Knowledge-Enhanced Adaptive Visual Compression (FOCUS) Framework for Few-Shot Whole Slide Image Classification

Główne pojęcia

The FOCUS framework leverages pathology foundation models and language-guided prompts to prioritize diagnostically relevant regions in whole slide images, significantly improving few-shot classification accuracy in computational pathology.

Streszczenie

• Bibliographic Information: Guo, Z., Xiong, C., Ma, J., Sun, Q., Feng, L., Wang, J., & Chen, H. (2024). FOCUS: Knowledge-enhanced Adaptive Visual Compression for Few-shot Whole Slide Image Classification. arXiv preprint arXiv:2411.14743v1.
• Research Objective: This paper introduces FOCUS, a novel framework designed to address the challenges of few-shot learning in computational pathology, specifically focusing on improving the classification accuracy of whole slide images (WSIs) with limited training data.
• Methodology: FOCUS employs a three-stage adaptive visual compression strategy:
  1. Global Redundancy Removal: Utilizes pre-trained pathology foundation models (FMs) to eliminate redundant visual information from WSIs through sliding-window similarity measurements.
  2. Language-Guided Visual Token Prioritization: Integrates pathology knowledge prompts generated from large language models (LLMs) to prioritize visual tokens (patches) based on their semantic relevance to textual descriptions of specific cancer subtypes.
  3. Sequential Visual Token Compression: Processes tokens sequentially, employing cosine similarity thresholding to eliminate local redundancies while preserving spatial coherence and important contextual information.
• Key Findings:
  • FOCUS consistently outperforms state-of-the-art methods in few-shot WSI classification tasks across three diverse pathology datasets (TCGA-NSCLC, CAMELYON, and UBC-OCEAN), demonstrating significant improvements in balanced accuracy, AUC, and F1 score.
  • The framework exhibits superior performance, particularly in the most challenging low-shot scenarios (e.g., 4-shot), highlighting its effectiveness in learning from limited data.
  • Ablation studies confirm the contribution of each module within FOCUS, with the three-stage compression strategy playing a crucial role in achieving high accuracy.
  • The choice of pathology FM significantly impacts performance, with CONCH, a vision-language model pre-trained on large-scale pathology image-caption pairs, consistently outperforming other FMs.
  • Utilizing different LLMs for generating pathology knowledge prompts also influences accuracy, indicating the importance of leveraging models with strong language modeling capabilities and domain-specific knowledge.
• Main Conclusions: FOCUS presents a novel and effective approach for few-shot WSI classification by leveraging the power of pathology FMs and language-guided prompts to focus on diagnostically relevant regions. This framework has the potential to significantly advance computational pathology, particularly in data-scarce settings, enabling more accurate and efficient diagnosis with limited training data.
• Significance: This research significantly contributes to the field of computational pathology by addressing the critical challenge of few-shot learning in WSI analysis. The proposed FOCUS framework offers a promising solution for improving diagnostic accuracy in real-world clinical settings where annotated data is often limited.
• Limitations and Future Research: While FOCUS demonstrates impressive performance, future research could explore:
  • Incorporating multi-scale information from WSIs to capture diagnostic features at different levels of detail.
  • Investigating the generalization capabilities of the framework across a wider range of cancer types and pathological conditions.
  • Exploring the potential of using FOCUS for other downstream tasks in computational pathology, such as tumor grading and prognosis prediction.

Statystyki

FOCUS achieves a Balanced ACC of 81.9% in the 4-shot setting on the TCGA-NSCLC dataset, outperforming the second-best method (ViLa-MIL) by 1.2%.
In the challenging 4-shot setting on the CAMELYON dataset, FOCUS achieves an ACC of 70.1%, significantly outperforming all baseline methods.
FOCUS achieves state-of-the-art AUC of 96.7% in the 16-shot setting on the UBC-OCEAN dataset, surpassing the previous best (DS- and TOP-MIL tied at 95.6%) by 1.1%.
CONCH consistently outperforms other FMs, achieving the highest Balanced ACC across all settings on the UBC-OCEAN dataset (70.4%, 77.3%, and 86.4% for 4-shot, 8-shot, and 16-shot, respectively).
Claude3.5-Sonnet achieved the highest Balanced ACC of 86.4% on the UBC-OCEAN dataset under 16-shots, followed by ChatGPT3.5-Turbo (84.8%) and OpenAI-o1-mini (84.6%).

Cytaty

Kluczowe wnioski z

FOCUS: Knowledge-enhanced Adaptive Visual Compression for Few-shot Whole Slide Image Classification

by Zhengrui Guo... o arxiv.org 11-25-2024

https://arxiv.org/pdf/2411.14743.pdf

Głębsze pytania

How might the FOCUS framework be adapted to incorporate other modalities of data commonly available in clinical settings, such as genomic information or radiology images, to further enhance diagnostic accuracy?

The FOCUS framework, primarily designed for few-shot whole slide image (WSI) classification, can be extended to incorporate multi-modal data like genomic information and radiology images. Here's how:
1. Genomic Information Integration:

Feature Fusion: Genomic data, often represented as high-dimensional vectors, can be integrated with compressed visual features from FOCUS using various fusion techniques.

Early Fusion: Concatenate genomic features with WSI patch embeddings before the knowledge-enhanced adaptive compression module. This allows the model to learn cross-modal interactions early on.
Late Fusion: Combine genomic features with the slide-level representation generated by the cross-modal aggregation module. This approach treats genomic data as complementary information for final classification.
Hybrid Fusion: Explore a combination of early and late fusion strategies to leverage both local patch-level and global slide-level interactions between genomic and visual data.

Genomic-aware Attention: Develop attention mechanisms that leverage genomic information to guide the visual token prioritization process. This could involve:

Cross-modal Attention: Compute attention scores based on both visual and genomic features, allowing the model to focus on patches with high relevance to both modalities.
Genomic-guided Prompting: Incorporate genomic information into the pathology knowledge prompts, enabling the model to prioritize patches exhibiting visual patterns associated with specific genomic alterations.
2. Radiology Image Incorporation:

Multi-input Architecture: Extend FOCUS to handle both WSI and radiology images as separate input branches. Each branch would have its own feature extractor and compression modules, with fusion occurring at a later stage.
Cross-modal Alignment: Employ techniques like contrastive learning or canonical correlation analysis to align the latent spaces of WSI and radiology image representations, facilitating cross-modal information transfer.
Region-of-Interest (ROI) Guidance: Utilize radiology images to identify potential ROIs within WSIs, allowing FOCUS to focus its analysis on regions with higher diagnostic significance.
Key Considerations:

Data Availability and Alignment: Ensure sufficient multi-modal data with appropriate alignment between WSIs, genomic profiles, and radiology images.
Model Complexity and Interpretability: Balance the benefits of multi-modal integration with potential increases in model complexity and challenges in interpreting model decisions.
Clinical Validation: Rigorously validate the performance of the extended FOCUS framework in real-world clinical settings to assess its impact on diagnostic accuracy and clinical decision-making.

While FOCUS demonstrates strong performance in few-shot settings, could the reliance on pre-trained foundation models and large language models potentially introduce biases or limit the framework's generalizability to under-represented patient populations or rare cancer subtypes?

Yes, the reliance on pre-trained foundation models (FMs) and large language models (LLMs) in FOCUS, while advantageous, could introduce biases and limit generalizability, particularly for under-represented populations and rare cancer subtypes.
Potential Biases and Limitations:

Data Bias in Pre-training: FMs and LLMs are trained on massive datasets, which may not adequately represent the diversity of patient demographics, disease presentations, or staining variations in histopathology. This can lead to biased predictions, particularly for groups under-represented in the training data.
Domain Shift: FMs trained on specific types of pathology images might not generalize well to rare cancer subtypes with unique morphological characteristics. Similarly, LLMs trained on general language data might not capture the nuances of specialized pathology terminology.
Lack of Explainability: The black-box nature of deep learning models, including FMs and LLMs, makes it challenging to identify and mitigate biases embedded within their learned representations.
Mitigating Biases and Enhancing Generalizability:

Diverse and Representative Training Data: Advocate for and contribute to the development of large, publicly available pathology datasets that encompass diverse patient populations, cancer subtypes, and staining techniques.
Fine-tuning and Domain Adaptation: Fine-tune pre-trained FMs and LLMs on datasets specifically curated for under-represented groups or rare cancer subtypes. Explore domain adaptation techniques to bridge the gap between the pre-training domain and the target domain.
Bias Detection and Mitigation Techniques: Employ bias detection tools and techniques to identify and quantify potential biases in model predictions. Implement bias mitigation strategies during training, such as adversarial training or data augmentation, to promote fairness.
Explainable AI (XAI): Integrate XAI methods into FOCUS to provide insights into the model's decision-making process, enabling clinicians to understand and potentially challenge biased predictions.
Addressing Rare Cancer Subtypes:

Few-shot and Zero-shot Learning: Leverage the few-shot capabilities of FOCUS to train models with limited data for rare subtypes. Explore zero-shot learning approaches that enable the model to generalize to unseen classes.
Data Augmentation and Synthesis: Employ data augmentation techniques to increase the size and diversity of training data for rare subtypes. Investigate the use of synthetic data generation methods to create realistic pathology images.
Collaboration and Data Sharing: Foster collaborations between research institutions and clinical centers to pool data and expertise for rare cancer subtype modeling.

Considering the increasing prevalence of digital pathology and the potential for integrating artificial intelligence into clinical workflows, what ethical considerations and regulatory frameworks need to be addressed to ensure responsible and equitable deployment of frameworks like FOCUS in real-world healthcare systems?

The integration of AI frameworks like FOCUS in digital pathology presents significant ethical and regulatory challenges that necessitate careful consideration for responsible and equitable deployment.
Ethical Considerations:

Bias and Fairness: As discussed earlier, mitigating bias in algorithms and datasets is crucial to ensure equitable access to healthcare and avoid disparities in diagnosis and treatment.
Transparency and Explainability: Black-box AI models raise concerns about transparency. Clinicians and patients need to understand how AI-driven diagnoses are made to trust and accept them. Explainable AI (XAI) methods are essential to address this.
Privacy and Data Security: Pathology images and associated patient data are highly sensitive. Robust data de-identification, secure storage, and access control mechanisms are paramount to maintain patient privacy.
Clinical Validation and Liability: Thorough clinical validation is non-negotiable before deploying AI systems in real-world settings. Clear guidelines on liability in case of misdiagnosis or errors involving AI are needed.
Human Oversight and Accountability: AI should augment, not replace, pathologists. Maintaining human oversight in the diagnostic process is crucial, with clear lines of accountability for decisions.
Regulatory Frameworks:

FDA Approval and Medical Device Regulations: AI systems intended for clinical diagnosis, like FOCUS, may fall under the purview of regulatory bodies like the FDA. Compliance with medical device regulations, including pre-market approval pathways, is essential.
Data Protection and Privacy Laws: Adherence to data protection laws, such as HIPAA in the United States or GDPR in Europe, is mandatory to safeguard patient data privacy and security.
Guidelines for Ethical AI in Healthcare: Developing and adhering to ethical guidelines specific to AI in healthcare is crucial. Organizations like the WHO and professional bodies like the American Medical Association are actively working on such guidelines.
Ensuring Responsible Deployment:

Multi-stakeholder Engagement: Engage clinicians, patients, ethicists, regulators, and AI developers in the design, development, and deployment of AI systems to address diverse perspectives.
Continuous Monitoring and Evaluation: Implement mechanisms for continuous monitoring of AI system performance, bias detection, and feedback loops for improvement.
Education and Training: Provide comprehensive education and training to healthcare professionals on the capabilities, limitations, and ethical implications of AI in pathology.
Public Engagement and Trust Building: Foster public awareness and understanding of AI in healthcare through transparent communication and engagement initiatives to build trust.
By proactively addressing these ethical considerations and adhering to evolving regulatory frameworks, we can harness the potential of AI frameworks like FOCUS to improve patient care while upholding the highest standards of responsibility and equity in healthcare.