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Oct 22

PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

  • 22 authors
·
May 16, 2024

Multiple Instance Learning Framework with Masked Hard Instance Mining for Whole Slide Image Classification

The whole slide image (WSI) classification is often formulated as a multiple instance learning (MIL) problem. Since the positive tissue is only a small fraction of the gigapixel WSI, existing MIL methods intuitively focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting hard-to-classify instances. Some literature has revealed that hard examples are beneficial for modeling a discriminative boundary accurately. By applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which uses a Siamese structure (Teacher-Student) with a consistency constraint to explore the potential hard instances. With several instance masking strategies based on attention scores, MHIM-MIL employs a momentum teacher to implicitly mine hard instances for training the student model, which can be any attention-based MIL model. This counter-intuitive strategy essentially enables the student to learn a better discriminating boundary. Moreover, the student is used to update the teacher with an exponential moving average (EMA), which in turn identifies new hard instances for subsequent training iterations and stabilizes the optimization. Experimental results on the CAMELYON-16 and TCGA Lung Cancer datasets demonstrate that MHIM-MIL outperforms other latest methods in terms of performance and training cost. The code is available at: https://github.com/DearCaat/MHIM-MIL.

  • 6 authors
·
Jul 27, 2023

Rethinking Multiple Instance Learning for Whole Slide Image Classification: A Good Instance Classifier is All You Need

Weakly supervised whole slide image classification is usually formulated as a multiple instance learning (MIL) problem, where each slide is treated as a bag, and the patches cut out of it are treated as instances. Existing methods either train an instance classifier through pseudo-labeling or aggregate instance features into a bag feature through attention mechanisms and then train a bag classifier, where the attention scores can be used for instance-level classification. However, the pseudo instance labels constructed by the former usually contain a lot of noise, and the attention scores constructed by the latter are not accurate enough, both of which affect their performance. In this paper, we propose an instance-level MIL framework based on contrastive learning and prototype learning to effectively accomplish both instance classification and bag classification tasks. To this end, we propose an instance-level weakly supervised contrastive learning algorithm for the first time under the MIL setting to effectively learn instance feature representation. We also propose an accurate pseudo label generation method through prototype learning. We then develop a joint training strategy for weakly supervised contrastive learning, prototype learning, and instance classifier training. Extensive experiments and visualizations on four datasets demonstrate the powerful performance of our method. Codes will be available.

  • 5 authors
·
Jul 5, 2023

PresentBench: A Fine-Grained Rubric-Based Benchmark for Slide Generation

Slides serve as a critical medium for conveying information in presentation-oriented scenarios such as academia, education, and business. Despite their importance, creating high-quality slide decks remains time-consuming and cognitively demanding. Recent advances in generative models, such as Nano Banana Pro, have made automated slide generation increasingly feasible. However, existing evaluations of slide generation are often coarse-grained and rely on holistic judgments, making it difficult to accurately assess model capabilities or track meaningful advances in the field. In practice, the lack of fine-grained, verifiable evaluation criteria poses a critical bottleneck for both research and real-world deployment. In this paper, we propose PresentBench, a fine-grained, rubric-based benchmark for evaluating automated real-world slide generation. It contains 238 evaluation instances, each supplemented with background materials required for slide creation. Moreover, we manually design an average of 54.1 checklist items per instance, each formulated as a binary question, to enable fine-grained, instance-specific evaluation of the generated slide decks. Extensive experiments show that PresentBench provides more reliable evaluation results than existing methods, and exhibits significantly stronger alignment with human preferences. Furthermore, our benchmark reveals that NotebookLM significantly outperforms other slide generation methods, highlighting substantial recent progress in this domain.

Multistain Pretraining for Slide Representation Learning in Pathology

Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valuable in computational pathology. These models hold the potential to advance critical tasks such as few-shot classification, slide retrieval, and patient stratification. Existing approaches for slide representation learning extend the principles of SSL from small images (e.g., 224 x 224 patches) to entire slides, usually by aligning two different augmentations (or views) of the slide. Yet the resulting representation remains constrained by the limited clinical and biological diversity of the views. Instead, we postulate that slides stained with multiple markers, such as immunohistochemistry, can be used as different views to form a rich task-agnostic training signal. To this end, we introduce Madeleine, a multimodal pretraining strategy for slide representation learning. Madeleine is trained with a dual global-local cross-stain alignment objective on large cohorts of breast cancer samples (N=4,211 WSIs across five stains) and kidney transplant samples (N=12,070 WSIs across four stains). We demonstrate the quality of slide representations learned by Madeleine on various downstream evaluations, ranging from morphological and molecular classification to prognostic prediction, comprising 21 tasks using 7,299 WSIs from multiple medical centers. Code is available at https://github.com/mahmoodlab/MADELEINE.

  • 10 authors
·
Aug 5, 2024

BigCell: Generating Gigapixel Whole-Slide Images

Whole-slide images (WSIs) are gigapixel-scale digital scans of histopathology tissue and serve as the primary basis for cancer diagnosis. Existing histopathology generative models operate at the patch scale, producing fixed-size tiles of at most 1024times1024 pixels which encompass only a small fraction of the WSI. In contrast, text reports for clinical diagnoses and slide-level diagnostic labels -- the supervision that exists at scale -- operate at the whole-slide level. We present BigCell, the first approach to generate coherent whole-slide histopathology images at native gigapixel resolution. BigCell trains a flow-matching transformer at 2048times2048 pixels on over 120,000 publicly available WSIs spanning multiple organ types. Conditioning on embeddings from pathology foundation models and using an inference-time sliding-window pipeline, BigCell generates coherent images of up to 32,768times32,768 pixels, outperforming prior tile generators on both tile-level and slide-level fidelity metrics. To make gigapixel synthesis practical, we introduce an adaptive scheduling strategy that prioritizes important slide regions, speeding up image generation by over 3\ttimes with minimal quality degradation. Furthermore, we propose the first text-to-image synthesis at 8k resolution by training a separate model that produces dense conditioning grids directly from pathology text reports. We demonstrate that augmenting with synthetic samples improves slide-level few-shot classification performance by up to 18 % over baselines trained on real data.

From Patches to Patients: A study of the tile-to-slide performance transferability in Digital Pathology

Foundation Models (FMs) have recently redefined the state-of-the-art in histopathology by providing robust representations for whole-slide image (WSI) analysis. However, selecting the optimal foundation model (FM) for a specific clinical cohort currently requires multiple preprocessing steps, followed by computationally expensive feature extraction and the training of a Multiple Instance Learning (MIL) aggregator for every model. In this work, we investigate whether efficient tile-level linear probing can serve as a reliable proxy for slide-level performance, reducing the need to run full slide-level pipelines for every candidate encoder. We benchmark 19 state-of-the-art FMs on 42 slide-level and 16 tile-level tasks, comparing tile probing metrics against slide-level outcomes using ABMIL and Mean Pooling aggregations. We observe a high correlation between tile and slide performance across varying task difficulties, indicating that encoder representation quality is the primary determinant of WSI success. Sensitivity analyses show that transferability is stable across models and is more influenced by cohort sizes and numbers of tiles per slide than by average task difficulty. We also measure the agreement in best performing models between tile and slide-level tasks, showing tile benchmarks reliably shortlist strong candidates. Overall, our study indicates that tile-level benchmarking provides an efficient and practical first step for narrowing down candidate models, while slide-level evaluation remains essential for final validation on clinical tasks.

  • 5 authors
·
Jun 8

SlideChat: A Large Vision-Language Assistant for Whole-Slide Pathology Image Understanding

Despite the progress made by multimodal large language models (MLLMs) in computational pathology, they remain limited by a predominant focus on patch-level analysis, missing essential contextual information at the whole-slide level. The lack of large-scale instruction datasets and the gigapixel scale of whole slide images (WSIs) pose significant developmental challenges. In this paper, we present SlideChat, the first vision-language assistant capable of understanding gigapixel whole-slide images, exhibiting excellent multimodal conversational capability and response complex instruction across diverse pathology scenarios. To support its development, we created SlideInstruction, the largest instruction-following dataset for WSIs consisting of 4.2K WSI captions and 176K VQA pairs with multiple categories. Furthermore, we propose SlideBench, a multimodal benchmark that incorporates captioning and VQA tasks to assess SlideChat's capabilities in varied clinical settings such as microscopy, diagnosis. Compared to both general and specialized MLLMs, SlideChat exhibits exceptional capabilities achieving state-of-the-art performance on 18 of 22 tasks. For example, it achieved an overall accuracy of 81.17% on SlideBench-VQA (TCGA), and 54.15% on SlideBench-VQA (BCNB). We will fully release SlideChat, SlideInstruction and SlideBench as open-source resources to facilitate research and development in computational pathology.

  • 11 authors
·
Oct 15, 2024

Animation Needs Attention: A Holistic Approach to Slides Animation Comprehension with Visual-Language Models

Slide animations, such as fade-in, fly-in, and wipe, are critical for audience engagement, efficient information delivery, and vivid visual expression. However, most AI-driven slide-generation tools still lack native animation support, and existing vision-language models (VLMs) struggle with animation tasks due to the absence of public datasets and limited temporal-reasoning capabilities. To address this gap, we release the first public dataset for slide-animation modeling: 12,000 triplets of natural-language descriptions, animation JSON files, and rendered videos, collectively covering every built-in PowerPoint effect. Using this resource, we fine-tune Qwen-2.5-VL-7B with Low-Rank Adaptation (LoRA) and achieve consistent improvements over GPT-4.1 and Gemini-2.5-Pro in BLEU-4, ROUGE-L, SPICE, and our Coverage-Order-Detail Assessment (CODA) metric, which evaluates action coverage, temporal order, and detail fidelity. On a manually created test set of slides, the LoRA model increases BLEU-4 by around 60%, ROUGE-L by 30%, and shows significant improvements in CODA-detail. This demonstrates that low-rank adaptation enables reliable temporal reasoning and generalization beyond synthetic data. Overall, our dataset, LoRA-enhanced model, and CODA metric provide a rigorous benchmark and foundation for future research on VLM-based dynamic slide generation.

  • 7 authors
·
Jul 5, 2025

PRISM2: Unlocking Multi-Modal General Pathology AI with Clinical Dialogue

Recent rapid progress in the field of computational pathology has been enabled by foundation models. These models are beginning to move beyond encoding image patches towards whole-slide understanding but their clinical utility remains limited. In this work, we present PRISM2, a multimodal slide-level foundation model trained on data from 700,000 diagnostic specimen-report pairs, the largest vision (2.3 million whole slide images) and language (14M question-answer pairs) histopathology dataset to date. By learning through clinical-dialogue supervision, PRISM2 aligns histomorphologic features with the language of diagnostic reasoning, producing slide-level representations that support both direct diagnostic question-answering and transferable embeddings for downstream tasks. Without additional training, PRISM2 matches or exceeds the cancer-detection performance of clinical-grade products. This is observed without loss of generality on other tasks, where PRISM2 achieves top performance. Finally, using survival prediction as the example, we show that task-specific finetuning with a large dataset can outperform task-specific models, further improving performance. These results demonstrate how language-supervised pretraining provides a scalable, clinically grounded signal for learning generalizable pathology representations, bridging human diagnostic reasoning and foundation-model performance.

  • 19 authors
·
Oct 30, 2025

SlideBank: A Persistent Hierarchical Evidence Bank for Consistent Whole-Slide Reasoning

Whole-slide images (WSIs) are challenging for vision-language reasoning because diagnostically relevant morphology is sparse, heterogeneous, and distributed across gigapixel-scale images and multiple spatial resolutions. Existing WSI models and pathology agents can aggregate slide features or actively acquire evidence, but the information retained after exploration is often difficult to access semantically while preserving its connection to the original visual evidence. We introduce SlideBank, a training-free framework that represents each WSI as a persistent, concept-indexed, and spatially grounded evidence bank. SlideBank performs question-independent coarse-to-fine exploration to identify informative regions and multi-scale views, converts them into explicit morphological observations, and grounds pathology signals to their supporting patches and WSI coordinates. At inference time, questions are routed to relevant signals and evidence scales, and the linked global, regional, and patch evidence is integrated through confidence-based cross-level consensus. Experiments on WSI-VQA and SlideBench-BCNB show that with Patho-R1, SlideBank reaches 52.77% on WSI-VQA and with Quilt-LLaVA, it reaches 50.92% average accuracy on SlideBench-BCNB, while structured signal-guided retrieval consistently outperforms random evidence sampling. Reusing the same bank across repeated queries further achieves over 99% rephrasing consistency and substantially reduces amortized inference cost through persistent evidence reuse.

  • 9 authors
·
Aug 30

SlidesGen-Bench: Evaluating Slides Generation via Computational and Quantitative Metrics

The rapid evolution of Large Language Models (LLMs) has fostered diverse paradigms for automated slide generation, ranging from code-driven layouts to image-centric synthesis. However, evaluating these heterogeneous systems remains challenging, as existing protocols often struggle to provide comparable scores across architectures or rely on uncalibrated judgments. In this paper, we introduce SlidesGen-Bench, a benchmark designed to evaluate slide generation through a lens of three core principles: universality, quantification, and reliability. First, to establish a unified evaluation framework, we ground our analysis in the visual domain, treating terminal outputs as renderings to remain agnostic to the underlying generation method. Second, we propose a computational approach that quantitatively assesses slides across three distinct dimensions - Content, Aesthetics, and Editability - offering reproducible metrics where prior works relied on subjective or reference-dependent proxies. Finally, to ensure high correlation with human preference, we construct the Slides-Align1.5k dataset, a human preference aligned dataset covering slides from nine mainstream generation systems across seven scenarios. Our experiments demonstrate that SlidesGen-Bench achieves a higher degree of alignment with human judgment than existing evaluation pipelines. Our code and data are available at https://github.com/YunqiaoYang/SlidesGen-Bench.

  • 9 authors
·
Jan 14

Semantic Document Derendering: SVG Reconstruction via Vision-Language Modeling

Multimedia documents such as slide presentations and posters are designed to be interactive and easy to modify. Yet, they are often distributed in a static raster format, which limits editing and customization. Restoring their editability requires converting these raster images back into structured vector formats. However, existing geometric raster-vectorization methods, which rely on low-level primitives like curves and polygons, fall short at this task. Specifically, when applied to complex documents like slides, they fail to preserve the high-level structure, resulting in a flat collection of shapes where the semantic distinction between image and text elements is lost. To overcome this limitation, we address the problem of semantic document derendering by introducing SliDer, a novel framework that uses Vision-Language Models (VLMs) to derender slide images as compact and editable Scalable Vector Graphic (SVG) representations. SliDer detects and extracts attributes from individual image and text elements in a raster input and organizes them into a coherent SVG format. Crucially, the model iteratively refines its predictions during inference in a process analogous to human design, generating SVG code that more faithfully reconstructs the original raster upon rendering. Furthermore, we introduce Slide2SVG, a novel dataset comprising raster-SVG pairs of slide documents curated from real-world scientific presentations, to facilitate future research in this domain. Our results demonstrate that SliDer achieves a reconstruction LPIPS of 0.069 and is favored by human evaluators in 82.9% of cases compared to the strongest zero-shot VLM baseline.

  • 6 authors
·
Nov 17, 2025

Look before Transcription: End-to-End SlideASR with Visually-Anchored Policy Optimization

Automatic speech recognition (ASR) systems often struggle with domain-specific terminology, especially in specialized settings such as academic lectures. To address this, we define the SlideASR task, which leverages the rich visual information from presentation slides to improve transcription accuracy. Existing pipeline methods for this task tend to be complex and underperform. Although omni-modal large language models (OLLMs) provide a promising end-to-end framework, they frequently fail in practice by degenerating into simple optical character recognition (OCR) systems. To overcome this, we propose Visually-Anchored Policy Optimization (VAPO), a novel post-training method designed to control the model's reasoning process. Drawing on the Chain-of-Thought reasoning paradigm, VAPO enforces a structured "Look before Transcription" procedure using a <think><answer> format. Specifically, the model first performs OCR on the slide content within the think step, then generates the transcription by referencing this recognized visual information in the answer step. This reasoning process is optimized via reinforcement learning with four distinct rewards targeting format compliance, OCR accuracy, ASR quality, and visual anchoring consistency. To support further research, we construct SlideASR-Bench, a new entity-rich benchmark consisting of a synthetic dataset for training and testing, and a challenging real-world set for evaluation. Extensive experiments demonstrate that VAPO significantly improves recognition of domain-specific terms, establishing an effective end-to-end paradigm for SlideASR.

  • 5 authors
·
Oct 8, 2025

PPTBench: Towards Holistic Evaluation of Large Language Models for PowerPoint Layout and Design Understanding

PowerPoint presentations combine rich textual content with structured visual layouts, making them a natural testbed for evaluating the multimodal reasoning and layout understanding abilities of modern MLLMs. However, existing benchmarks focus solely on narrow subtasks while overlooking layout-centric challenges, which are central to real-world slide creation and editing. To bridge this gap, we introduce PPTBench, a comprehensive multimodal benchmark for evaluating LLMs on PowerPoint-related tasks. Leveraging a diverse source of 958 PPTX files, PPTBench evaluates models across four categories with 4,439 samples, including Detection, Understanding, Modification, and Generation. Our experiments reveal a substantial gap between semantic understanding and visual-layout reasoning in current MLLMs: models can interpret slide content but fail to produce coherent spatial arrangements. Ablation and further analysis show that current MLLMs struggle to combine visual cues with JSON-based layout structures and fail to integrate visual information into their API planning ability. And case studies visually expose systematic layout errors such as misalignment and element overlap. These findings provides a new perspective on evaluating VLLMs in PPT scenarios, highlighting challenges and directions for future research on visual-structural reasoning and coherent slide generation. All datasets and code are fully released to support reproducibility and future research.

  • 5 authors
·
Dec 2, 2025

SlideTailor: Personalized Presentation Slide Generation for Scientific Papers

Automatic presentation slide generation can greatly streamline content creation. However, since preferences of each user may vary, existing under-specified formulations often lead to suboptimal results that fail to align with individual user needs. We introduce a novel task that conditions paper-to-slides generation on user-specified preferences. We propose a human behavior-inspired agentic framework, SlideTailor, that progressively generates editable slides in a user-aligned manner. Instead of requiring users to write their preferences in detailed textual form, our system only asks for a paper-slides example pair and a visual template - natural and easy-to-provide artifacts that implicitly encode rich user preferences across content and visual style. Despite the implicit and unlabeled nature of these inputs, our framework effectively distills and generalizes the preferences to guide customized slide generation. We also introduce a novel chain-of-speech mechanism to align slide content with planned oral narration. Such a design significantly enhances the quality of generated slides and enables downstream applications like video presentations. To support this new task, we construct a benchmark dataset that captures diverse user preferences, with carefully designed interpretable metrics for robust evaluation. Extensive experiments demonstrate the effectiveness of our framework.

Multimodal Lecture Presentations Dataset: Understanding Multimodality in Educational Slides

Lecture slide presentations, a sequence of pages that contain text and figures accompanied by speech, are constructed and presented carefully in order to optimally transfer knowledge to students. Previous studies in multimedia and psychology attribute the effectiveness of lecture presentations to their multimodal nature. As a step toward developing AI to aid in student learning as intelligent teacher assistants, we introduce the Multimodal Lecture Presentations dataset as a large-scale benchmark testing the capabilities of machine learning models in multimodal understanding of educational content. Our dataset contains aligned slides and spoken language, for 180+ hours of video and 9000+ slides, with 10 lecturers from various subjects (e.g., computer science, dentistry, biology). We introduce two research tasks which are designed as stepping stones towards AI agents that can explain (automatically captioning a lecture presentation) and illustrate (synthesizing visual figures to accompany spoken explanations) educational content. We provide manual annotations to help implement these two research tasks and evaluate state-of-the-art models on them. Comparing baselines and human student performances, we find that current models struggle in (1) weak crossmodal alignment between slides and spoken text, (2) learning novel visual mediums, (3) technical language, and (4) long-range sequences. Towards addressing this issue, we also introduce PolyViLT, a multimodal transformer trained with a multi-instance learning loss that is more effective than current approaches. We conclude by shedding light on the challenges and opportunities in multimodal understanding of educational presentations.

  • 5 authors
·
Aug 17, 2022

Solving the Catastrophic Forgetting Problem in Generalized Category Discovery

Generalized Category Discovery (GCD) aims to identify a mix of known and novel categories within unlabeled data sets, providing a more realistic setting for image recognition. Essentially, GCD needs to remember existing patterns thoroughly to recognize novel categories. Recent state-of-the-art method SimGCD transfers the knowledge from known-class data to the learning of novel classes through debiased learning. However, some patterns are catastrophically forgot during adaptation and thus lead to poor performance in novel categories classification. To address this issue, we propose a novel learning approach, LegoGCD, which is seamlessly integrated into previous methods to enhance the discrimination of novel classes while maintaining performance on previously encountered known classes. Specifically, we design two types of techniques termed as Local Entropy Regularization (LER) and Dual-views Kullback Leibler divergence constraint (DKL). The LER optimizes the distribution of potential known class samples in unlabeled data, thus ensuring the preservation of knowledge related to known categories while learning novel classes. Meanwhile, DKL introduces Kullback Leibler divergence to encourage the model to produce a similar prediction distribution of two view samples from the same image. In this way, it successfully avoids mismatched prediction and generates more reliable potential known class samples simultaneously. Extensive experiments validate that the proposed LegoGCD effectively addresses the known category forgetting issue across all datasets, eg, delivering a 7.74% and 2.51% accuracy boost on known and novel classes in CUB, respectively. Our code is available at: https://github.com/Cliffia123/LegoGCD.

  • 8 authors
·
Jan 9, 2025

Mixed Magnification Aggregation for Generalizable Region-Level Representations in Computational Pathology

In recent years, a standard computational pathology workflow has emerged where whole slide images are cropped into tiles, these tiles are processed using a foundation model, and task-specific models are built using the resulting representations. At least 15 different foundation models have been proposed, and the vast majority are trained exclusively with tiles using the 20times magnification. However, it is well known that certain histologic features can only be discerned with larger context windows and requires a pathologist to zoom in and out when analyzing a whole slide image. Furthermore, creating 224times224 pixel crops at 20times leads to a large number of tiles per slide, which can be gigapixel in size. To more accurately capture multi-resolution features and investigate the possibility of reducing the number of representations per slide, we propose a region-level mixing encoder. Our approach jointly fuses image tile representations of a mixed magnification foundation model using a masked embedding modeling pretraining step. We explore a design space for pretraining the proposed mixed-magnification region aggregators and evaluate our models on transfer to biomarker prediction tasks representing various cancer types. Results demonstrate cancer dependent improvements in predictive performance, highlighting the importance of spatial context and understanding.

  • 10 authors
·
Feb 24

Enhancing Instance-Level Image Classification with Set-Level Labels

Instance-level image classification tasks have traditionally relied on single-instance labels to train models, e.g., few-shot learning and transfer learning. However, set-level coarse-grained labels that capture relationships among instances can provide richer information in real-world scenarios. In this paper, we present a novel approach to enhance instance-level image classification by leveraging set-level labels. We provide a theoretical analysis of the proposed method, including recognition conditions for fast excess risk rate, shedding light on the theoretical foundations of our approach. We conducted experiments on two distinct categories of datasets: natural image datasets and histopathology image datasets. Our experimental results demonstrate the effectiveness of our approach, showcasing improved classification performance compared to traditional single-instance label-based methods. Notably, our algorithm achieves 13% improvement in classification accuracy compared to the strongest baseline on the histopathology image classification benchmarks. Importantly, our experimental findings align with the theoretical analysis, reinforcing the robustness and reliability of our proposed method. This work bridges the gap between instance-level and set-level image classification, offering a promising avenue for advancing the capabilities of image classification models with set-level coarse-grained labels.

  • 4 authors
·
Nov 8, 2023

Few-Shot Class-Incremental Learning via Training-Free Prototype Calibration

Real-world scenarios are usually accompanied by continuously appearing classes with scare labeled samples, which require the machine learning model to incrementally learn new classes and maintain the knowledge of base classes. In this Few-Shot Class-Incremental Learning (FSCIL) scenario, existing methods either introduce extra learnable components or rely on a frozen feature extractor to mitigate catastrophic forgetting and overfitting problems. However, we find a tendency for existing methods to misclassify the samples of new classes into base classes, which leads to the poor performance of new classes. In other words, the strong discriminability of base classes distracts the classification of new classes. To figure out this intriguing phenomenon, we observe that although the feature extractor is only trained on base classes, it can surprisingly represent the semantic similarity between the base and unseen new classes. Building upon these analyses, we propose a simple yet effective Training-frEE calibratioN (TEEN) strategy to enhance the discriminability of new classes by fusing the new prototypes (i.e., mean features of a class) with weighted base prototypes. In addition to standard benchmarks in FSCIL, TEEN demonstrates remarkable performance and consistent improvements over baseline methods in the few-shot learning scenario. Code is available at: https://github.com/wangkiw/TEEN

  • 5 authors
·
Dec 8, 2023

PathAlign: A vision-language model for whole slide images in histopathology

Microscopic interpretation of histopathology images underlies many important diagnostic and treatment decisions. While advances in vision-language modeling raise new opportunities for analysis of such images, the gigapixel-scale size of whole slide images (WSIs) introduces unique challenges. Additionally, pathology reports simultaneously highlight key findings from small regions while also aggregating interpretation across multiple slides, often making it difficult to create robust image-text pairs. As such, pathology reports remain a largely untapped source of supervision in computational pathology, with most efforts relying on region-of-interest annotations or self-supervision at the patch-level. In this work, we develop a vision-language model based on the BLIP-2 framework using WSIs paired with curated text from pathology reports. This enables applications utilizing a shared image-text embedding space, such as text or image retrieval for finding cases of interest, as well as integration of the WSI encoder with a frozen large language model (LLM) for WSI-based generative text capabilities such as report generation or AI-in-the-loop interactions. We utilize a de-identified dataset of over 350,000 WSIs and diagnostic text pairs, spanning a wide range of diagnoses, procedure types, and tissue types. We present pathologist evaluation of text generation and text retrieval using WSI embeddings, as well as results for WSI classification and workflow prioritization (slide-level triaging). Model-generated text for WSIs was rated by pathologists as accurate, without clinically significant error or omission, for 78% of WSIs on average. This work demonstrates exciting potential capabilities for language-aligned WSI embeddings.

  • 17 authors
·
Jun 27, 2024

AEM: Attention Entropy Maximization for Multiple Instance Learning based Whole Slide Image Classification

Multiple Instance Learning (MIL) has demonstrated effectiveness in analyzing whole slide images (WSIs), yet it often encounters overfitting challenges in real-world applications, particularly in the form of attention over-concentration. While existing methods to alleviate this issue introduce complex modules or processing steps, such as multiple-stage training and teacher-student distillation, this paper proposes a simple yet effective regularization: Attention Entropy Maximization (AEM). Motivated by our investigation revealing a positive correlation between attention entropy and model performance, AEM incorporates a negative entropy loss for attention values into the standard MIL framework, penalizing overly concentrated attention and encouraging the model to consider a broader range of informative regions in WSIs, potentially improving its generalization capabilities. Compared to existing overfitting mitigation methods, our AEM approach offers advantages of simplicity, efficiency, and versatility. It requires no additional modules or processing steps, involves only one hyperparameter, and demonstrates compatibility with MIL frameworks and techniques. These advantages make AEM particularly attractive for practical applications. We evaluate AEM on three benchmark datasets, demonstrating consistent performance improvements over existing methods. Furthermore, AEM shows high versatility, integrating effectively with four feature extractors, two advanced MIL frameworks, three attention mechanisms, and Subsampling augmentation technique. The source code is available at https://github.com/dazhangyu123/AEM.

  • 7 authors
·
Jun 17, 2024

A Multimodal Knowledge-enhanced Whole-slide Pathology Foundation Model

Remarkable strides in computational pathology have been made in the task-agnostic foundation model that advances the performance of a wide array of downstream clinical tasks. Despite the promising performance, there are still several challenges. First, prior works have resorted to either vision-only or image-caption data, disregarding pathology reports with more clinically authentic information from pathologists and gene expression profiles which respectively offer distinct knowledge for versatile clinical applications. Second, the current progress in pathology FMs predominantly concentrates on the patch level, where the restricted context of patch-level pretraining fails to capture whole-slide patterns. Even recent slide-level FMs still struggle to provide whole-slide context for patch representation. In this study, for the first time, we develop a pathology foundation model incorporating three levels of modalities: pathology slides, pathology reports, and gene expression data, which resulted in 26,169 slide-level modality pairs from 10,275 patients across 32 cancer types, amounting to over 116 million pathological patch images. To leverage these data for CPath, we propose a novel whole-slide pretraining paradigm that injects the multimodal whole-slide context into the patch representation, called Multimodal Self-TAught PRetraining (mSTAR). The proposed paradigm revolutionizes the pretraining workflow for CPath, enabling the pathology FM to acquire the whole-slide context. To the best of our knowledge, this is the first attempt to incorporate three modalities at the whole-slide context for enhancing pathology FMs. To systematically evaluate the capabilities of mSTAR, we built the largest spectrum of oncological benchmark, spanning 7 categories of oncological applications in 15 types of 97 practical oncological tasks.

  • 19 authors
·
Jul 22, 2024

Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification

In the application of Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) classification, attention mechanisms often focus on a subset of discriminative instances, which are closely linked to overfitting. To mitigate overfitting, we present Attention-Challenging MIL (ACMIL). ACMIL combines two techniques based on separate analyses for attention value concentration. Firstly, UMAP of instance features reveals various patterns among discriminative instances, with existing attention mechanisms capturing only some of them. To remedy this, we introduce Multiple Branch Attention (MBA) to capture more discriminative instances using multiple attention branches. Secondly, the examination of the cumulative value of Top-K attention scores indicates that a tiny number of instances dominate the majority of attention. In response, we present Stochastic Top-K Instance Masking (STKIM), which masks out a portion of instances with Top-K attention values and allocates their attention values to the remaining instances. The extensive experimental results on three WSI datasets with two pre-trained backbones reveal that our ACMIL outperforms state-of-the-art methods. Additionally, through heatmap visualization and UMAP visualization, this paper extensively illustrates ACMIL's effectiveness in suppressing attention value concentration and overcoming the overfitting challenge. The source code is available at https://github.com/dazhangyu123/ACMIL.

  • 6 authors
·
Nov 13, 2023

Pathology-CoT: Learning Visual Chain-of-Thought Agent from Expert Whole Slide Image Diagnosis Behavior

Diagnosing a whole-slide image is an interactive, multi-stage process involving changes in magnification and movement between fields. Although recent pathology foundation models are strong, practical agentic systems that decide what field to examine next, adjust magnification, and deliver explainable diagnoses are still lacking. The blocker is data: scalable, clinically aligned supervision of expert viewing behavior that is tacit and experience-based, not written in textbooks or online, and therefore absent from large language model training. We introduce the AI Session Recorder, which works with standard WSI viewers to unobtrusively record routine navigation and convert the viewer logs into standardized behavioral commands (inspect or peek at discrete magnifications) and bounding boxes. A lightweight human-in-the-loop review turns AI-drafted rationales into the Pathology-CoT dataset, a form of paired "where to look" and "why it matters" supervision produced at roughly six times lower labeling time. Using this behavioral data, we build Pathologist-o3, a two-stage agent that first proposes regions of interest and then performs behavior-guided reasoning. On gastrointestinal lymph-node metastasis detection, it achieved 84.5% precision, 100.0% recall, and 75.4% accuracy, exceeding the state-of-the-art OpenAI o3 model and generalizing across backbones. To our knowledge, this constitutes one of the first behavior-grounded agentic systems in pathology. Turning everyday viewer logs into scalable, expert-validated supervision, our framework makes agentic pathology practical and establishes a path to human-aligned, upgradeable clinical AI.

zhihuanglab Zhi Huang Lab
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Oct 6, 2025 2

Modeling Collaborator: Enabling Subjective Vision Classification With Minimal Human Effort via LLM Tool-Use

From content moderation to wildlife conservation, the number of applications that require models to recognize nuanced or subjective visual concepts is growing. Traditionally, developing classifiers for such concepts requires substantial manual effort measured in hours, days, or even months to identify and annotate data needed for training. Even with recently proposed Agile Modeling techniques, which enable rapid bootstrapping of image classifiers, users are still required to spend 30 minutes or more of monotonous, repetitive data labeling just to train a single classifier. Drawing on Fiske's Cognitive Miser theory, we propose a new framework that alleviates manual effort by replacing human labeling with natural language interactions, reducing the total effort required to define a concept by an order of magnitude: from labeling 2,000 images to only 100 plus some natural language interactions. Our framework leverages recent advances in foundation models, both large language models and vision-language models, to carve out the concept space through conversation and by automatically labeling training data points. Most importantly, our framework eliminates the need for crowd-sourced annotations. Moreover, our framework ultimately produces lightweight classification models that are deployable in cost-sensitive scenarios. Across 15 subjective concepts and across 2 public image classification datasets, our trained models outperform traditional Agile Modeling as well as state-of-the-art zero-shot classification models like ALIGN, CLIP, CuPL, and large visual question-answering models like PaLI-X.

  • 13 authors
·
Mar 4, 2024 1

Multiple Instance Learning Framework with Masked Hard Instance Mining for Gigapixel Histopathology Image Analysis

Digitizing pathological images into gigapixel Whole Slide Images (WSIs) has opened new avenues for Computational Pathology (CPath). As positive tissue comprises only a small fraction of gigapixel WSIs, existing Multiple Instance Learning (MIL) methods typically focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting challenging ones. Recent studies have shown that hard examples are crucial for accurately modeling discriminative boundaries. Applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which utilizes a Siamese structure with a consistency constraint to explore the hard instances. Using a class-aware instance probability, MHIM-MIL employs a momentum teacher to mask salient instances and implicitly mine hard instances for training the student model. To obtain diverse, non-redundant hard instances, we adopt large-scale random masking while utilizing a global recycle network to mitigate the risk of losing key features. Furthermore, the student updates the teacher using an exponential moving average, which identifies new hard instances for subsequent training iterations and stabilizes optimization. Experimental results on cancer diagnosis, subtyping, survival analysis tasks, and 12 benchmarks demonstrate that MHIM-MIL outperforms the latest methods in both performance and efficiency. The code is available at: https://github.com/DearCaat/MHIM-MIL.

  • 6 authors
·
Sep 14, 2025 2

Histopathological Image Classification based on Self-Supervised Vision Transformer and Weak Labels

Whole Slide Image (WSI) analysis is a powerful method to facilitate the diagnosis of cancer in tissue samples. Automating this diagnosis poses various issues, most notably caused by the immense image resolution and limited annotations. WSIs commonly exhibit resolutions of 100Kx100K pixels. Annotating cancerous areas in WSIs on the pixel level is prohibitively labor-intensive and requires a high level of expert knowledge. Multiple instance learning (MIL) alleviates the need for expensive pixel-level annotations. In MIL, learning is performed on slide-level labels, in which a pathologist provides information about whether a slide includes cancerous tissue. Here, we propose Self-ViT-MIL, a novel approach for classifying and localizing cancerous areas based on slide-level annotations, eliminating the need for pixel-wise annotated training data. Self-ViT- MIL is pre-trained in a self-supervised setting to learn rich feature representation without relying on any labels. The recent Vision Transformer (ViT) architecture builds the feature extractor of Self-ViT-MIL. For localizing cancerous regions, a MIL aggregator with global attention is utilized. To the best of our knowledge, Self-ViT- MIL is the first approach to introduce self-supervised ViTs in MIL-based WSI analysis tasks. We showcase the effectiveness of our approach on the common Camelyon16 dataset. Self-ViT-MIL surpasses existing state-of-the-art MIL-based approaches in terms of accuracy and area under the curve (AUC).

  • 6 authors
·
Oct 17, 2022

Adaptive Confidence Smoothing for Generalized Zero-Shot Learning

Generalized zero-shot learning (GZSL) is the problem of learning a classifier where some classes have samples and others are learned from side information, like semantic attributes or text description, in a zero-shot learning fashion (ZSL). Training a single model that operates in these two regimes simultaneously is challenging. Here we describe a probabilistic approach that breaks the model into three modular components, and then combines them in a consistent way. Specifically, our model consists of three classifiers: A "gating" model that makes soft decisions if a sample is from a "seen" class, and two experts: a ZSL expert, and an expert model for seen classes. We address two main difficulties in this approach: How to provide an accurate estimate of the gating probability without any training samples for unseen classes; and how to use expert predictions when it observes samples outside of its domain. The key insight to our approach is to pass information between the three models to improve each one's accuracy, while maintaining the modular structure. We test our approach, adaptive confidence smoothing (COSMO), on four standard GZSL benchmark datasets and find that it largely outperforms state-of-the-art GZSL models. COSMO is also the first model that closes the gap and surpasses the performance of generative models for GZSL, even-though it is a light-weight model that is much easier to train and tune. Notably, COSMO offers a new view for developing zero-shot models. Thanks to COSMO's modular structure, instead of trying to perform well both on seen and on unseen classes, models can focus on accurate classification of unseen classes, and later consider seen class models.

  • 2 authors
·
Dec 24, 2018

Wide and Deep Neural Networks Achieve Optimality for Classification

While neural networks are used for classification tasks across domains, a long-standing open problem in machine learning is determining whether neural networks trained using standard procedures are optimal for classification, i.e., whether such models minimize the probability of misclassification for arbitrary data distributions. In this work, we identify and construct an explicit set of neural network classifiers that achieve optimality. Since effective neural networks in practice are typically both wide and deep, we analyze infinitely wide networks that are also infinitely deep. In particular, using the recent connection between infinitely wide neural networks and Neural Tangent Kernels, we provide explicit activation functions that can be used to construct networks that achieve optimality. Interestingly, these activation functions are simple and easy to implement, yet differ from commonly used activations such as ReLU or sigmoid. More generally, we create a taxonomy of infinitely wide and deep networks and show that these models implement one of three well-known classifiers depending on the activation function used: (1) 1-nearest neighbor (model predictions are given by the label of the nearest training example); (2) majority vote (model predictions are given by the label of the class with greatest representation in the training set); or (3) singular kernel classifiers (a set of classifiers containing those that achieve optimality). Our results highlight the benefit of using deep networks for classification tasks, in contrast to regression tasks, where excessive depth is harmful.

  • 3 authors
·
Apr 29, 2022

What does a platypus look like? Generating customized prompts for zero-shot image classification

Open-vocabulary models are a promising new paradigm for image classification. Unlike traditional classification models, open-vocabulary models classify among any arbitrary set of categories specified with natural language during inference. This natural language, called "prompts", typically consists of a set of hand-written templates (e.g., "a photo of a {}") which are completed with each of the category names. This work introduces a simple method to generate higher accuracy prompts, without relying on any explicit knowledge of the task domain and with far fewer hand-constructed sentences. To achieve this, we combine open-vocabulary models with large language models (LLMs) to create Customized Prompts via Language models (CuPL, pronounced "couple"). In particular, we leverage the knowledge contained in LLMs in order to generate many descriptive sentences that contain important discriminating characteristics of the image categories. This allows the model to place a greater importance on these regions in the image when making predictions. We find that this straightforward and general approach improves accuracy on a range of zero-shot image classification benchmarks, including over one percentage point gain on ImageNet. Finally, this simple baseline requires no additional training and remains completely zero-shot. Code available at https://github.com/sarahpratt/CuPL.

  • 4 authors
·
Sep 7, 2022

MOOZY: A Patient-First Foundation Model for Computational Pathology

Computational pathology needs whole-slide image (WSI) foundation models that transfer across diverse clinical tasks, yet current approaches remain largely slide-centric, often depend on private data and expensive paired-report supervision, and do not explicitly model relationships among multiple slides from the same patient. We present MOOZY, a patient-first pathology foundation model in which the patient case, not the individual slide, is the core unit of representation. MOOZY explicitly models dependencies across all slides from the same patient via a case transformer during pretraining, combining multi-stage open self-supervision with scaled low-cost task supervision. In Stage 1, we pretrain a vision-only slide encoder on 77,134 public slide feature grids using masked self-distillation. In Stage 2, we align these representations with clinical semantics using a case transformer and multi-task supervision over 333 tasks from 56 public datasets, including 205 classification and 128 survival tasks across four endpoints. Across eight held-out tasks with five-fold frozen-feature probe evaluation, MOOZY achieves best or tied-best performance on most metrics and improves macro averages over TITAN by +7.37%, +5.50%, and +7.83% and over PRISM by +8.83%, +10.70%, and +9.78% for weighted F1, weighted ROC-AUC, and balanced accuracy, respectively. MOOZY is also parameter efficient with 85.77M parameters, 14x smaller than GigaPath. These results demonstrate that open, reproducible patient-level pretraining yields transferable embeddings, providing a practical path toward scalable patient-first histopathology foundation models.

AeSlides: Incentivizing Aesthetic Layout in LLM-Based Slide Generation via Verifiable Rewards

Large language models (LLMs) have demonstrated strong potential in agentic tasks, particularly in slide generation. However, slide generation poses a fundamental challenge: the generation process is text-centric, whereas its quality is governed by visual aesthetics. This modality gap leads current models to frequently produce slides with aesthetically suboptimal layouts. Existing solutions typically rely either on heavy visual reflection, which incurs high inference cost yet yields limited gains; or on fine-tuning with large-scale datasets, which still provides weak and indirect aesthetic supervision. In contrast, the explicit use of aesthetic principles as supervision remains unexplored. In this work, we present AeSlides, a reinforcement learning framework with verifiable rewards for Aesthetic layout supervision in Slide generation. We introduce a suite of meticulously designed verifiable metrics to quantify slide layout quality, capturing key layout issues in an accurate, efficient, and low-cost manner. Leveraging these verifiable metrics, we develop a GRPO-based reinforcement learning method that directly optimizes slide generation models for aesthetically coherent layouts. With only 5K training prompts on GLM-4.7-Flash, AeSlides improves aspect ratio compliance from 36% to 85%, while reducing whitespace by 44%, element collisions by 43%, and visual imbalance by 28%. Human evaluation further shows a substantial improvement in overall quality, increasing scores from 3.31 to 3.56 (+7.6%), outperforming both model-based reward optimization and reflection-based agentic approaches, and even edging out Claude-Sonnet-4.5. These results demonstrate that such a verifiable aesthetic paradigm provides an efficient and scalable approach to aligning slide generation with human aesthetic preferences. Our repository is available at https://github.com/ympan0508/aeslides.

  • 9 authors
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Apr 20

The Unreasonable Effectiveness of Easy Training Data for Hard Tasks

How can we train models to perform well on hard test data when hard training data is by definition difficult to label correctly? This question has been termed the scalable oversight problem and has drawn increasing attention as language models have continually improved. In this paper, we present the surprising conclusion that current language models often generalize relatively well from easy to hard data, even performing as well as "oracle" models trained on hard data. We demonstrate this kind of easy-to-hard generalization using simple training methods like in-context learning, linear classifier heads, and QLoRA for seven different measures of datapoint hardness, including six empirically diverse human hardness measures (like grade level) and one model-based measure (loss-based). Furthermore, we show that even if one cares most about model performance on hard data, it can be better to collect and train on easy data rather than hard data, since hard data is generally noisier and costlier to collect. Our experiments use open models up to 70b in size and four publicly available question-answering datasets with questions ranging in difficulty from 3rd grade science questions to college level STEM questions and general-knowledge trivia. We conclude that easy-to-hard generalization in LMs is surprisingly strong for the tasks studied, suggesting the scalable oversight problem may be easier than previously thought. Our code is available at https://github.com/allenai/easy-to-hard-generalization

  • 4 authors
·
Jan 12, 2024

STARC-9: A Large-scale Dataset for Multi-Class Tissue Classification for CRC Histopathology

Multi-class tissue-type classification of colorectal cancer (CRC) histopathologic images is a significant step in the development of downstream machine learning models for diagnosis and treatment planning. However, existing public CRC datasets often lack morphologic diversity, suffer from class imbalance, and contain low-quality image tiles, limiting model performance and generalizability. To address these issues, we introduce STARC-9 (STAnford coloRectal Cancer), a large-scale dataset for multi-class tissue classification. STARC-9 contains 630,000 hematoxylin and eosin-stained image tiles uniformly sampled across nine clinically relevant tissue classes (70,000 tiles per class) from 200 CRC patients at the Stanford University School of Medicine. The dataset was built using a novel framework, DeepCluster++, designed to ensure intra-class diversity and reduce manual curation. First, an encoder from a histopathology-specific autoencoder extracts feature vectors from tiles within each whole-slide image. Then, K-means clustering groups morphologically similar tiles, followed by equal-frequency binning to sample diverse morphologic patterns within each class. The selected tiles are subsequently verified by expert gastrointestinal pathologists to ensure accuracy. This semi-automated process significantly reduces manual effort while producing high-quality, diverse tiles. To evaluate STARC-9, we benchmarked convolutional neural networks, transformers, and pathology-specific foundation models on multi-class CRC tissue classification and segmentation tasks, showing superior generalizability compared to models trained on existing datasets. Although we demonstrate the utility of DeepCluster++ on CRC as a pilot use-case, it is a flexible framework that can be used for constructing high-quality datasets from large WSI repositories across a wide range of cancer and non-cancer applications.

  • 8 authors
·
Oct 31, 2025

LADDER: Language Driven Slice Discovery and Error Rectification

Error slice discovery is crucial to diagnose and mitigate model errors. Current clustering or discrete attribute-based slice discovery methods face key limitations: 1) clustering results in incoherent slices, while assigning discrete attributes to slices leads to incomplete coverage of error patterns due to missing or insufficient attributes; 2) these methods lack complex reasoning, preventing them from fully explaining model biases; 3) they fail to integrate domain knowledge, limiting their usage in specialized fields \eg radiology. We propose\ladder (Language-Driven Discovery and Error Rectification), to address the limitations by: (1) leveraging the flexibility of natural language to address incompleteness, (2) employing LLM's latent domain knowledge and advanced reasoning to analyze sentences and derive testable hypotheses directly, identifying biased attributes, and form coherent error slices without clustering. Existing mitigation methods typically address only the worst-performing group, often amplifying errors in other subgroups. In contrast,\ladder generates pseudo attributes from the discovered hypotheses to mitigate errors across all biases without explicit attribute annotations or prior knowledge of bias. Rigorous evaluations on 6 datasets spanning natural and medical images -- comparing 200+ classifiers with diverse architectures, pretraining strategies, and LLMs -- show that\ladder consistently outperforms existing baselines in discovering and mitigating biases.

BostonU Boston University
·
Jul 31, 2024

Quilt-1M: One Million Image-Text Pairs for Histopathology

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

  • 8 authors
·
Jun 19, 2023

Visually Impaired Aid using Convolutional Neural Networks, Transfer Learning, and Particle Competition and Cooperation

Navigation and mobility are some of the major problems faced by visually impaired people in their daily lives. Advances in computer vision led to the proposal of some navigation systems. However, most of them require expensive and/or heavy hardware. In this paper we propose the use of convolutional neural networks (CNN), transfer learning, and semi-supervised learning (SSL) to build a framework aimed at the visually impaired aid. It has low computational costs and, therefore, may be implemented on current smartphones, without relying on any additional equipment. The smartphone camera can be used to automatically take pictures of the path ahead. Then, they will be immediately classified, providing almost instantaneous feedback to the user. We also propose a dataset to train the classifiers, including indoor and outdoor situations with different types of light, floor, and obstacles. Many different CNN architectures are evaluated as feature extractors and classifiers, by fine-tuning weights pre-trained on a much larger dataset. The graph-based SSL method, known as particle competition and cooperation, is also used for classification, allowing feedback from the user to be incorporated without retraining the underlying network. 92\% and 80\% classification accuracy is achieved in the proposed dataset in the best supervised and SSL scenarios, respectively.

  • 2 authors
·
May 9, 2020

Koala-36M: A Large-scale Video Dataset Improving Consistency between Fine-grained Conditions and Video Content

As visual generation technologies continue to advance, the scale of video datasets has expanded rapidly, and the quality of these datasets is critical to the performance of video generation models. We argue that temporal splitting, detailed captions, and video quality filtering are three key factors that determine dataset quality. However, existing datasets exhibit various limitations in these areas. To address these challenges, we introduce Koala-36M, a large-scale, high-quality video dataset featuring accurate temporal splitting, detailed captions, and superior video quality. The core of our approach lies in improving the consistency between fine-grained conditions and video content. Specifically, we employ a linear classifier on probability distributions to enhance the accuracy of transition detection, ensuring better temporal consistency. We then provide structured captions for the splitted videos, with an average length of 200 words, to improve text-video alignment. Additionally, we develop a Video Training Suitability Score (VTSS) that integrates multiple sub-metrics, allowing us to filter high-quality videos from the original corpus. Finally, we incorporate several metrics into the training process of the generation model, further refining the fine-grained conditions. Our experiments demonstrate the effectiveness of our data processing pipeline and the quality of the proposed Koala-36M dataset. Our dataset and code will be released at https://koala36m.github.io/.

  • 13 authors
·
Oct 10, 2024

PLUTO: Pathology-Universal Transformer

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

  • 33 authors
·
May 13, 2024

An accurate detection is not all you need to combat label noise in web-noisy datasets

Training a classifier on web-crawled data demands learning algorithms that are robust to annotation errors and irrelevant examples. This paper builds upon the recent empirical observation that applying unsupervised contrastive learning to noisy, web-crawled datasets yields a feature representation under which the in-distribution (ID) and out-of-distribution (OOD) samples are linearly separable. We show that direct estimation of the separating hyperplane can indeed offer an accurate detection of OOD samples, and yet, surprisingly, this detection does not translate into gains in classification accuracy. Digging deeper into this phenomenon, we discover that the near-perfect detection misses a type of clean examples that are valuable for supervised learning. These examples often represent visually simple images, which are relatively easy to identify as clean examples using standard loss- or distance-based methods despite being poorly separated from the OOD distribution using unsupervised learning. Because we further observe a low correlation with SOTA metrics, this urges us to propose a hybrid solution that alternates between noise detection using linear separation and a state-of-the-art (SOTA) small-loss approach. When combined with the SOTA algorithm PLS, we substantially improve SOTA results for real-world image classification in the presence of web noise github.com/PaulAlbert31/LSA

  • 6 authors
·
Jul 7, 2024 4

PathReasoner-R1: Instilling Structured Reasoning into Pathology Vision-Language Model via Knowledge-Guided Policy Optimization

Vision-Language Models (VLMs) are advancing computational pathology with superior visual understanding capabilities. However, current systems often reduce diagnosis to directly output conclusions without verifiable evidence-linked reasoning, which severely limits clinical trust and hinders expert error rectification. To address these barriers, we construct PathReasoner, the first large-scale dataset of whole-slide image (WSI) reasoning. Unlike previous work reliant on unverified distillation, we develop a rigorous knowledge-guided generation pipeline. By leveraging medical knowledge graphs, we explicitly align structured pathological findings and clinical reasoning with diagnoses, generating over 20K high-quality instructional samples. Based on the database, we propose PathReasoner-R1, which synergizes trajectory-masked supervised fine-tuning with reasoning-oriented reinforcement learning to instill structured chain-of-thought capabilities. To ensure medical rigor, we engineer a knowledge-aware multi-granular reward function incorporating an Entity Reward mechanism strictly aligned with knowledge graphs. This effectively guides the model to optimize for logical consistency rather than mere outcome matching, thereby enhancing robustness. Extensive experiments demonstrate that PathReasoner-R1 achieves state-of-the-art performance on both PathReasoner and public benchmarks across various image scales, equipping pathology models with transparent, clinically grounded reasoning capabilities. Dataset and code are available at https://github.com/cyclexfy/PathReasoner-R1.

  • 5 authors
·
Jan 29

ProAPO: Progressively Automatic Prompt Optimization for Visual Classification

Vision-language models (VLMs) have made significant progress in image classification by training with large-scale paired image-text data. Their performances largely depend on the prompt quality. While recent methods show that visual descriptions generated by large language models (LLMs) enhance the generalization of VLMs, class-specific prompts may be inaccurate or lack discrimination due to the hallucination in LLMs. In this paper, we aim to find visually discriminative prompts for fine-grained categories with minimal supervision and no human-in-the-loop. An evolution-based algorithm is proposed to progressively optimize language prompts from task-specific templates to class-specific descriptions. Unlike optimizing templates, the search space shows an explosion in class-specific candidate prompts. This increases prompt generation costs, iterative times, and the overfitting problem. To this end, we first introduce several simple yet effective edit-based and evolution-based operations to generate diverse candidate prompts by one-time query of LLMs. Then, two sampling strategies are proposed to find a better initial search point and reduce traversed categories, saving iteration costs. Moreover, we apply a novel fitness score with entropy constraints to mitigate overfitting. In a challenging one-shot image classification setting, our method outperforms existing textual prompt-based methods and improves LLM-generated description methods across 13 datasets. Meanwhile, we demonstrate that our optimal prompts improve adapter-based methods and transfer effectively across different backbones.

  • 8 authors
·
Feb 27, 2025

Simple Token-Efficient Vision-Language Model for Case-level Pathology Synoptic Report Generation

Generating clinically useful pathology reports for pathology cases from whole-slide images (WSIs) is challenging due to gigapixel resolution, long visual-token sequences, and the complexity of case-level reasoning, where a single case may contain multiple WSIs with heterogeneous tissues and ambiguous findings. We present a simple token-efficient vision--language model for case-level synoptic report generation that remains practical under constrained GPU memory. Our architecture follows a minimal three-component design: a frozen pathology patch encoder, a lightweight two-layer MLP vision-language aligner, and a large language model decoder, with an explicit WSI marker token to separate slides within a case. Training proceeds in two supervised stages: (1) aligner-only WSI captioning using heterogeneous WSI-text pairs, and (2) case-level supervised fine-tuning on case-report pairs for structured report generation. To reduce sequence length, we represent each slide using 512 times 512 patches at 5times magnification, which reduces the average sequence length by up to 64times times compared to the commonly used 20times patches. Combined with efficient training techniques, we enable practical training with only half a NVIDIA H100 GPU. Across both training stages, our approach achieves high ROUGE-L/METEOR/BLEU-4 scores while being substantially more efficient in memory and runtime. In AI-based evaluations, our model is consistently preferred over strong baselines. Extensive ablations characterize performance-efficiency trade-offs and identify simple choices that improve robustness in multi-WSI settings. Overall, this work provides a strong, reproducible baseline for efficient pathology report generation, lowering the barrier to multi-WSI VLM research under limited compute.

  • 4 authors
·
May 28

FOLD-SE: An Efficient Rule-based Machine Learning Algorithm with Scalable Explainability

We present FOLD-SE, an efficient, explainable machine learning algorithm for classification tasks given tabular data containing numerical and categorical values. FOLD-SE generates a set of default rules-essentially a stratified normal logic program-as an (explainable) trained model. Explainability provided by FOLD-SE is scalable, meaning that regardless of the size of the dataset, the number of learned rules and learned literals stay quite small while good accuracy in classification is maintained. A model with smaller number of rules and literals is easier to understand for human beings. FOLD-SE is competitive with state-of-the-art machine learning algorithms such as XGBoost and Multi-Layer Perceptrons (MLP) wrt accuracy of prediction. However, unlike XGBoost and MLP, the FOLD-SE algorithm is explainable. The FOLD-SE algorithm builds upon our earlier work on developing the explainable FOLD-R++ machine learning algorithm for binary classification and inherits all of its positive features. Thus, pre-processing of the dataset, using techniques such as one-hot encoding, is not needed. Like FOLD-R++, FOLD-SE uses prefix sum to speed up computations resulting in FOLD-SE being an order of magnitude faster than XGBoost and MLP in execution speed. The FOLD-SE algorithm outperforms FOLD-R++ as well as other rule-learning algorithms such as RIPPER in efficiency, performance and scalability, especially for large datasets. A major reason for scalable explainability of FOLD-SE is the use of a literal selection heuristics based on Gini Impurity, as opposed to Information Gain used in FOLD-R++. A multi-category classification version of FOLD-SE is also presented.

  • 2 authors
·
Aug 16, 2022 1