A Survey on Computational Pathology Foundation Models: Datasets, Adaptation Strategies, and Evaluation Tasks

Computational pathology foundation models (CPathFMs) have emerged as a powerful approach for analyzing histopathological data, leveraging self-supervised learning to extract robust feature representations from unlabeled whole-slide images. These models, categorized into uni-modal and multi-modal frameworks, have demonstrated promise in automating complex pathology tasks such as segmentation, classification, and biomarker discovery. However, the development of CPathFMs presents significant challenges, such as limited data accessibility, high variability across datasets, the necessity for domain-specific adaptation, and the lack of standardized evaluation benchmarks. This survey provides a comprehensive review of CPathFMs in computational pathology, focusing on datasets, adaptation strategies, and evaluation tasks. We analyze key techniques, such as contrastive learning and multi-modal integration, and highlight existing gaps in current research. Finally, we explore future directions from four perspectives for advancing CPathFMs. This survey serves as a valuable resource for researchers, clinicians, and AI practitioners, guiding the advancement of CPathFMs toward robust and clinically applicable AI-driven pathology solutions.

Fair In-Context Learning via Latent Concept Variables

The emerging in-context learning (ICL) ability of large language models (LLMs) has prompted their use for predictive tasks in various domains with different types of data facilitated by serialization methods. However, with increasing applications in high-stakes domains, it has been shown that LLMs can inherit social bias and discrimination from their pre-training data. In this work, we investigate this inherent bias in LLMs during in-context learning with tabular data. We focus on an optimal demonstration selection approach that utilizes latent concept variables for resource-efficient task adaptation. We design data augmentation strategies that reduce correlation between predictive outcomes and sensitive variables helping to promote fairness during latent concept learning. We utilize the learned concept and select demonstrations from a training dataset to obtain fair predictions during inference while maintaining model utility. The latent concept variable is learned using a smaller internal LLM and the selected demonstrations can be used for inference with larger external LLMs. We empirically verify that the fair latent variable approach improves fairness results on tabular datasets compared to multiple heuristic demonstration selection methods.

Soft Prompting for Unlearning in Large Language Models

The widespread popularity of Large Language Models (LLMs), partly due to their unique ability to perform in-context learning, has also brought to light the importance of ethical and safety considerations when deploying these pre-trained models. In this work, we focus on investigating machine unlearning for LLMs motivated by data protection regulations. In contrast to the growing literature on fine-tuning methods to achieve unlearning, we focus on a comparatively lightweight alternative called soft prompting to realize the unlearning of a subset of training data. With losses designed to enforce forgetting as well as utility preservation, our framework \textbf{S}oft \textbf{P}rompting for \textbf{U}n\textbf{l}earning (SPUL) learns prompt tokens that can be appended to an arbitrary query to induce unlearning of specific examples at inference time without updating LLM parameters. We conduct a rigorous evaluation of the proposed method and our results indicate that SPUL can significantly improve the trade-off between utility and forgetting in the context of text classification with LLMs. We further validate our method using multiple LLMs to highlight the scalability of our framework and provide detailed insights into the choice of hyperparameters and the influence of the size of unlearning data. Our implementation is available at \url{https://github.com/karuna-bhaila/llm_unlearning}.

Beyond Human Vision: The Role of Large Vision Language Models in Microscope Image Analysis

Vision language models (VLMs) have recently emerged and gained the spotlight for their ability to comprehend the dual modality of image and textual data. VLMs such as LLaVA, ChatGPT-4, and Gemini have recently shown impressive performance on tasks such as natural image captioning, visual question answering (VQA), and spatial reasoning. Additionally, a universal segmentation model by Meta AI, Segment Anything Model (SAM) shows unprecedented performance at isolating objects from unforeseen images. Since medical experts, biologists, and materials scientists routinely examine microscopy or medical images in conjunction with textual information in the form of captions, literature, or reports, and draw conclusions of great importance and merit, it is indubitably essential to test the performance of VLMs and foundation models such as SAM, on these images. In this study, we charge ChatGPT, LLaVA, Gemini, and SAM with classification, segmentation, counting, and VQA tasks on a variety of microscopy images. We observe that ChatGPT and Gemini are impressively able to comprehend the visual features in microscopy images, while SAM is quite capable at isolating artefacts in a general sense. However, the performance is not close to that of a domain expert - the models are readily encumbered by the introduction of impurities, defects, artefact overlaps and diversity present in the images.

Causal Diffusion Autoencoders: Toward Counterfactual Generation via Diffusion Probabilistic Models

Diffusion probabilistic models (DPMs) have become the state-of-the-art in high-quality image generation. However, DPMs have an arbitrary noisy latent space with no interpretable or controllable semantics. Although there has been significant research effort to improve image sample quality, there is little work on representation-controlled generation using diffusion models. Specifically, causal modeling and controllable counterfactual generation using DPMs is an underexplored area. In this work, we propose CausalDiffAE, a diffusion-based causal representation learning framework to enable counterfactual generation according to a specified causal model. Our key idea is to use an encoder to extract high-level semantically meaningful causal variables from high-dimensional data and model stochastic variation using reverse diffusion. We propose a causal encoding mechanism that maps high-dimensional data to causally related latent factors and parameterize the causal mechanisms among latent factors using neural networks. To enforce the disentanglement of causal variables, we formulate a variational objective and leverage auxiliary label information in a prior to regularize the latent space. We propose a DDIM-based counterfactual generation procedure subject to do-interventions. Finally, to address the limited label supervision scenario, we also study the application of CausalDiffAE when a part of the training data is unlabeled, which also enables granular control over the strength of interventions in generating counterfactuals during inference. We empirically show that CausalDiffAE learns a disentangled latent space and is capable of generating high-quality counterfactual images.

Privacy Preserving Prompt Engineering: A Survey

Pre-trained language models (PLMs) have demonstrated significant proficiency in solving a wide range of general natural language processing (NLP) tasks. Researchers have observed a direct correlation between the performance of these models and their sizes. As a result, the sizes of these models have notably expanded in recent years, persuading researchers to adopt the term large language models (LLMs) to characterize the larger-sized PLMs. The size expansion comes with a distinct capability called in-context learning (ICL), which represents a special form of prompting and allows the models to be utilized through the presentation of demonstration examples without modifications to the model parameters. Although interesting, privacy concerns have become a major obstacle in its widespread usage. Multiple studies have examined the privacy risks linked to ICL and prompting in general, and have devised techniques to alleviate these risks. Thus, there is a necessity to organize these mitigation techniques for the benefit of the community. This survey provides a systematic overview of the privacy protection methods employed during ICL and prompting in general. We review, analyze, and compare different methods under this paradigm. Furthermore, we provide a summary of the resources accessible for the development of these frameworks. Finally, we discuss the limitations of these frameworks and offer a detailed examination of the promising areas that necessitate further exploration.

Robust Influence-based Training Methods for Noisy Brain MRI

Correctly classifying brain tumors is imperative to the prompt and accurate treatment of a patient. While several classification algorithms based on classical image processing or deep learning methods have been proposed to rapidly classify tumors in MR images, most assume the unrealistic setting of noise-free training data. In this work, we study a difficult but realistic setting of training a deep learning model on noisy MR images to classify brain tumors. We propose two training methods that are robust to noisy MRI training data, Influence-based Sample Reweighing (ISR) and Influence-based Sample Perturbation (ISP), which are based on influence functions from robust statistics. Using the influence functions, in ISR, we adaptively reweigh training examples according to how helpful/harmful they are to the training process, while in ISP, we craft and inject helpful perturbation proportional to the influence score. Both ISR and ISP harden the classification model against noisy training data without significantly affecting the generalization ability of the model on test data. We conduct empirical evaluations over a common brain tumor dataset and compare ISR and ISP to three baselines. Our empirical results show that ISR and ISP can efficiently train deep learning models robust against noisy training data.

DP-TabICL: In-Context Learning with Differentially Private Tabular Data

In-context learning (ICL) enables large language models (LLMs) to adapt to new tasks by conditioning on demonstrations of question-answer pairs and it has been shown to have comparable performance to costly model retraining and fine-tuning. Recently, ICL has been extended to allow tabular data to be used as demonstration examples by serializing individual records into natural language formats. However, it has been shown that LLMs can leak information contained in prompts, and since tabular data often contain sensitive information, understanding how to protect the underlying tabular data used in ICL is a critical area of research. This work serves as an initial investigation into how to use differential privacy (DP) -- the long-established gold standard for data privacy and anonymization -- to protect tabular data used in ICL. Specifically, we investigate the application of DP mechanisms for private tabular ICL via data privatization prior to serialization and prompting. We formulate two private ICL frameworks with provable privacy guarantees in both the local (LDP-TabICL) and global (GDP-TabICL) DP scenarios via injecting noise into individual records or group statistics, respectively. We evaluate our DP-based frameworks on eight real-world tabular datasets and across multiple ICL and DP settings. Our evaluations show that DP-based ICL can protect the privacy of the underlying tabular data while achieving comparable performance to non-LLM baselines, especially under high privacy regimes.

On Large Visual Language Models for Medical Imaging Analysis: An Empirical Study

Recently, large language models (LLMs) have taken the spotlight in natural language processing. Further, integrating LLMs with vision enables the users to explore emergent abilities with multimodal data. Visual language models (VLMs), such as LLaVA, Flamingo, or CLIP, have demonstrated impressive performance on various visio-linguistic tasks. Consequently, there are enormous applications of large models that could be potentially used in the biomedical imaging field. Along that direction, there is a lack of related work to show the ability of large models to diagnose the diseases. In this work, we study the zero-shot and few-shot robustness of VLMs on the medical imaging analysis tasks. Our comprehensive experiments demonstrate the effectiveness of VLMs in analyzing biomedical images such as brain MRIs, microscopic images of blood cells, and chest X-rays.

Dynamic Environment Responsive Online Meta-Learning with Fairness Awareness

The fairness-aware online learning framework has emerged as a potent tool within the context of continuous lifelong learning. In this scenario, the learner's objective is to progressively acquire new tasks as they arrive over time, while also guaranteeing statistical parity among various protected sub-populations, such as race and gender, when it comes to the newly introduced tasks. A significant limitation of current approaches lies in their heavy reliance on the i.i.d (independent and identically distributed) assumption concerning data, leading to a static regret analysis of the framework. Nevertheless, it's crucial to note that achieving low static regret does not necessarily translate to strong performance in dynamic environments characterized by tasks sampled from diverse distributions. In this paper, to tackle the fairness-aware online learning challenge in evolving settings, we introduce a unique regret measure, FairSAR, by incorporating long-term fairness constraints into a strongly adapted loss regret framework. Moreover, to determine an optimal model parameter at each time step, we introduce an innovative adaptive fairness-aware online meta-learning algorithm, referred to as FairSAOML. This algorithm possesses the ability to adjust to dynamic environments by effectively managing bias control and model accuracy. The problem is framed as a bi-level convex-concave optimization, considering both the model's primal and dual parameters, which pertain to its accuracy and fairness attributes, respectively. Theoretical analysis yields sub-linear upper bounds for both loss regret and the cumulative violation of fairness constraints. Our experimental evaluation on various real-world datasets in dynamic environments demonstrates that our proposed FairSAOML algorithm consistently outperforms alternative approaches rooted in the most advanced prior online learning methods.