

Peng Tang, Yang Nan, Tobias Lasser

Many skin lesion analysis (SLA) methods recently focused on developing a multi-modal-based multi-label classification method due to two factors. The first is multi-modal data, i.e., clinical and dermoscopy images, which can provide complementary information to obtain more accurate results than single-modal data. The second one is that multi-label classification, i.e., seven-point checklist (SPC) criteria as an auxiliary classification task can not only boost the diagnostic accuracy of melanoma in the deep learning (DL) pipeline but also provide more useful functions to the clinical doctor as it is commonly used in clinical dermatologist's diagnosis. However, most methods only focus on designing a better module for multi-modal data fusion; few methods explore utilizing the label correlation between SPC and skin disease for performance improvement. This study fills the gap that introduces a Graph Convolution Network (GCN) to exploit prior co-occurrence between each category as a correlation matrix into the DL model for the multi-label classification. However, directly applying GCN degraded the performances in our experiments; we attribute this to the weak generalization ability of GCN in the scenario of insufficient statistical samples of medical data. We tackle this issue by proposing a Graph-Ensemble Learning Model (GELN) that views the prediction from GCN as complementary information of the predictions from the fusion model and adaptively fuses them by a weighted averaging scheme, which can utilize the valuable information from GCN while avoiding its negative influences as much as possible. To evaluate our method, we conduct experiments on public datasets. The results illustrate that our GELN can consistently improve the classification performance on different datasets and that the proposed method can achieve state-of-the-art performance in SPC and diagnosis classification.

IVFeb 28, 2024Code
MambaMIR: An Arbitrary-Masked Mamba for Joint Medical Image Reconstruction and Uncertainty Estimation

Jiahao Huang, Liutao Yang, Fanwen Wang et al.

The recent Mamba model has shown remarkable adaptability for visual representation learning, including in medical imaging tasks. This study introduces MambaMIR, a Mamba-based model for medical image reconstruction, as well as its Generative Adversarial Network-based variant, MambaMIR-GAN. Our proposed MambaMIR inherits several advantages, such as linear complexity, global receptive fields, and dynamic weights, from the original Mamba model. The innovated arbitrary-mask mechanism effectively adapt Mamba to our image reconstruction task, providing randomness for subsequent Monte Carlo-based uncertainty estimation. Experiments conducted on various medical image reconstruction tasks, including fast MRI and SVCT, which cover anatomical regions such as the knee, chest, and abdomen, have demonstrated that MambaMIR and MambaMIR-GAN achieve comparable or superior reconstruction results relative to state-of-the-art methods. Additionally, the estimated uncertainty maps offer further insights into the reliability of the reconstruction quality. The code is publicly available at https://github.com/ayanglab/MambaMIR.

LGJan 14
Interpretable Probability Estimation with LLMs via Shapley Reconstruction

Yang Nan, Qihao Wen, Jiahao Wang et al.

Large Language Models (LLMs) demonstrate potential to estimate the probability of uncertain events, by leveraging their extensive knowledge and reasoning capabilities. This ability can be applied to support intelligent decision-making across diverse fields, such as financial forecasting and preventive healthcare. However, directly prompting LLMs for probability estimation faces significant challenges: their outputs are often noisy, and the underlying predicting process is opaque. In this paper, we propose PRISM: Probability Reconstruction via Shapley Measures, a framework that brings transparency and precision to LLM-based probability estimation. PRISM decomposes an LLM's prediction by quantifying the marginal contribution of each input factor using Shapley values. These factor-level contributions are then aggregated to reconstruct a calibrated final estimate. In our experiments, we demonstrate PRISM improves predictive accuracy over direct prompting and other baselines, across multiple domains including finance, healthcare, and agriculture. Beyond performance, PRISM provides a transparent prediction pipeline: our case studies visualize how individual factors shape the final estimate, helping build trust in LLM-based decision support systems.

LGFeb 2
Embedding Perturbation may Better Reflect the Uncertainty in LLM Reasoning

Qihao Wen, Jiahao Wang, Yang Nan et al.

Large language Models (LLMs) have achieved significant breakthroughs across diverse domains; however, they can still produce unreliable or misleading outputs. For responsible LLM application, Uncertainty Quantification (UQ) techniques are used to estimate a model's uncertainty about its outputs, indicating the likelihood that those outputs may be problematic. For LLM reasoning tasks, it is essential to estimate the uncertainty not only for the final answer, but also for the intermediate steps of the reasoning, as this can enable more fine-grained and targeted interventions. In this study, we explore what UQ metrics better reflect the LLM's ``intermediate uncertainty''during reasoning. Our study reveals that an LLMs' incorrect reasoning steps tend to contain tokens which are highly sensitive to the perturbations on the preceding token embeddings. In this way, incorrect (uncertain) intermediate steps can be readily identified using this sensitivity score as guidance in practice. In our experiments, we show such perturbation-based metric achieves stronger uncertainty quantification performance compared with baseline methods such as token (generation) probability and token entropy. Besides, different from approaches that rely on multiple sampling, the perturbation-based metrics offer better simplicity and efficiency.

IVOct 9, 2023
High Accuracy and Cost-Saving Active Learning 3D WD-UNet for Airway Segmentation

Shiyi Wang, Yang Nan, Simon Walsh et al.

We propose a novel Deep Active Learning (DeepAL) model-3D Wasserstein Discriminative UNet (WD-UNet) for reducing the annotation effort of medical 3D Computed Tomography (CT) segmentation. The proposed WD-UNet learns in a semi-supervised way and accelerates learning convergence to meet or exceed the prediction metrics of supervised learning models. Our method can be embedded with different Active Learning (AL) strategies and different network structures. The model is evaluated on 3D lung airway CT scans for medical segmentation and show that the use of uncertainty metric, which is parametrized as an input of query strategy, leads to more accurate prediction results than some state-of-the-art Deep Learning (DL) supervised models, e.g.,3DUNet and 3D CEUNet. Compared to the above supervised DL methods, our WD-UNet not only saves the cost of annotation for radiologists but also saves computational resources. WD-UNet uses a limited amount of annotated data (35% of the total) to achieve better predictive metrics with a more efficient deep learning model algorithm.

CLFeb 24, 2025Code
Measuring Data Diversity for Instruction Tuning: A Systematic Analysis and A Reliable Metric

Yuming Yang, Yang Nan, Junjie Ye et al.

Data diversity is crucial for the instruction tuning of large language models. Existing studies have explored various diversity-aware data selection methods to construct high-quality datasets and enhance model performance. However, the fundamental problem of precisely defining and measuring data diversity remains underexplored, limiting clear guidance for data engineering. To address this, we systematically analyze 11 existing diversity measurement methods by evaluating their correlation with model performance through extensive fine-tuning experiments. Our results indicate that a reliable diversity measure should properly account for both inter-sample differences and the information density in the sample space. Building on this, we propose NovelSum, a new diversity metric based on sample-level "novelty." Experiments on both simulated and real-world data show that NovelSum accurately captures diversity variations and achieves a 0.97 correlation with instruction-tuned model performance, highlighting its value in guiding data engineering practices. With NovelSum as an optimization objective, we further develop a greedy, diversity-oriented data selection strategy that outperforms existing approaches, validating both the effectiveness and practical significance of our metric. The code is available at https://github.com/UmeanNever/NovelSum.

IVSep 4, 2024
Coupling AI and Citizen Science in Creation of Enhanced Training Dataset for Medical Image Segmentation

Amir Syahmi, Xiangrong Lu, Yinxuan Li et al.

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

CVOct 17, 2024Code
Deep Generative Models Unveil Patterns in Medical Images Through Vision-Language Conditioning

Xiaodan Xing, Junzhi Ning, Yang Nan et al.

Deep generative models have significantly advanced medical imaging analysis by enhancing dataset size and quality. Beyond mere data augmentation, our research in this paper highlights an additional, significant capacity of deep generative models: their ability to reveal and demonstrate patterns in medical images. We employ a generative structure with hybrid conditions, combining clinical data and segmentation masks to guide the image synthesis process. Furthermore, we innovatively transformed the tabular clinical data into textual descriptions. This approach simplifies the handling of missing values and also enables us to leverage large pre-trained vision-language models that investigate the relations between independent clinical entries and comprehend general terms, such as gender and smoking status. Our approach differs from and presents a more challenging task than traditional medical report-guided synthesis due to the less visual correlation of our clinical information with the images. To overcome this, we introduce a text-visual embedding mechanism that strengthens the conditions, ensuring the network effectively utilizes the provided information. Our pipeline is generalizable to both GAN-based and diffusion models. Experiments on chest CT, particularly focusing on the smoking status, demonstrated a consistent intensity shift in the lungs which is in agreement with clinical observations, indicating the effectiveness of our method in capturing and visualizing the impact of specific attributes on medical image patterns. Our methods offer a new avenue for the early detection and precise visualization of complex clinical conditions with deep generative models. All codes are https://github.com/junzhin/DGM-VLC.

LGOct 21, 2025Code
BAPO: Stabilizing Off-Policy Reinforcement Learning for LLMs via Balanced Policy Optimization with Adaptive Clipping

Zhiheng Xi, Xin Guo, Yang Nan et al.

Reinforcement learning (RL) has recently become the core paradigm for aligning and strengthening large language models (LLMs). Yet, applying RL in off-policy settings--where stale data from past policies are used for training--improves sample efficiency, but remains challenging: policy entropy declines sharply, optimization often becomes unstable and may even collapse. Through theoretical and empirical analysis, we identify two key insights: (i) an imbalance in optimization, where negative-advantage samples dominate the policy gradient, suppressing useful behaviors and risking gradient explosions; and (ii) the derived Entropy-Clip Rule, which reveals that the fixed clipping mechanism in PPO-like objectives systematically blocks entropy-increasing updates, thereby driving the policy toward over-exploitation at the expense of exploration. Building on these insights, we propose BAlanced Policy Optimization with Adaptive Clipping (BAPO), a simple yet effective method that dynamically adjusts clipping bounds to adaptively re-balance positive and negative contributions, preserve entropy, and stabilize RL optimization. Across diverse off-policy scenarios--including sample replay and partial rollout--BAPO achieves fast, stable, and data-efficient training. On AIME 2024 and AIME 2025 benchmarks, our 7B BAPO model surpasses open-source counterparts such as SkyWork-OR1-7B, while our 32B BAPO model not only achieves state-of-the-art results among models of the same scale but also outperforms leading proprietary systems like o3-mini and Gemini-2.5-Flash-Thinking.

CLJun 17, 2024Code
Beyond Boundaries: Learning a Universal Entity Taxonomy across Datasets and Languages for Open Named Entity Recognition

Yuming Yang, Wantong Zhao, Caishuang Huang et al.

Open Named Entity Recognition (NER), which involves identifying arbitrary types of entities from arbitrary domains, remains challenging for Large Language Models (LLMs). Recent studies suggest that fine-tuning LLMs on extensive NER data can boost their performance. However, training directly on existing datasets neglects their inconsistent entity definitions and redundant data, limiting LLMs to dataset-specific learning and hindering out-of-domain adaptation. To address this, we present B2NERD, a compact dataset designed to guide LLMs' generalization in Open NER under a universal entity taxonomy. B2NERD is refined from 54 existing English and Chinese datasets using a two-step process. First, we detect inconsistent entity definitions across datasets and clarify them by distinguishable label names to construct a universal taxonomy of 400+ entity types. Second, we address redundancy using a data pruning strategy that selects fewer samples with greater category and semantic diversity. Comprehensive evaluation shows that B2NERD significantly enhances LLMs' Open NER capabilities. Our B2NER models, trained on B2NERD, outperform GPT-4 by 6.8-12.0 F1 points and surpass previous methods in 3 out-of-domain benchmarks across 15 datasets and 6 languages. The data, models, and code are publicly available at https://github.com/UmeanNever/B2NER.

IVOct 31, 2021Code
Calibrating the Dice loss to handle neural network overconfidence for biomedical image segmentation

Michael Yeung, Leonardo Rundo, Yang Nan et al.

The Dice similarity coefficient (DSC) is both a widely used metric and loss function for biomedical image segmentation due to its robustness to class imbalance. However, it is well known that the DSC loss is poorly calibrated, resulting in overconfident predictions that cannot be usefully interpreted in biomedical and clinical practice. Performance is often the only metric used to evaluate segmentations produced by deep neural networks, and calibration is often neglected. However, calibration is important for translation into biomedical and clinical practice, providing crucial contextual information to model predictions for interpretation by scientists and clinicians. In this study, we provide a simple yet effective extension of the DSC loss, named the DSC++ loss, that selectively modulates the penalty associated with overconfident, incorrect predictions. As a standalone loss function, the DSC++ loss achieves significantly improved calibration over the conventional DSC loss across six well-validated open-source biomedical imaging datasets, including both 2D binary and 3D multi-class segmentation tasks. Similarly, we observe significantly improved calibration when integrating the DSC++ loss into four DSC-based loss functions. Finally, we use softmax thresholding to illustrate that well calibrated outputs enable tailoring of recall-precision bias, which is an important post-processing technique to adapt the model predictions to suit the biomedical or clinical task. The DSC++ loss overcomes the major limitation of the DSC loss, providing a suitable loss function for training deep learning segmentation models for use in biomedical and clinical practice. Source code is available at: https://github.com/mlyg/DicePlusPlus.

IVDec 21, 2023
Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge

Yang Nan, Xiaodan Xing, Shiyi Wang et al.

Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway trees remains prohibitively time-consuming. While significant efforts have been made towards enhancing airway modelling, current public-available datasets concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023' (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for prognosis, a strong airway-derived biomarker (Hazard ratio>1.5, p<0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.

LGMay 15, 2024
When AI Eats Itself: On the Caveats of AI Autophagy

Xiaodan Xing, Fadong Shi, Jiahao Huang et al.

Generative Artificial Intelligence (AI) technologies and large models are producing realistic outputs across various domains, such as images, text, speech, and music. Creating these advanced generative models requires significant resources, particularly large and high-quality datasets. To minimise training expenses, many algorithm developers use data created by the models themselves as a cost-effective training solution. However, not all synthetic data effectively improve model performance, necessitating a strategic balance in the use of real versus synthetic data to optimise outcomes. Currently, the previously well-controlled integration of real and synthetic data is becoming uncontrollable. The widespread and unregulated dissemination of synthetic data online leads to the contamination of datasets traditionally compiled through web scraping, now mixed with unlabeled synthetic data. This trend, known as the AI autophagy phenomenon, suggests a future where generative AI systems may increasingly consume their own outputs without discernment, raising concerns about model performance, reliability, and ethical implications. What will happen if generative AI continuously consumes itself without discernment? What measures can we take to mitigate the potential adverse effects? To address these research questions, this study examines the existing literature, delving into the consequences of AI autophagy, analyzing the associated risks, and exploring strategies to mitigate its impact. Our aim is to provide a comprehensive perspective on this phenomenon advocating for a balanced approach that promotes the sustainable development of generative AI technologies in the era of large models.

CVDec 7, 2023
Joint-Individual Fusion Structure with Fusion Attention Module for Multi-Modal Skin Cancer Classification

Peng Tang, Xintong Yan, Yang Nan et al.

Most convolutional neural network (CNN) based methods for skin cancer classification obtain their results using only dermatological images. Although good classification results have been shown, more accurate results can be achieved by considering the patient's metadata, which is valuable clinical information for dermatologists. Current methods only use the simple joint fusion structure (FS) and fusion modules (FMs) for the multi-modal classification methods, there still is room to increase the accuracy by exploring more advanced FS and FM. Therefore, in this paper, we design a new fusion method that combines dermatological images (dermoscopy images or clinical images) and patient metadata for skin cancer classification from the perspectives of FS and FM. First, we propose a joint-individual fusion (JIF) structure that learns the shared features of multi-modality data and preserves specific features simultaneously. Second, we introduce a fusion attention (FA) module that enhances the most relevant image and metadata features based on both the self and mutual attention mechanism to support the decision-making pipeline. We compare the proposed JIF-MMFA method with other state-of-the-art fusion methods on three different public datasets. The results show that our JIF-MMFA method improves the classification results for all tested CNN backbones and performs better than the other fusion methods on the three public datasets, demonstrating our method's effectiveness and robustness

99.4AIMar 31
ASI-Evolve: AI Accelerates AI

Weixian Xu, Tiantian Mi, Yixiu Liu et al.

Can AI accelerate the development of AI itself? While recent agentic systems have shown strong performance on well-scoped tasks with rapid feedback, it remains unclear whether they can tackle the costly, long-horizon, and weakly supervised research loops that drive real AI progress. We present ASI-Evolve, an agentic framework for AI-for-AI research that closes this loop through a learn-design-experiment-analyze cycle. ASI-Evolve augments standard evolutionary agents with two key components: a cognition base that injects accumulated human priors into each round of exploration, and a dedicated analyzer that distills complex experimental outcomes into reusable insights for future iterations. To our knowledge, ASI-Evolve is the first unified framework to demonstrate AI-driven discovery across three central components of AI development: data, architectures, and learning algorithms. In neural architecture design, it discovered 105 SOTA linear attention architectures, with the best discovered model surpassing DeltaNet by +0.97 points, nearly 3x the gain of recent human-designed improvements. In pretraining data curation, the evolved pipeline improves average benchmark performance by +3.96 points, with gains exceeding 18 points on MMLU. In reinforcement learning algorithm design, discovered algorithms outperform GRPO by up to +12.5 points on AMC32, +11.67 points on AIME24, and +5.04 points on OlympiadBench. We further provide initial evidence that this AI-for-AI paradigm can transfer beyond the AI stack through experiments in mathematics and biomedicine. Together, these results suggest that ASI-Evolve represents a promising step toward enabling AI to accelerate AI across the foundational stages of development, offering early evidence for the feasibility of closed-loop AI research.

AIJul 24, 2025
AlphaGo Moment for Model Architecture Discovery

Yixiu Liu, Yang Nan, Weixian Xu et al.

While AI systems demonstrate exponentially improving capabilities, the pace of AI research itself remains linearly bounded by human cognitive capacity, creating an increasingly severe development bottleneck. We present ASI-Arch, the first demonstration of Artificial Superintelligence for AI research (ASI4AI) in the critical domain of neural architecture discovery--a fully autonomous system that shatters this fundamental constraint by enabling AI to conduct its own architectural innovation. Moving beyond traditional Neural Architecture Search (NAS), which is fundamentally limited to exploring human-defined spaces, we introduce a paradigm shift from automated optimization to automated innovation. ASI-Arch can conduct end-to-end scientific research in the domain of architecture discovery, autonomously hypothesizing novel architectural concepts, implementing them as executable code, training and empirically validating their performance through rigorous experimentation and past experience. ASI-Arch conducted 1,773 autonomous experiments over 20,000 GPU hours, culminating in the discovery of 106 innovative, state-of-the-art (SOTA) linear attention architectures. Like AlphaGo's Move 37 that revealed unexpected strategic insights invisible to human players, our AI-discovered architectures demonstrate emergent design principles that systematically surpass human-designed baselines and illuminate previously unknown pathways for architectural innovation. Crucially, we establish the first empirical scaling law for scientific discovery itself--demonstrating that architectural breakthroughs can be scaled computationally, transforming research progress from a human-limited to a computation-scalable process. We provide comprehensive analysis of the emergent design patterns and autonomous research capabilities that enabled these breakthroughs, establishing a blueprint for self-accelerating AI systems.

CLJul 21, 2025
Interaction as Intelligence: Deep Research With Human-AI Partnership

Lyumanshan Ye, Xiaojie Cai, Xinkai Wang et al.

This paper introduces "Interaction as Intelligence" research series, presenting a reconceptualization of human-AI relationships in deep research tasks. Traditional approaches treat interaction merely as an interface for accessing AI capabilities-a conduit between human intent and machine output. We propose that interaction itself constitutes a fundamental dimension of intelligence. As AI systems engage in extended thinking processes for research tasks, meaningful interaction transitions from an optional enhancement to an essential component of effective intelligence. Current deep research systems adopt an "input-wait-output" paradigm where users initiate queries and receive results after black-box processing. This approach leads to error cascade effects, inflexible research boundaries that prevent question refinement during investigation, and missed opportunities for expertise integration. To address these limitations, we introduce Deep Cognition, a system that transforms the human role from giving instructions to cognitive oversight-a mode of engagement where humans guide AI thinking processes through strategic intervention at critical junctures. Deep cognition implements three key innovations: (1)Transparent, controllable, and interruptible interaction that reveals AI reasoning and enables intervention at any point; (2)Fine-grained bidirectional dialogue; and (3)Shared cognitive context where the system observes and adapts to user behaviors without explicit instruction. User evaluation demonstrates that this cognitive oversight paradigm outperforms the strongest baseline across six key metrics: Transparency(+20.0%), Fine-Grained Interaction(+29.2%), Real-Time Intervention(+18.5%), Ease of Collaboration(+27.7%), Results-Worth-Effort(+8.8%), and Interruptibility(+20.7%). Evaluations on challenging research problems show 31.8% to 50.0% points of improvements over deep research systems.

CVMar 12, 2025
Revisiting Medical Image Retrieval via Knowledge Consolidation

Yang Nan, Huichi Zhou, Xiaodan Xing et al.

As artificial intelligence and digital medicine increasingly permeate healthcare systems, robust governance frameworks are essential to ensure ethical, secure, and effective implementation. In this context, medical image retrieval becomes a critical component of clinical data management, playing a vital role in decision-making and safeguarding patient information. Existing methods usually learn hash functions using bottleneck features, which fail to produce representative hash codes from blended embeddings. Although contrastive hashing has shown superior performance, current approaches often treat image retrieval as a classification task, using category labels to create positive/negative pairs. Moreover, many methods fail to address the out-of-distribution (OOD) issue when models encounter external OOD queries or adversarial attacks. In this work, we propose a novel method to consolidate knowledge of hierarchical features and optimisation functions. We formulate the knowledge consolidation by introducing Depth-aware Representation Fusion (DaRF) and Structure-aware Contrastive Hashing (SCH). DaRF adaptively integrates shallow and deep representations into blended features, and SCH incorporates image fingerprints to enhance the adaptability of positive/negative pairings. These blended features further facilitate OOD detection and content-based recommendation, contributing to a secure AI-driven healthcare environment. Moreover, we present a content-guided ranking to improve the robustness and reproducibility of retrieval results. Our comprehensive assessments demonstrate that the proposed method could effectively recognise OOD samples and significantly outperform existing approaches in medical image retrieval (p<0.05). In particular, our method achieves a 5.6-38.9% improvement in mean Average Precision on the anatomical radiology dataset.

CVFeb 12, 2024
Make it more specific: A novel uncertainty based airway segmentation application on 3D U-Net and its variants

Shiyi Wang, Yang Nan, Felder Federico N et al.

Each medical segmentation task should be considered with a specific AI algorithm based on its scenario so that the most accurate prediction model can be obtained. The most popular algorithms in medical segmentation, 3D U-Net and its variants, can directly implement the task of lung trachea segmentation, but its failure to consider the special tree-like structure of the trachea suggests that there is much room for improvement in its segmentation accuracy. Therefore, a research gap exists because a great amount of state-of-the-art DL algorithms are vanilla 3D U-Net structures, which do not introduce the various performance-enhancing modules that come with special natural image modality in lung airway segmentation. In this paper, we proposed two different network structures Branch-Level U-Net (B-UNet) and Branch-Level CE-UNet (B-CE-UNet) which are based on U-Net structure and compared the prediction results with the same dataset. Specially, both of the two networks add branch loss and central line loss to learn the feature of fine branch endings of the airways. Uncertainty estimation algorithms are also included to attain confident predictions and thereby, increase the overall trustworthiness of our whole model. In addition, predictions of the lung trachea based on the maximum connectivity rate were calculated and extracted during post-processing for segmentation refinement and pruning.

CLSep 20, 2025
Analyzing the Effects of Supervised Fine-Tuning on Model Knowledge from Token and Parameter Levels

Junjie Ye, Yuming Yang, Yang Nan et al.

Large language models (LLMs) acquire substantial world knowledge during pre-training, which is further shaped by post-training techniques such as supervised fine-tuning (SFT). However, the impact of SFT on a model's knowledge remains underexplored, limiting our ability to control knowledge change behavior in fine-tuned models. To address this gap, we evaluate closed-book question answering (CBQA) performance across five LLMs from the LLaMA-2 and LLaMA-3 families. Surprisingly, models fine-tuned on 1,920 samples perform up to 14% worse than those fine-tuned on only 240 samples. Furthermore, varying the level of knowledge mastery in the fine-tuning data leads to performance fluctuations of over 12%. To investigate these effects, we analyze model behavior at both the token and parameter levels. Our analysis reveals that up to 90% of parameter updates during SFT do not contribute to knowledge enhancement. Restoring these updates can improve performance on the CBQA task, depending on the characteristics of the fine-tuning data. These insights offer practical guidance for developing fine-tuning strategies that more effectively strengthen model knowledge.

CLAug 28, 2025
Can Multiple Responses from an LLM Reveal the Sources of Its Uncertainty?

Yang Nan, Pengfei He, Ravi Tandon et al.

Large language models (LLMs) have delivered significant breakthroughs across diverse domains but can still produce unreliable or misleading outputs, posing critical challenges for real-world applications. While many recent studies focus on quantifying model uncertainty, relatively little work has been devoted to \textit{diagnosing the source of uncertainty}. In this study, we show that, when an LLM is uncertain, the patterns of disagreement among its multiple generated responses contain rich clues about the underlying cause of uncertainty. To illustrate this point, we collect multiple responses from a target LLM and employ an auxiliary LLM to analyze their patterns of disagreement. The auxiliary model is tasked to reason about the likely source of uncertainty, such as whether it stems from ambiguity in the input question, a lack of relevant knowledge, or both. In cases involving knowledge gaps, the auxiliary model also identifies the specific missing facts or concepts contributing to the uncertainty. In our experiment, we validate our framework on AmbigQA, OpenBookQA, and MMLU-Pro, confirming its generality in diagnosing distinct uncertainty sources. Such diagnosis shows the potential for relevant manual interventions that improve LLM performance and reliability.

AIJun 27, 2024
Learning Pareto Set for Multi-Objective Continuous Robot Control

Tianye Shu, Ke Shang, Cheng Gong et al.

For a control problem with multiple conflicting objectives, there exists a set of Pareto-optimal policies called the Pareto set instead of a single optimal policy. When a multi-objective control problem is continuous and complex, traditional multi-objective reinforcement learning (MORL) algorithms search for many Pareto-optimal deep policies to approximate the Pareto set, which is quite resource-consuming. In this paper, we propose a simple and resource-efficient MORL algorithm that learns a continuous representation of the Pareto set in a high-dimensional policy parameter space using a single hypernet. The learned hypernet can directly generate various well-trained policy networks for different user preferences. We compare our method with two state-of-the-art MORL algorithms on seven multi-objective continuous robot control problems. Experimental results show that our method achieves the best overall performance with the least training parameters. An interesting observation is that the Pareto set is well approximated by a curved line or surface in a high-dimensional parameter space. This observation will provide insight for researchers to design new MORL algorithms.

IVJun 23, 2024
Fuzzy Attention-based Border Rendering Network for Lung Organ Segmentation

Sheng Zhang, Yang Nan, Yingying Fang et al.

Automatic lung organ segmentation on CT images is crucial for lung disease diagnosis. However, the unlimited voxel values and class imbalance of lung organs can lead to false-negative/positive and leakage issues in advanced methods. Additionally, some slender lung organs are easily lost during the recycled down/up-sample procedure, e.g., bronchioles & arterioles, causing severe discontinuity issue. Inspired by these, this paper introduces an effective lung organ segmentation method called Fuzzy Attention-based Border Rendering (FABR) network. Since fuzzy logic can handle the uncertainty in feature extraction, hence the fusion of deep networks and fuzzy sets should be a viable solution for better performance. Meanwhile, unlike prior top-tier methods that operate on all regular dense points, our FABR depicts lung organ regions as cube-trees, focusing only on recycle-sampled border vulnerable points, rendering the severely discontinuous, false-negative/positive organ regions with a novel Global-Local Cube-tree Fusion (GLCF) module. All experimental results, on four challenging datasets of airway & artery, demonstrate that our method can achieve the favorable performance significantly.

CVJun 3, 2024
Deep asymmetric mixture model for unsupervised cell segmentation

Yang Nan, Guang Yang

Automated cell segmentation has become increasingly crucial for disease diagnosis and drug discovery, as manual delineation is excessively laborious and subjective. To address this issue with limited manual annotation, researchers have developed semi/unsupervised segmentation approaches. Among these approaches, the Deep Gaussian mixture model plays a vital role due to its capacity to facilitate complex data distributions. However, these models assume that the data follows symmetric normal distributions, which is inapplicable for data that is asymmetrically distributed. These models also obstacles weak generalization capacity and are sensitive to outliers. To address these issues, this paper presents a novel asymmetric mixture model for unsupervised cell segmentation. This asymmetric mixture model is built by aggregating certain multivariate Gaussian mixture models with log-likelihood and self-supervised-based optimization functions. The proposed asymmetric mixture model outperforms (nearly 2-30% gain in dice coefficient, p<0.05) the existing state-of-the-art unsupervised models on cell segmentation including the segment anything.

CVMay 25, 2023
You Don't Have to Be Perfect to Be Amazing: Unveil the Utility of Synthetic Images

Xiaodan Xing, Federico Felder, Yang Nan et al.

Synthetic images generated from deep generative models have the potential to address data scarcity and data privacy issues. The selection of synthesis models is mostly based on image quality measurements, and most researchers favor synthetic images that produce realistic images, i.e., images with good fidelity scores, such as low Fréchet Inception Distance (FID) and high Peak Signal-To-Noise Ratio (PSNR). However, the quality of synthetic images is not limited to fidelity, and a wide spectrum of metrics should be evaluated to comprehensively measure the quality of synthetic images. In addition, quality metrics are not truthful predictors of the utility of synthetic images, and the relations between these evaluation metrics are not yet clear. In this work, we have established a comprehensive set of evaluators for synthetic images, including fidelity, variety, privacy, and utility. By analyzing more than 100k chest X-ray images and their synthetic copies, we have demonstrated that there is an inevitable trade-off between synthetic image fidelity, variety, and privacy. In addition, we have empirically demonstrated that the utility score does not require images with both high fidelity and high variety. For intra- and cross-task data augmentation, mode-collapsed images and low-fidelity images can still demonstrate high utility. Finally, our experiments have also showed that it is possible to produce images with both high utility and privacy, which can provide a strong rationale for the use of deep generative models in privacy-preserving applications. Our study can shore up comprehensive guidance for the evaluation of synthetic images and elicit further developments for utility-aware deep generative models in medical image synthesis.

IVMay 3, 2023
The Beauty or the Beast: Which Aspect of Synthetic Medical Images Deserves Our Focus?

Xiaodan Xing, Yang Nan, Federico Felder et al.

Training medical AI algorithms requires large volumes of accurately labeled datasets, which are difficult to obtain in the real world. Synthetic images generated from deep generative models can help alleviate the data scarcity problem, but their effectiveness relies on their fidelity to real-world images. Typically, researchers select synthesis models based on image quality measurements, prioritizing synthetic images that appear realistic. However, our empirical analysis shows that high-fidelity and visually appealing synthetic images are not necessarily superior. In fact, we present a case where low-fidelity synthetic images outperformed their high-fidelity counterparts in downstream tasks. Our findings highlight the importance of comprehensive analysis before incorporating synthetic data into real-world applications. We hope our results will raise awareness among the research community of the value of low-fidelity synthetic images in medical AI algorithm training.

NEJan 18, 2022
Benchmarking Subset Selection from Large Candidate Solution Sets in Evolutionary Multi-objective Optimization

Ke Shang, Tianye Shu, Hisao Ishibuchi et al.

In the evolutionary multi-objective optimization (EMO) field, the standard practice is to present the final population of an EMO algorithm as the output. However, it has been shown that the final population often includes solutions which are dominated by other solutions generated and discarded in previous generations. Recently, a new EMO framework has been proposed to solve this issue by storing all the non-dominated solutions generated during the evolution in an archive and selecting a subset of solutions from the archive as the output. The key component in this framework is the subset selection from the archive which usually stores a large number of candidate solutions. However, most studies on subset selection focus on small candidate solution sets for environmental selection. There is no benchmark test suite for large-scale subset selection. This paper aims to fill this research gap by proposing a benchmark test suite for subset selection from large candidate solution sets, and comparing some representative methods using the proposed test suite. The proposed test suite together with the benchmarking studies provides a baseline for researchers to understand, use, compare, and develop subset selection methods in the EMO field.

AIJan 17, 2022
Data Harmonisation for Information Fusion in Digital Healthcare: A State-of-the-Art Systematic Review, Meta-Analysis and Future Research Directions

Yang Nan, Javier Del Ser, Simon Walsh et al.

Removing the bias and variance of multicentre data has always been a challenge in large scale digital healthcare studies, which requires the ability to integrate clinical features extracted from data acquired by different scanners and protocols to improve stability and robustness. Previous studies have described various computational approaches to fuse single modality multicentre datasets. However, these surveys rarely focused on evaluation metrics and lacked a checklist for computational data harmonisation studies. In this systematic review, we summarise the computational data harmonisation approaches for multi-modality data in the digital healthcare field, including harmonisation strategies and evaluation metrics based on different theories. In addition, a comprehensive checklist that summarises common practices for data harmonisation studies is proposed to guide researchers to report their research findings more effectively. Last but not least, flowcharts presenting possible ways for methodology and metric selection are proposed and the limitations of different methods have been surveyed for future research.

NEApr 20, 2021
Hypervolume-Optimal $μ$-Distributions on Line/Plane-based Pareto Fronts in Three Dimensions

Ke Shang, Hisao Ishibuchi, Weiyu Chen et al.

Hypervolume is widely used in the evolutionary multi-objective optimization (EMO) field to evaluate the quality of a solution set. For a solution set with $μ$ solutions on a Pareto front, a larger hypervolume means a better solution set. Investigating the distribution of the solution set with the largest hypervolume is an important topic in EMO, which is the so-called hypervolume optimal $μ$-distribution. Theoretical results have shown that the $μ$ solutions are uniformly distributed on a linear Pareto front in two dimensions. However, the $μ$ solutions are not always uniformly distributed on a single-line Pareto front in three dimensions. They are only uniform when the single-line Pareto front has one constant objective. In this paper, we further investigate the hypervolume optimal $μ$-distribution in three dimensions. We consider the line- and plane-based Pareto fronts. For the line-based Pareto fronts, we extend the single-line Pareto front to two-line and three-line Pareto fronts, where each line has one constant objective. For the plane-based Pareto fronts, the linear triangular and inverted triangular Pareto fronts are considered. First, we show that the $μ$ solutions are not always uniformly distributed on the line-based Pareto fronts. The uniformity depends on how the lines are combined. Then, we show that a uniform solution set on the plane-based Pareto front is not always optimal for hypervolume maximization. It is locally optimal with respect to a $(μ+1)$ selection scheme. Our results can help researchers in the community to better understand and utilize the hypervolume indicator.

IVDec 2, 2019
The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge

Nicholas Heller, Fabian Isensee, Klaus H. Maier-Hein et al.

There is a large body of literature linking anatomic and geometric characteristics of kidney tumors to perioperative and oncologic outcomes. Semantic segmentation of these tumors and their host kidneys is a promising tool for quantitatively characterizing these lesions, but its adoption is limited due to the manual effort required to produce high-quality 3D segmentations of these structures. Recently, methods based on deep learning have shown excellent results in automatic 3D segmentation, but they require large datasets for training, and there remains little consensus on which methods perform best. The 2019 Kidney and Kidney Tumor Segmentation challenge (KiTS19) was a competition held in conjunction with the 2019 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) which sought to address these issues and stimulate progress on this automatic segmentation problem. A training set of 210 cross sectional CT images with kidney tumors was publicly released with corresponding semantic segmentation masks. 106 teams from five continents used this data to develop automated systems to predict the true segmentation masks on a test set of 90 CT images for which the corresponding ground truth segmentations were kept private. These predictions were scored and ranked according to their average So rensen-Dice coefficient between the kidney and tumor across all 90 cases. The winning team achieved a Dice of 0.974 for kidney and 0.851 for tumor, approaching the inter-annotator performance on kidney (0.983) but falling short on tumor (0.923). This challenge has now entered an "open leaderboard" phase where it serves as a challenging benchmark in 3D semantic segmentation.

CVDec 20, 2017
Partial Labeled Gastric Tumor Segmentation via patch-based Reiterative Learning

Yang Nan, Gianmarc Coppola, Qiaokang Liang et al.

Gastric cancer is the second leading cause of cancer-related deaths worldwide, and the major hurdle in biomedical image analysis is the determination of the cancer extent. This assignment has high clinical relevance and would generally require vast microscopic assessment by pathologists. Recent advances in deep learning have produced inspiring results on biomedical image segmentation, while its outcome is reliant on comprehensive annotation. This requires plenty of labor costs, for the ground truth must be annotated meticulously by pathologists. In this paper, a reiterative learning framework was presented to train our network on partial annotated biomedical images, and superior performance was achieved without any pre-trained or further manual annotation. We eliminate the boundary error of patch-based model through our overlapped region forecast algorithm. Through these advisable methods, a mean intersection over union coefficient (IOU) of 0.883 and mean accuracy of 91.09% on the partial labeled dataset was achieved, which made us win the 2017 China Big Data & Artificial Intelligence Innovation and Entrepreneurship Competitions.