Expanding Training Data for Endoscopic Phenotyping of Eosinophilic Esophagitis

Eosinophilic esophagitis (EoE) is a chronic esophageal disorder marked by eosinophil-dominated inflammation. Diagnosing EoE usually involves endoscopic inspection of the esophageal mucosa and obtaining esophageal biopsies for histologic confirmation. Recent advances have seen AI-assisted endoscopic imaging, guided by the EREFS system, emerge as a potential alternative to reduce reliance on invasive histological assessments. Despite these advancements, significant challenges persist due to the limited availability of data for training AI models - a common issue even in the development of AI for more prevalent diseases. This study seeks to improve the performance of deep learning-based EoE phenotype classification by augmenting our training data with a diverse set of images from online platforms, public datasets, and electronic textbooks increasing our dataset from 435 to 7050 images. We utilized the Data-efficient Image Transformer for image classification and incorporated attention map visualizations to boost interpretability. The findings show that our expanded dataset and model enhancements improved diagnostic accuracy, robustness, and comprehensive analysis, enhancing patient outcomes.

Unified Coding for Both Human Perception and Generalized Machine Analytics with CLIP Supervision

The image compression model has long struggled with adaptability and generalization, as the decoded bitstream typically serves only human or machine needs and fails to preserve information for unseen visual tasks. Therefore, this paper innovatively introduces supervision obtained from multimodal pre-training models and incorporates adaptive multi-objective optimization tailored to support both human visual perception and machine vision simultaneously with a single bitstream, denoted as Unified and Generalized Image Coding for Machine (UG-ICM). Specifically, to get rid of the reliance between compression models with downstream task supervision, we introduce Contrastive Language-Image Pre-training (CLIP) models into the training constraint for improved generalization. Global-to-instance-wise CLIP supervision is applied to help obtain hierarchical semantics that make models more generalizable for the tasks relying on the information of different granularity. Furthermore, for supporting both human and machine visions with only a unifying bitstream, we incorporate a conditional decoding strategy that takes as conditions human or machine preferences, enabling the bitstream to be decoded into different versions for corresponding preferences. As such, our proposed UG-ICM is fully trained in a self-supervised manner, i.e., without awareness of any specific downstream models and tasks. The extensive experiments have shown that the proposed UG-ICM is capable of achieving remarkable improvements in various unseen machine analytics tasks, while simultaneously providing perceptually satisfying images.

Prism: Mining Task-aware Domains in Non-i.i.d. IMU Data for Flexible User Perception

A wide range of user perception applications leverage inertial measurement unit (IMU) data for online prediction. However, restricted by the non-i.i.d. nature of IMU data collected from mobile devices, most systems work well only in a controlled setting (e.g., for a specific user in particular postures), limiting application scenarios. To achieve uncontrolled online prediction on mobile devices, referred to as the flexible user perception (FUP) problem, is attractive but hard. In this paper, we propose a novel scheme, called Prism, which can obtain high FUP accuracy on mobile devices. The core of Prism is to discover task-aware domains embedded in IMU dataset, and to train a domain-aware model on each identified domain. To this end, we design an expectation-maximization (EM) algorithm to estimate latent domains with respect to the specific downstream perception task. Finally, the best-fit model can be automatically selected for use by comparing the test sample and all identified domains in the feature space. We implement Prism on various mobile devices and conduct extensive experiments. Results demonstrate that Prism can achieve the best FUP performance with a low latency.

GloFinder: AI-empowered QuPath Plugin for WSI-level Glomerular Detection, Visualization, and Curation

Artificial intelligence (AI) has demonstrated significant success in automating the detection of glomeruli, the key functional units of the kidney, from whole slide images (WSIs) in kidney pathology. However, existing open-source tools are often distributed as source code or Docker containers, requiring advanced programming skills that hinder accessibility for non-programmers, such as clinicians. Additionally, current models are typically trained on a single dataset and lack flexibility in adjusting confidence levels for predictions. To overcome these challenges, we introduce GloFinder, a QuPath plugin designed for single-click automated glomeruli detection across entire WSIs with online editing through the graphical user interface (GUI). GloFinder employs CircleNet, an anchor-free detection framework utilizing circle representations for precise object localization, with models trained on approximately 160,000 manually annotated glomeruli. To further enhance accuracy, the plugin incorporates Weighted Circle Fusion (WCF), an ensemble method that combines confidence scores from multiple CircleNet models to produce refined predictions, achieving superior performance in glomerular detection. GloFinder enables direct visualization and editing of results in QuPath, facilitating seamless interaction for clinicians and providing a powerful tool for nephropathology research and clinical practice.

Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology

Segmenting glomerular intraglomerular tissue and lesions traditionally depends on detailed morphological evaluations by expert nephropathologists, a labor-intensive process susceptible to interobserver variability. Our group previously developed the Glo-In-One toolkit for integrated detection and segmentation of glomeruli. In this study, we leverage the Glo-In-One toolkit to version 2 with fine-grained segmentation capabilities, curating 14 distinct labels for tissue regions, cells, and lesions across a dataset of 23,529 annotated glomeruli across human and mouse histopathology data. To our knowledge, this dataset is among the largest of its kind to date.In this study, we present a single dynamic head deep learning architecture designed to segment 14 classes within partially labeled images of human and mouse pathology data. Our model was trained using a training set derived from 368 annotated kidney whole-slide images (WSIs) to identify 5 key intraglomerular tissues covering Bowman's capsule, glomerular tuft, mesangium, mesangial cells, and podocytes. Additionally, the network segments 9 glomerular lesion classes including adhesion, capsular drop, global sclerosis, hyalinosis, mesangial lysis, microaneurysm, nodular sclerosis, mesangial expansion, and segmental sclerosis. The glomerulus segmentation model achieved a decent performance compared with baselines, and achieved a 76.5 % average Dice Similarity Coefficient (DSC). Additional, transfer learning from rodent to human for glomerular lesion segmentation model has enhanced the average segmentation accuracy across different types of lesions by more than 3 %, as measured by Dice scores. The Glo-In-One-v2 model and trained weight have been made publicly available at https: //github.com/hrlblab/Glo-In-One_v2.

How Good Are We? Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment

Training AI foundation models has emerged as a promising large-scale learning approach for addressing real-world healthcare challenges, including digital pathology. While many of these models have been developed for tasks like disease diagnosis and tissue quantification using extensive and diverse training datasets, their readiness for deployment on some arguably simplest tasks, such as nuclei segmentation within a single organ (e.g., the kidney), remains uncertain. This paper seeks to answer this key question, "How good are we?", by thoroughly evaluating the performance of recent cell foundation models on a curated multi-center, multi-disease, and multi-species external testing dataset. Additionally, we tackle a more challenging question, "How can we improve?", by developing and assessing human-in-the-loop data enrichment strategies aimed at enhancing model performance while minimizing the reliance on pixel-level human annotation. To address the first question, we curated a multicenter, multidisease, and multispecies dataset consisting of 2,542 kidney whole slide images (WSIs). Three state-of-the-art (SOTA) cell foundation models-Cellpose, StarDist, and CellViT-were selected for evaluation. To tackle the second question, we explored data enrichment algorithms by distilling predictions from the different foundation models with a human-in-the-loop framework, aiming to further enhance foundation model performance with minimal human efforts. Our experimental results showed that all three foundation models improved over their baselines with model fine-tuning with enriched data. Interestingly, the baseline model with the highest F1 score does not yield the best segmentation outcomes after fine-tuning. This study establishes a benchmark for the development and deployment of cell vision foundation models tailored for real-world data applications.

LLM Unlearning via Loss Adjustment with Only Forget Data

Unlearning in Large Language Models (LLMs) is essential for ensuring ethical and responsible AI use, especially in addressing privacy leak, bias, safety, and evolving regulations. Existing approaches to LLM unlearning often rely on retain data or a reference LLM, yet they struggle to adequately balance unlearning performance with overall model utility. This challenge arises because leveraging explicit retain data or implicit knowledge of retain data from a reference LLM to fine-tune the model tends to blur the boundaries between the forgotten and retain data, as different queries often elicit similar responses. In this work, we propose eliminating the need to retain data or the reference LLM for response calibration in LLM unlearning. Recognizing that directly applying gradient ascent on the forget data often leads to optimization instability and poor performance, our method guides the LLM on what not to respond to, and importantly, how to respond, based on the forget data. Hence, we introduce Forget data only Loss AjustmenT (FLAT), a "flat" loss adjustment approach which addresses these issues by maximizing f-divergence between the available template answer and the forget answer only w.r.t. the forget data. The variational form of the defined f-divergence theoretically provides a way of loss adjustment by assigning different importance weights for the learning w.r.t. template responses and the forgetting of responses subject to unlearning. Empirical results demonstrate that our approach not only achieves superior unlearning performance compared to existing methods but also minimizes the impact on the model's retained capabilities, ensuring high utility across diverse tasks, including copyrighted content unlearning on Harry Potter dataset and MUSE Benchmark, and entity unlearning on the TOFU dataset.

Alignment-Enhanced Decoding:Defending via Token-Level Adaptive Refining of Probability Distributions

Large language models are susceptible to jailbreak attacks, which can result in the generation of harmful content. While prior defenses mitigate these risks by perturbing or inspecting inputs, they ignore competing objectives, the underlying cause of alignment failures. In this paper, we propose Alignment-Enhanced Decoding (AED), a novel defense that employs adaptive decoding to address the root causes of jailbreak issues. We first define the Competitive Index to quantify alignment failures and utilize feedback from self-evaluation to compute post-alignment logits. Then, AED adaptively combines AED and post-alignment logits with the original logits to obtain harmless and helpful distributions. Consequently, our method enhances safety alignment while maintaining helpfulness. We conduct experiments across five models and four common jailbreaks, with the results validating the effectiveness of our approach. Code is available at https://github.com/GIGABaozi/AED.git.

Assessment of Cell Nuclei AI Foundation Models in Kidney Pathology

Cell nuclei instance segmentation is a crucial task in digital kidney pathology. Traditional automatic segmentation methods often lack generalizability when applied to unseen datasets. Recently, the success of foundation models (FMs) has provided a more generalizable solution, potentially enabling the segmentation of any cell type. In this study, we perform a large-scale evaluation of three widely used state-of-the-art (SOTA) cell nuclei foundation models (Cellpose, StarDist, and CellViT). Specifically, we created a highly diverse evaluation dataset consisting of 2,542 kidney whole slide images (WSIs) collected from both human and rodent sources, encompassing various tissue types, sizes, and staining methods. To our knowledge, this is the largest-scale evaluation of its kind to date. Our quantitative analysis of the prediction distribution reveals a persistent performance gap in kidney pathology. Among the evaluated models, CellViT demonstrated superior performance in segmenting nuclei in kidney pathology. However, none of the foundation models are perfect; a performance gap remains in general nuclei segmentation for kidney pathology.

Adapting Mouse Pathological Model to Human Glomerular Lesion Segmentation

Moving from animal models to human applications in preclinical research encompasses a broad spectrum of disciplines in medical science. A fundamental element in the development of new drugs, treatments, diagnostic methods, and in deepening our understanding of disease processes is the accurate measurement of kidney tissues. Past studies have demonstrated the viability of translating glomeruli segmentation techniques from mouse models to human applications. Yet, these investigations tend to neglect the complexities involved in segmenting pathological glomeruli affected by different lesions. Such lesions present a wider range of morphological variations compared to healthy glomerular tissue, which are arguably more valuable than normal glomeruli in clinical practice. Furthermore, data on lesions from animal models can be more readily scaled up from disease models and whole kidney biopsies. This brings up a question: ``\textit{Can a pathological segmentation model trained on mouse models be effectively applied to human patients?}" To answer this question, we introduced GLAM, a deep learning study for fine-grained segmentation of human kidney lesions using a mouse model, addressing mouse-to-human transfer learning, by evaluating different learning strategies for segmenting human pathological lesions using zero-shot transfer learning and hybrid learning by leveraging mouse samples. From the results, the hybrid learning model achieved superior performance.