arXiv subjects

Yutong Xie

Publications and source records attributed to Yutong Xie.

At least 73 records · Page 4Linked to original sources

arXiv2025

MapExplorer: New Content Generation from Low-Dimensional Visualizations

Low-dimensional visualizations, or "projection maps," are widely used in scientific and creative domains to interpret large-scale and complex datasets. These visualizations not only aid in understanding existing knowledge spaces but also implicitly guide exploration into unknown areas. Although techniques such as t-SNE and UMAP can generate these maps, there exists no systematic method for leveraging them to generate new content. To address this, we introduce MapExplorer, a novel knowledge discovery task that translates coordinates within any projection map into coherent, contextually aligned textual content. This allows users to interactively explore and uncover insights embedded in the maps. To evaluate the performance of MapExplorer methods, we propose Atometric, a fine-grained metric inspired by ROUGE that quantifies logical coherence and alignment between generated and reference text. Experiments on diverse datasets demonstrate the versatility of MapExplorer in generating scientific hypotheses, crafting synthetic personas, and devising strategies for attacking large language models-even with simple baseline methods. By bridging visualization and generation, our work highlights the potential of MapExplorer to enable intuitive human-AI collaboration in large-scale data exploration.

cs.AI↗

arXiv2025

Partial Label Clustering

Partial label learning (PLL) is a significant weakly supervised learning framework, where each training example corresponds to a set of candidate labels and only one label is the ground-truth label. For the first time, this paper investigates the partial label clustering problem, which takes advantage of the limited available partial labels to improve the clustering performance. Specifically, we first construct a weight matrix of examples based on their relationships in the feature space and disambiguate the candidate labels to estimate the ground-truth label based on the weight matrix. Then, we construct a set of must-link and cannot-link constraints based on the disambiguation results. Moreover, we propagate the initial must-link and cannot-link constraints based on an adversarial prior promoted dual-graph learning approach. Finally, we integrate weight matrix construction, label disambiguation, and pairwise constraints propagation into a joint model to achieve mutual enhancement. We also theoretically prove that a better disambiguated label matrix can help improve clustering performance. Comprehensive experiments demonstrate our method realizes superior performance when comparing with state-of-the-art constrained clustering methods, and outperforms PLL and semi-supervised PLL methods when only limited samples are annotated. The code is publicly available at https://github.com/xyt-ml/PLC.

cs.LG↗

arXiv2025

MMCLIP: Cross-modal Attention Masked Modelling for Medical Language-Image Pre-Training

Vision-and-language pretraining (VLP) in the medical field utilizes contrastive learning on image-text pairs to achieve effective transfer across tasks. Yet, current VLP approaches with the masked modeling strategy face two challenges when applied to the medical domain. First, current models struggle to accurately reconstruct key pathological features due to the scarcity of medical data. Second, most methods only adopt either paired image-text or image-only data, failing to exploit the combination of both paired and unpaired data. To this end, this paper proposes the MMCLIP (Masked Medical Contrastive Language-Image Pre-Training) framework to enhance pathological learning and feature learning via unpaired data. First, we introduce the attention-masked image modeling (AttMIM) and entity-driven masked language modeling module (EntMLM), which learns to reconstruct pathological visual and textual tokens via multi-modal feature interaction, thus improving medical-enhanced features. The AttMIM module masks a portion of the image features that are highly responsive to textual features. This allows MMCLIP to improve the reconstruction of highly similar image data in medicine efficiency. Second, our MMCLIP capitalizes unpaired data to enhance multimodal learning by introducing disease-kind prompts. The experimental results show that MMCLIP achieves SOTA for zero-shot and fine-tuning classification performance on five datasets. Our code will be available at https://github.com/AIGeeksGroup/MMCLIP.

cs.CV↗

arXiv2025

A Comprehensive Analysis of Mamba for 3D Volumetric Medical Image Segmentation

Mamba, with its selective State Space Models (SSMs), offers a more computationally efficient solution than Transformers for long-range dependency modeling. However, there is still a debate about its effectiveness in high-resolution 3D medical image segmentation. In this study, we present a comprehensive investigation into Mamba's capabilities in 3D medical image segmentation by tackling three pivotal questions: Can Mamba replace Transformers? Can it elevate multi-scale representation learning? Is complex scanning necessary to unlock its full potential? We evaluate Mamba's performance across three large public benchmarks-AMOS, TotalSegmentator, and BraTS. Our findings reveal that UlikeMamba, a U-shape Mamba-based network, consistently surpasses UlikeTrans, a U-shape Transformer-based network, particularly when enhanced with custom-designed 3D depthwise convolutions, boosting accuracy and computational efficiency. Further, our proposed multi-scale Mamba block demonstrates superior performance in capturing both fine-grained details and global context, especially in complex segmentation tasks, surpassing Transformer-based counterparts. We also critically assess complex scanning strategies, finding that simpler methods often suffice, while our Tri-scan approach delivers notable advantages in the most challenging scenarios. By integrating these advancements, we introduce a new network for 3D medical image segmentation, positioning Mamba as a transformative force that outperforms leading models such as nnUNet, CoTr, and U-Mamba, offering competitive accuracy with superior computational efficiency. This study provides key insights into Mamba's unique advantages, paving the way for more efficient and accurate approaches to 3D medical imaging.

cs.CV↗

arXiv2025

MMRC: A Large-Scale Benchmark for Understanding Multimodal Large Language Model in Real-World Conversation

Recent multimodal large language models (MLLMs) have demonstrated significant potential in open-ended conversation, generating more accurate and personalized responses. However, their abilities to memorize, recall, and reason in sustained interactions within real-world scenarios remain underexplored. This paper introduces MMRC, a Multi-Modal Real-world Conversation benchmark for evaluating six core open-ended abilities of MLLMs: information extraction, multi-turn reasoning, information update, image management, memory recall, and answer refusal. With data collected from real-world scenarios, MMRC comprises 5,120 conversations and 28,720 corresponding manually labeled questions, posing a significant challenge to existing MLLMs. Evaluations on 20 MLLMs in MMRC indicate an accuracy drop during open-ended interactions. We identify four common failure patterns: long-term memory degradation, inadequacies in updating factual knowledge, accumulated assumption of error propagation, and reluctance to say no. To mitigate these issues, we propose a simple yet effective NOTE-TAKING strategy, which can record key information from the conversation and remind the model during its responses, enhancing conversational capabilities. Experiments across six MLLMs demonstrate significant performance improvements.

cs.CL↗

arXiv2025

Bridging AI and Science: Implications from a Large-Scale Literature Analysis of AI4Science

Artificial Intelligence has proven to be a transformative tool for advancing scientific research across a wide range of disciplines. However, a significant gap still exists between AI and scientific communities, limiting the full potential of AI methods in driving broad scientific discovery. Existing efforts in identifying and bridging this gap have often relied on qualitative examination of small samples of literature, offering a limited perspective on the broader AI4Science landscape. In this work, we present a large-scale analysis of the AI4Science literature, starting by using large language models to identify scientific problems and AI methods in publications from top science and AI venues. Leveraging this new dataset, we quantitatively highlight key disparities between AI methods and scientific problems, revealing substantial opportunities for deeper AI integration across scientific disciplines. Furthermore, we explore the potential and challenges of facilitating collaboration between AI and scientific communities through the lens of link prediction. Our findings and tools aim to promote more impactful interdisciplinary collaborations and accelerate scientific discovery through deeper and broader AI integration. Our code and dataset are available at: https://github.com/charles-pyj/Bridging-AI-and-Science.

cs.AI↗

arXiv2025

UD-Mamba: A pixel-level uncertainty-driven Mamba model for medical image segmentation

Recent advancements have highlighted the Mamba framework, a state-space model known for its efficiency in capturing long-range dependencies with linear computational complexity. While Mamba has shown competitive performance in medical image segmentation, it encounters difficulties in modeling local features due to the sporadic nature of traditional location-based scanning methods and the complex, ambiguous boundaries often present in medical images. To overcome these challenges, we propose Uncertainty-Driven Mamba (UD-Mamba), which redefines the pixel-order scanning process by incorporating channel uncertainty into the scanning mechanism. UD-Mamba introduces two key scanning techniques: 1) sequential scanning, which prioritizes regions with high uncertainty by scanning in a row-by-row fashion, and 2) skip scanning, which processes columns vertically, moving from high-to-low or low-to-high uncertainty at fixed intervals. Sequential scanning efficiently clusters high-uncertainty regions, such as boundaries and foreground objects, to improve segmentation precision, while skip scanning enhances the interaction between background and foreground regions, allowing for timely integration of background information to support more accurate foreground inference. Recognizing the advantages of scanning from certain to uncertain areas, we introduce four learnable parameters to balance the importance of features extracted from different scanning methods. Additionally, a cosine consistency loss is employed to mitigate the drawbacks of transitioning between uncertain and certain regions during the scanning process. Our method demonstrates robust segmentation performance, validated across three distinct medical imaging datasets involving pathology, dermatological lesions, and cardiac tasks.

eess.IV↗

arXiv2025

Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

cs.CV↗

arXiv2024

How Different AI Chatbots Behave? Benchmarking Large Language Models in Behavioral Economics Games

The deployment of large language models (LLMs) in diverse applications requires a thorough understanding of their decision-making strategies and behavioral patterns. As a supplement to a recent study on the behavioral Turing test, this paper presents a comprehensive analysis of five leading LLM-based chatbot families as they navigate a series of behavioral economics games. By benchmarking these AI chatbots, we aim to uncover and document both common and distinct behavioral patterns across a range of scenarios. The findings provide valuable insights into the strategic preferences of each LLM, highlighting potential implications for their deployment in critical decision-making roles.

cs.AI↗

arXiv2024

A Survey of Medical Vision-and-Language Applications and Their Techniques

Medical vision-and-language models (MVLMs) have attracted substantial interest due to their capability to offer a natural language interface for interpreting complex medical data. Their applications are versatile and have the potential to improve diagnostic accuracy and decision-making for individual patients while also contributing to enhanced public health monitoring, disease surveillance, and policy-making through more efficient analysis of large data sets. MVLMS integrate natural language processing with medical images to enable a more comprehensive and contextual understanding of medical images alongside their corresponding textual information. Unlike general vision-and-language models trained on diverse, non-specialized datasets, MVLMs are purpose-built for the medical domain, automatically extracting and interpreting critical information from medical images and textual reports to support clinical decision-making. Popular clinical applications of MVLMs include automated medical report generation, medical visual question answering, medical multimodal segmentation, diagnosis and prognosis and medical image-text retrieval. Here, we provide a comprehensive overview of MVLMs and the various medical tasks to which they have been applied. We conduct a detailed analysis of various vision-and-language model architectures, focusing on their distinct strategies for cross-modal integration/exploitation of medical visual and textual features. We also examine the datasets used for these tasks and compare the performance of different models based on standardized evaluation metrics. Furthermore, we highlight potential challenges and summarize future research trends and directions. The full collection of papers and codes is available at: https://github.com/YtongXie/Medical-Vision-and-Language-Tasks-and-Methodologies-A-Survey.

cs.CV↗

arXiv2024

Instance-dependent Label Distribution Estimation for Learning with Label Noise

Noise transition matrix (NTM) estimation is a promising approach for learning with label noise. It can infer clean posterior probabilities, known as Label Distribution (LD), based on noisy ones and reduce the impact of noisy labels. However, this estimation is challenging, since the ground truth labels are not always available. Most existing methods estimate a global NTM using either correctly labeled samples (anchor points) or detected reliable samples (pseudo anchor points). These methods heavily rely on the existence of anchor points or the quality of pseudo ones, and the global NTM can hardly provide accurate label transition information for each sample, since the label noise in real applications is mostly instance-dependent. To address these challenges, we propose an Instance-dependent Label Distribution Estimation (ILDE) method to learn from noisy labels for image classification. The method's workflow has three major steps. First, we estimate each sample's noisy posterior probability, supervised by noisy labels. Second, since mislabeling probability closely correlates with inter-class correlation, we compute the inter-class correlation matrix to estimate the NTM, bypassing the need for (pseudo) anchor points. Moreover, for a precise approximation of the instance-dependent NTM, we calculate the inter-class correlation matrix using only mini-batch samples rather than the entire training dataset. Third, we transform the noisy posterior probability into instance-dependent LD by multiplying it with the estimated NTM, using the resulting LD for enhanced supervision to prevent DCNNs from memorizing noisy labels. The proposed ILDE method has been evaluated against several state-of-the-art methods on two synthetic and three real-world noisy datasets. Our results indicate that the proposed ILDE method outperforms all competing methods, no matter whether the noise is synthetic or real noise.

cs.CV↗

arXiv2024

RapidStream IR: Infrastructure for FPGA High-Level Physical Synthesis

The increasing complexity of large-scale FPGA accelerators poses significant challenges in achieving high performance while maintaining design productivity. High-level synthesis (HLS) has been adopted as a solution, but the mismatch between the high-level description and the physical layout often leads to suboptimal operating frequency. Although existing proposals for high-level physical synthesis, which use coarse-grained design partitioning, floorplanning, and pipelining to improve frequency, have gained traction, they lack a framework enabling (1) pipelining of real-world designs at arbitrary hierarchical levels, (2) integration of HLS blocks, vendor IPs, and handcrafted RTL designs, (3) portability to emerging new target FPGA devices, and (4) extensibility for the easy implementation of new design optimization tools. We present RapidStream IR, a practical high-level physical synthesis (HLPS) infrastructure for representing the composition of complex FPGA designs and exploring physical optimizations. Our approach introduces a flexible intermediate representation (IR) that captures interconnection protocols at arbitrary hierarchical levels, coarse-grained pipelining, and spatial information, enabling the creation of reusable passes for design frequency optimizations. RapidStream IR improves the frequency of a broad set of mixed-source designs by 7% to 62%, including large language models and genomics accelerators, and is portable to user-customizable new FPGA platforms. We further demonstrate its extensibility through case studies, showcasing the ability to facilitate future research.

cs.AR↗

arXiv2024

Act Like a Radiologist: Radiology Report Generation across Anatomical Regions

Automating radiology report generation can ease the reporting workload for radiologists. However, existing works focus mainly on the chest area due to the limited availability of public datasets for other regions. Besides, they often rely on naive data-driven approaches, e.g., a basic encoder-decoder framework with captioning loss, which limits their ability to recognise complex patterns across diverse anatomical regions. To address these issues, we propose X-RGen, a radiologist-minded report generation framework across six anatomical regions. In X-RGen, we seek to mimic the behaviour of human radiologists, breaking them down into four principal phases: 1) initial observation, 2) cross-region analysis, 3) medical interpretation, and 4) report formation. Firstly, we adopt an image encoder for feature extraction, akin to a radiologist's preliminary review. Secondly, we enhance the recognition capacity of the image encoder by analysing images and reports across various regions, mimicking how radiologists gain their experience and improve their professional ability from past cases. Thirdly, just as radiologists apply their expertise to interpret radiology images, we introduce radiological knowledge of multiple anatomical regions to further analyse the features from a clinical perspective. Lastly, we generate reports based on the medical-aware features using a typical auto-regressive text decoder. Both natural language generation (NLG) and clinical efficacy metrics show the effectiveness of X-RGen on six X-ray datasets. Our code and checkpoints are available at: https://github.com/YtongXie/X-RGen.

cs.CV↗

arXiv2024

MedUniSeg: 2D and 3D Medical Image Segmentation via a Prompt-driven Universal Model

Universal segmentation models offer significant potential in addressing a wide range of tasks by effectively leveraging discrete annotations. As the scope of tasks and modalities expands, it becomes increasingly important to generate and strategically position task- and modal-specific priors within the universal model. However, existing universal models often overlook the correlations between different priors, and the optimal placement and frequency of these priors remain underexplored. In this paper, we introduce MedUniSeg, a prompt-driven universal segmentation model designed for 2D and 3D multi-task segmentation across diverse modalities and domains. MedUniSeg employs multiple modal-specific prompts alongside a universal task prompt to accurately characterize the modalities and tasks. To generate the related priors, we propose the modal map (MMap) and the fusion and selection (FUSE) modules, which transform modal and task prompts into corresponding priors. These modal and task priors are systematically introduced at the start and end of the encoding process. We evaluate MedUniSeg on a comprehensive multi-modal upstream dataset consisting of 17 sub-datasets. The results demonstrate that MedUniSeg achieves superior multi-task segmentation performance, attaining a 1.2% improvement in the mean Dice score across the 17 upstream tasks compared to nnUNet baselines, while using less than 1/10 of the parameters. For tasks that underperform during the initial multi-task joint training, we freeze MedUniSeg and introduce new modules to re-learn these tasks. This approach yields an enhanced version, MedUniSeg*, which consistently outperforms MedUniSeg across all tasks. Moreover, MedUniSeg surpasses advanced self-supervised and supervised pre-trained models on six downstream tasks, establishing itself as a high-quality, highly generalizable pre-trained segmentation model.

cs.CV↗

arXiv2024

A Novel Perspective for Multi-modal Multi-label Skin Lesion Classification

The efficacy of deep learning-based Computer-Aided Diagnosis (CAD) methods for skin diseases relies on analyzing multiple data modalities (i.e., clinical+dermoscopic images, and patient metadata) and addressing the challenges of multi-label classification. Current approaches tend to rely on limited multi-modal techniques and treat the multi-label problem as a multiple multi-class problem, overlooking issues related to imbalanced learning and multi-label correlation. This paper introduces the innovative Skin Lesion Classifier, utilizing a Multi-modal Multi-label TransFormer-based model (SkinM2Former). For multi-modal analysis, we introduce the Tri-Modal Cross-attention Transformer (TMCT) that fuses the three image and metadata modalities at various feature levels of a transformer encoder. For multi-label classification, we introduce a multi-head attention (MHA) module to learn multi-label correlations, complemented by an optimisation that handles multi-label and imbalanced learning problems. SkinM2Former achieves a mean average accuracy of 77.27% and a mean diagnostic accuracy of 77.85% on the public Derm7pt dataset, outperforming state-of-the-art (SOTA) methods.

cs.CV↗

arXiv2024

Structural Attention: Rethinking Transformer for Unpaired Medical Image Synthesis

Unpaired medical image synthesis aims to provide complementary information for an accurate clinical diagnostics, and address challenges in obtaining aligned multi-modal medical scans. Transformer-based models excel in imaging translation tasks thanks to their ability to capture long-range dependencies. Although effective in supervised training settings, their performance falters in unpaired image synthesis, particularly in synthesizing structural details. This paper empirically demonstrates that, lacking strong inductive biases, Transformer can converge to non-optimal solutions in the absence of paired data. To address this, we introduce UNet Structured Transformer (UNest), a novel architecture incorporating structural inductive biases for unpaired medical image synthesis. We leverage the foundational Segment-Anything Model to precisely extract the foreground structure and perform structural attention within the main anatomy. This guides the model to learn key anatomical regions, thus improving structural synthesis under the lack of supervision in unpaired training. Evaluated on two public datasets, spanning three modalities, i.e., MR, CT, and PET, UNest improves recent methods by up to 19.30% across six medical image synthesis tasks. Our code is released at https://github.com/HieuPhan33/MICCAI2024-UNest.

cs.CV↗

arXiv2024

AdaCBM: An Adaptive Concept Bottleneck Model for Explainable and Accurate Diagnosis

The integration of vision-language models such as CLIP and Concept Bottleneck Models (CBMs) offers a promising approach to explaining deep neural network (DNN) decisions using concepts understandable by humans, addressing the black-box concern of DNNs. While CLIP provides both explainability and zero-shot classification capability, its pre-training on generic image and text data may limit its classification accuracy and applicability to medical image diagnostic tasks, creating a transfer learning problem. To maintain explainability and address transfer learning needs, CBM methods commonly design post-processing modules after the bottleneck module. However, this way has been ineffective. This paper takes an unconventional approach by re-examining the CBM framework through the lens of its geometrical representation as a simple linear classification system. The analysis uncovers that post-CBM fine-tuning modules merely rescale and shift the classification outcome of the system, failing to fully leverage the system's learning potential. We introduce an adaptive module strategically positioned between CLIP and CBM to bridge the gap between source and downstream domains. This simple yet effective approach enhances classification performance while preserving the explainability afforded by the framework. Our work offers a comprehensive solution that encompasses the entire process, from concept discovery to model training, providing a holistic recipe for leveraging the strengths of GPT, CLIP, and CBM.

cs.CV↗

arXiv2024

MASSW: A New Dataset and Benchmark Tasks for AI-Assisted Scientific Workflows

Scientific innovation relies on detailed workflows, which include critical steps such as analyzing literature, generating ideas, validating these ideas, interpreting results, and inspiring follow-up research. However, scientific publications that document these workflows are extensive and unstructured. This makes it difficult for both human researchers and AI systems to effectively navigate and explore the space of scientific innovation. To address this issue, we introduce MASSW, a comprehensive text dataset on Multi-Aspect Summarization of Scientific Workflows. MASSW includes more than 152,000 peer-reviewed publications from 17 leading computer science conferences spanning the past 50 years. Using Large Language Models (LLMs), we automatically extract five core aspects from these publications -- context, key idea, method, outcome, and projected impact -- which correspond to five key steps in the research workflow. These structured summaries facilitate a variety of downstream tasks and analyses. The quality of the LLM-extracted summaries is validated by comparing them with human annotations. We demonstrate the utility of MASSW through multiple novel machine-learning tasks that can be benchmarked using this new dataset, which make various types of predictions and recommendations along the scientific workflow. MASSW holds significant potential for researchers to create and benchmark new AI methods for optimizing scientific workflows and fostering scientific innovation in the field. Our dataset is openly available at \url{https://github.com/xingjian-zhang/massw}.

cs.CL↗