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Dec 12

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

Multimodal Multitask Representation Learning for Pathology Biobank Metadata Prediction

Metadata are general characteristics of the data in a well-curated and condensed format, and have been proven to be useful for decision making, knowledge discovery, and also heterogeneous data organization of biobank. Among all data types in the biobank, pathology is the key component of the biobank and also serves as the gold standard of diagnosis. To maximize the utility of biobank and allow the rapid progress of biomedical science, it is essential to organize the data with well-populated pathology metadata. However, manual annotation of such information is tedious and time-consuming. In the study, we develop a multimodal multitask learning framework to predict four major slide-level metadata of pathology images. The framework learns generalizable representations across tissue slides, pathology reports, and case-level structured data. We demonstrate improved performance across all four tasks with the proposed method compared to a single modal single task baseline on two test sets, one external test set from a distinct data source (TCGA) and one internal held-out test set (TTH). In the test sets, the performance improvements on the averaged area under receiver operating characteristic curve across the four tasks are 16.48% and 9.05% on TCGA and TTH, respectively. Such pathology metadata prediction system may be adopted to mitigate the effort of expert annotation and ultimately accelerate the data-driven research by better utilization of the pathology biobank.

  • 5 authors
·
Sep 17, 2019

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

On the Importance of Text Preprocessing for Multimodal Representation Learning and Pathology Report Generation

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.

  • 6 authors
·
Feb 26

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

Fine-Tuning and Training of DenseNet for Histopathology Image Representation Using TCGA Diagnostic Slides

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

  • 22 authors
·
Jan 19, 2021

Molecular-driven Foundation Model for Oncologic Pathology

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

  • 18 authors
·
Jan 27

MambaMIL: Enhancing Long Sequence Modeling with Sequence Reordering in Computational Pathology

Multiple Instance Learning (MIL) has emerged as a dominant paradigm to extract discriminative feature representations within Whole Slide Images (WSIs) in computational pathology. Despite driving notable progress, existing MIL approaches suffer from limitations in facilitating comprehensive and efficient interactions among instances, as well as challenges related to time-consuming computations and overfitting. In this paper, we incorporate the Selective Scan Space State Sequential Model (Mamba) in Multiple Instance Learning (MIL) for long sequence modeling with linear complexity, termed as MambaMIL. By inheriting the capability of vanilla Mamba, MambaMIL demonstrates the ability to comprehensively understand and perceive long sequences of instances. Furthermore, we propose the Sequence Reordering Mamba (SR-Mamba) aware of the order and distribution of instances, which exploits the inherent valuable information embedded within the long sequences. With the SR-Mamba as the core component, MambaMIL can effectively capture more discriminative features and mitigate the challenges associated with overfitting and high computational overhead. Extensive experiments on two public challenging tasks across nine diverse datasets demonstrate that our proposed framework performs favorably against state-of-the-art MIL methods. The code is released at https://github.com/isyangshu/MambaMIL.

  • 3 authors
·
Mar 11, 2024

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

H-DenseUNet: Hybrid Densely Connected UNet for Liver and Tumor Segmentation from CT Volumes

Liver cancer is one of the leading causes of cancer death. To assist doctors in hepatocellular carcinoma diagnosis and treatment planning, an accurate and automatic liver and tumor segmentation method is highly demanded in the clinical practice. Recently, fully convolutional neural networks (FCNs), including 2D and 3D FCNs, serve as the back-bone in many volumetric image segmentation. However, 2D convolutions can not fully leverage the spatial information along the third dimension while 3D convolutions suffer from high computational cost and GPU memory consumption. To address these issues, we propose a novel hybrid densely connected UNet (H-DenseUNet), which consists of a 2D DenseUNet for efficiently extracting intra-slice features and a 3D counterpart for hierarchically aggregating volumetric contexts under the spirit of the auto-context algorithm for liver and tumor segmentation. We formulate the learning process of H-DenseUNet in an end-to-end manner, where the intra-slice representations and inter-slice features can be jointly optimized through a hybrid feature fusion (HFF) layer. We extensively evaluated our method on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge and 3DIRCADb Dataset. Our method outperformed other state-of-the-arts on the segmentation results of tumors and achieved very competitive performance for liver segmentation even with a single model.

  • 6 authors
·
Sep 21, 2017

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

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

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

Generating Narrated Lecture Videos from Slides with Synchronized Highlights

Turning static slides into engaging video lectures takes considerable time and effort, requiring presenters to record explanations and visually guide their audience through the material. We introduce an end-to-end system designed to automate this process entirely. Given a slide deck, this system synthesizes a video lecture featuring AI-generated narration synchronized precisely with dynamic visual highlights. These highlights automatically draw attention to the specific concept being discussed, much like an effective presenter would. The core technical contribution is a novel highlight alignment module. This module accurately maps spoken phrases to locations on a given slide using diverse strategies (e.g., Levenshtein distance, LLM-based semantic analysis) at selectable granularities (line or word level) and utilizes timestamp-providing Text-to-Speech (TTS) for timing synchronization. We demonstrate the system's effectiveness through a technical evaluation using a manually annotated slide dataset with 1000 samples, finding that LLM-based alignment achieves high location accuracy (F1 > 92%), significantly outperforming simpler methods, especially on complex, math-heavy content. Furthermore, the calculated generation cost averages under $1 per hour of video, offering potential savings of two orders of magnitude compared to conservative estimates of manual production costs. This combination of high accuracy and extremely low cost positions this approach as a practical and scalable tool for transforming static slides into effective, visually-guided video lectures.

  • 1 authors
·
May 5

Paper2Video: Automatic Video Generation from Scientific Papers

Academic presentation videos have become an essential medium for research communication, yet producing them remains highly labor-intensive, often requiring hours of slide design, recording, and editing for a short 2 to 10 minutes video. Unlike natural video, presentation video generation involves distinctive challenges: inputs from research papers, dense multi-modal information (text, figures, tables), and the need to coordinate multiple aligned channels such as slides, subtitles, speech, and human talker. To address these challenges, we introduce PaperTalker, the first benchmark of 101 research papers paired with author-created presentation videos, slides, and speaker metadata. We further design four tailored evaluation metrics--Meta Similarity, PresentArena, PresentQuiz, and IP Memory--to measure how videos convey the paper's information to the audience. Building on this foundation, we propose PaperTalker, the first multi-agent framework for academic presentation video generation. It integrates slide generation with effective layout refinement by a novel effective tree search visual choice, cursor grounding, subtitling, speech synthesis, and talking-head rendering, while parallelizing slide-wise generation for efficiency. Experiments on Paper2Video demonstrate that the presentation videos produced by our approach are more faithful and informative than existing baselines, establishing a practical step toward automated and ready-to-use academic video generation. Our dataset, agent, and code are available at https://github.com/showlab/Paper2Video.

showlab Show Lab
·
Oct 6 2

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

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

Harmonizing Visual Text Comprehension and Generation

In this work, we present TextHarmony, a unified and versatile multimodal generative model proficient in comprehending and generating visual text. Simultaneously generating images and texts typically results in performance degradation due to the inherent inconsistency between vision and language modalities. To overcome this challenge, existing approaches resort to modality-specific data for supervised fine-tuning, necessitating distinct model instances. We propose Slide-LoRA, which dynamically aggregates modality-specific and modality-agnostic LoRA experts, partially decoupling the multimodal generation space. Slide-LoRA harmonizes the generation of vision and language within a singular model instance, thereby facilitating a more unified generative process. Additionally, we develop a high-quality image caption dataset, DetailedTextCaps-100K, synthesized with a sophisticated closed-source MLLM to enhance visual text generation capabilities further. Comprehensive experiments across various benchmarks demonstrate the effectiveness of the proposed approach. Empowered by Slide-LoRA, TextHarmony achieves comparable performance to modality-specific fine-tuning results with only a 2% increase in parameters and shows an average improvement of 2.5% in visual text comprehension tasks and 4.0% in visual text generation tasks. Our work delineates the viability of an integrated approach to multimodal generation within the visual text domain, setting a foundation for subsequent inquiries.

  • 10 authors
·
Jul 23, 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

PASS: Presentation Automation for Slide Generation and Speech

In today's fast-paced world, effective presentations have become an essential tool for communication in both online and offline meetings. The crafting of a compelling presentation requires significant time and effort, from gathering key insights to designing slides that convey information clearly and concisely. However, despite the wealth of resources available, people often find themselves manually extracting crucial points, analyzing data, and organizing content in a way that ensures clarity and impact. Furthermore, a successful presentation goes beyond just the slides; it demands rehearsal and the ability to weave a captivating narrative to fully engage the audience. Although there has been some exploration of automating document-to-slide generation, existing research is largely centered on converting research papers. In addition, automation of the delivery of these presentations has yet to be addressed. We introduce PASS, a pipeline used to generate slides from general Word documents, going beyond just research papers, which also automates the oral delivery of the generated slides. PASS analyzes user documents to create a dynamic, engaging presentation with an AI-generated voice. Additionally, we developed an LLM-based evaluation metric to assess our pipeline across three critical dimensions of presentations: relevance, coherence, and redundancy. The data and codes are available at https://github.com/AggarwalTushar/PASS.

  • 2 authors
·
Jan 11

Revisiting Data Challenges of Computational Pathology: A Pack-based Multiple Instance Learning Framework

Computational pathology (CPath) digitizes pathology slides into whole slide images (WSIs), enabling analysis for critical healthcare tasks such as cancer diagnosis and prognosis. However, WSIs possess extremely long sequence lengths (up to 200K), significant length variations (from 200 to 200K), and limited supervision. These extreme variations in sequence length lead to high data heterogeneity and redundancy. Conventional methods often compromise on training efficiency and optimization to preserve such heterogeneity under limited supervision. To comprehensively address these challenges, we propose a pack-based MIL framework. It packs multiple sampled, variable-length feature sequences into fixed-length ones, enabling batched training while preserving data heterogeneity. Moreover, we introduce a residual branch that composes discarded features from multiple slides into a hyperslide which is trained with tailored labels. It offers multi-slide supervision while mitigating feature loss from sampling. Meanwhile, an attention-driven downsampler is introduced to compress features in both branches to reduce redundancy. By alleviating these challenges, our approach achieves an accuracy improvement of up to 8% while using only 12% of the training time in the PANDA(UNI). Extensive experiments demonstrate that focusing data challenges in CPath holds significant potential in the era of foundation models. The code is https://github.com/FangHeng/PackMIL

  • 5 authors
·
Sep 25

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

Stationary Representations: Optimally Approximating Compatibility and Implications for Improved Model Replacements

Learning compatible representations enables the interchangeable use of semantic features as models are updated over time. This is particularly relevant in search and retrieval systems where it is crucial to avoid reprocessing of the gallery images with the updated model. While recent research has shown promising empirical evidence, there is still a lack of comprehensive theoretical understanding about learning compatible representations. In this paper, we demonstrate that the stationary representations learned by the d-Simplex fixed classifier optimally approximate compatibility representation according to the two inequality constraints of its formal definition. This not only establishes a solid foundation for future works in this line of research but also presents implications that can be exploited in practical learning scenarios. An exemplary application is the now-standard practice of downloading and fine-tuning new pre-trained models. Specifically, we show the strengths and critical issues of stationary representations in the case in which a model undergoing sequential fine-tuning is asynchronously replaced by downloading a better-performing model pre-trained elsewhere. Such a representation enables seamless delivery of retrieval service (i.e., no reprocessing of gallery images) and offers improved performance without operational disruptions during model replacement. Code available at: https://github.com/miccunifi/iamcl2r.

  • 4 authors
·
May 4, 2024

Compositional 3D-aware Video Generation with LLM Director

Significant progress has been made in text-to-video generation through the use of powerful generative models and large-scale internet data. However, substantial challenges remain in precisely controlling individual concepts within the generated video, such as the motion and appearance of specific characters and the movement of viewpoints. In this work, we propose a novel paradigm that generates each concept in 3D representation separately and then composes them with priors from Large Language Models (LLM) and 2D diffusion models. Specifically, given an input textual prompt, our scheme consists of three stages: 1) We leverage LLM as the director to first decompose the complex query into several sub-prompts that indicate individual concepts within the video~(e.g., scene, objects, motions), then we let LLM to invoke pre-trained expert models to obtain corresponding 3D representations of concepts. 2) To compose these representations, we prompt multi-modal LLM to produce coarse guidance on the scales and coordinates of trajectories for the objects. 3) To make the generated frames adhere to natural image distribution, we further leverage 2D diffusion priors and use Score Distillation Sampling to refine the composition. Extensive experiments demonstrate that our method can generate high-fidelity videos from text with diverse motion and flexible control over each concept. Project page: https://aka.ms/c3v.

  • 6 authors
·
Aug 31, 2024 2

A General-Purpose Self-Supervised Model for Computational Pathology

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

  • 20 authors
·
Aug 29, 2023

RepVideo: Rethinking Cross-Layer Representation for Video Generation

Video generation has achieved remarkable progress with the introduction of diffusion models, which have significantly improved the quality of generated videos. However, recent research has primarily focused on scaling up model training, while offering limited insights into the direct impact of representations on the video generation process. In this paper, we initially investigate the characteristics of features in intermediate layers, finding substantial variations in attention maps across different layers. These variations lead to unstable semantic representations and contribute to cumulative differences between features, which ultimately reduce the similarity between adjacent frames and negatively affect temporal coherence. To address this, we propose RepVideo, an enhanced representation framework for text-to-video diffusion models. By accumulating features from neighboring layers to form enriched representations, this approach captures more stable semantic information. These enhanced representations are then used as inputs to the attention mechanism, thereby improving semantic expressiveness while ensuring feature consistency across adjacent frames. Extensive experiments demonstrate that our RepVideo not only significantly enhances the ability to generate accurate spatial appearances, such as capturing complex spatial relationships between multiple objects, but also improves temporal consistency in video generation.

  • 6 authors
·
Jan 15 3

TAMPAR: Visual Tampering Detection for Parcel Logistics in Postal Supply Chains

Due to the steadily rising amount of valuable goods in supply chains, tampering detection for parcels is becoming increasingly important. In this work, we focus on the use-case last-mile delivery, where only a single RGB image is taken and compared against a reference from an existing database to detect potential appearance changes that indicate tampering. We propose a tampering detection pipeline that utilizes keypoint detection to identify the eight corner points of a parcel. This permits applying a perspective transformation to create normalized fronto-parallel views for each visible parcel side surface. These viewpoint-invariant parcel side surface representations facilitate the identification of signs of tampering on parcels within the supply chain, since they reduce the problem to parcel side surface matching with pair-wise appearance change detection. Experiments with multiple classical and deep learning-based change detection approaches are performed on our newly collected TAMpering detection dataset for PARcels, called TAMPAR. We evaluate keypoint and change detection separately, as well as in a unified system for tampering detection. Our evaluation shows promising results for keypoint (Keypoint AP 75.76) and tampering detection (81% accuracy, F1-Score 0.83) on real images. Furthermore, a sensitivity analysis for tampering types, lens distortion and viewing angles is presented. Code and dataset are available at https://a-nau.github.io/tampar.

  • 4 authors
·
Nov 6, 2023

Improving Prototypical Parts Abstraction for Case-Based Reasoning Explanations Designed for the Kidney Stone Type Recognition

The in-vivo identification of the kidney stone types during an ureteroscopy would be a major medical advance in urology, as it could reduce the time of the tedious renal calculi extraction process, while diminishing infection risks. Furthermore, such an automated procedure would make possible to prescribe anti-recurrence treatments immediately. Nowadays, only few experienced urologists are able to recognize the kidney stone types in the images of the videos displayed on a screen during the endoscopy. Thus, several deep learning (DL) models have recently been proposed to automatically recognize the kidney stone types using ureteroscopic images. However, these DL models are of black box nature whicl limits their applicability in clinical settings. This contribution proposes a case-based reasoning DL model which uses prototypical parts (PPs) and generates local and global descriptors. The PPs encode for each class (i.e., kidney stone type) visual feature information (hue, saturation, intensity and textures) similar to that used by biologists. The PPs are optimally generated due a new loss function used during the model training. Moreover, the local and global descriptors of PPs allow to explain the decisions ("what" information, "where in the images") in an understandable way for biologists and urologists. The proposed DL model has been tested on a database including images of the six most widespread kidney stone types. The overall average classification accuracy was 90.37. When comparing this results with that of the eight other DL models of the kidney stone state-of-the-art, it can be seen that the valuable gain in explanability was not reached at the expense of accuracy which was even slightly increased with respect to that (88.2) of the best method of the literature. These promising and interpretable results also encourage urologists to put their trust in AI-based solutions.

  • 8 authors
·
Sep 19, 2024

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

  • 9 authors
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Jul 12

Aladdin: Zero-Shot Hallucination of Stylized 3D Assets from Abstract Scene Descriptions

What constitutes the "vibe" of a particular scene? What should one find in "a busy, dirty city street", "an idyllic countryside", or "a crime scene in an abandoned living room"? The translation from abstract scene descriptions to stylized scene elements cannot be done with any generality by extant systems trained on rigid and limited indoor datasets. In this paper, we propose to leverage the knowledge captured by foundation models to accomplish this translation. We present a system that can serve as a tool to generate stylized assets for 3D scenes described by a short phrase, without the need to enumerate the objects to be found within the scene or give instructions on their appearance. Additionally, it is robust to open-world concepts in a way that traditional methods trained on limited data are not, affording more creative freedom to the 3D artist. Our system demonstrates this using a foundation model "team" composed of a large language model, a vision-language model and several image diffusion models, which communicate using an interpretable and user-editable intermediate representation, thus allowing for more versatile and controllable stylized asset generation for 3D artists. We introduce novel metrics for this task, and show through human evaluations that in 91% of the cases, our system outputs are judged more faithful to the semantics of the input scene description than the baseline, thus highlighting the potential of this approach to radically accelerate the 3D content creation process for 3D artists.

  • 4 authors
·
Jun 9, 2023

JM3D & JM3D-LLM: Elevating 3D Representation with Joint Multi-modal Cues

The rising importance of 3D representation learning, pivotal in computer vision, autonomous driving, and robotics, is evident. However, a prevailing trend, which straightforwardly resorted to transferring 2D alignment strategies to the 3D domain, encounters three distinct challenges: (1) Information Degradation: This arises from the alignment of 3D data with mere single-view 2D images and generic texts, neglecting the need for multi-view images and detailed subcategory texts. (2) Insufficient Synergy: These strategies align 3D representations to image and text features individually, hampering the overall optimization for 3D models. (3) Underutilization: The fine-grained information inherent in the learned representations is often not fully exploited, indicating a potential loss in detail. To address these issues, we introduce JM3D, a comprehensive approach integrating point cloud, text, and image. Key contributions include the Structured Multimodal Organizer (SMO), enriching vision-language representation with multiple views and hierarchical text, and the Joint Multi-modal Alignment (JMA), combining language understanding with visual representation. Our advanced model, JM3D-LLM, marries 3D representation with large language models via efficient fine-tuning. Evaluations on ModelNet40 and ScanObjectNN establish JM3D's superiority. The superior performance of JM3D-LLM further underscores the effectiveness of our representation transfer approach. Our code and models are available at https://github.com/Mr-Neko/JM3D.

  • 6 authors
·
Oct 14, 2023

Uni4D-LLM: A Unified SpatioTemporal-Aware VLM for 4D Understanding and Generation

Vision-language models (VLMs) have demonstrated strong performance in 2D scene understanding and generation, but extending this unification to the physical world remains an open challenge. Existing 3D and 4D approaches typically embed scene geometry into autoregressive model for semantic understanding and diffusion model for content generation. This paradigm gap prevents a single model from jointly handling both tasks, especially in dynamic 4D settings where spatiotemporal modeling is critical. We propose Uni4D-LLM, the first unified VLM framework with spatiotemporal awareness for 4D scene understanding and generation. Our design is guided by two key insights: 1) Unification requires a shared representation. We extract semantic features for understanding and noisy-injected appearance features for generation, incorporate 4D geometric cues, and fuse them into a spatiotemporal-aware visual representation through adaptive cross-attention. 2) Unification requires a shared architecture. Both autoregression and diffusion are built on Transformer backbones, and this enables integration into a single LLM with task-specific heads. By aligning visual and linguistic representations, our Uni4D-LLM produces predictions for both understanding and generation within one Transformer-based framework. We further apply instruction fine-tuning on diverse 4D vision-language datasets to improve generalization across tasks. Extensive experiments on multiple benchmarks demonstrate that Uni4D-LLM achieves competitive or superior results compared to state-of-the-art models and offers the first true unification of 4D scene understanding and generation.

  • 2 authors
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Sep 28

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.

Recent Advance in 3D Object and Scene Generation: A Survey

In recent years, the demand for 3D content has grown exponentially with intelligent upgrading of interactive media, extended reality (XR), and Metaverse industries. In order to overcome the limitation of traditional manual modeling approaches, such as labor-intensive workflows and prolonged production cycles, revolutionary advances have been achieved through the convergence of novel 3D representation paradigms and artificial intelligence generative technologies. In this survey, we conduct a systematically review of the cutting-edge achievements in static 3D object and scene generation, as well as establish a comprehensive technical framework through systematic categorization. Specifically, we initiate our analysis with mainstream 3D object representations, followed by in-depth exploration of two principal technical pathways in object generation: data-driven supervised learning methods and deep generative model-based approaches. Regarding scene generation, we focus on three dominant paradigms: layout-guided compositional synthesis, 2D prior-based scene generation, and rule-driven modeling. Finally, we critically examine persistent challenges in 3D generation and propose potential research directions for future investigation. This survey aims to provide readers with a structured understanding of state-of-the-art 3D generation technologies while inspiring researchers to undertake more exploration in this domain.

  • 3 authors
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Apr 15

Hi3DEval: Advancing 3D Generation Evaluation with Hierarchical Validity

Despite rapid advances in 3D content generation, quality assessment for the generated 3D assets remains challenging. Existing methods mainly rely on image-based metrics and operate solely at the object level, limiting their ability to capture spatial coherence, material authenticity, and high-fidelity local details. 1) To address these challenges, we introduce Hi3DEval, a hierarchical evaluation framework tailored for 3D generative content. It combines both object-level and part-level evaluation, enabling holistic assessments across multiple dimensions as well as fine-grained quality analysis. Additionally, we extend texture evaluation beyond aesthetic appearance by explicitly assessing material realism, focusing on attributes such as albedo, saturation, and metallicness. 2) To support this framework, we construct Hi3DBench, a large-scale dataset comprising diverse 3D assets and high-quality annotations, accompanied by a reliable multi-agent annotation pipeline. We further propose a 3D-aware automated scoring system based on hybrid 3D representations. Specifically, we leverage video-based representations for object-level and material-subject evaluations to enhance modeling of spatio-temporal consistency and employ pretrained 3D features for part-level perception. Extensive experiments demonstrate that our approach outperforms existing image-based metrics in modeling 3D characteristics and achieves superior alignment with human preference, providing a scalable alternative to manual evaluations. The project page is available at https://zyh482.github.io/Hi3DEval/.

  • 8 authors
·
Aug 7 3

PresentAgent: Multimodal Agent for Presentation Video Generation

We present PresentAgent, a multimodal agent that transforms long-form documents into narrated presentation videos. While existing approaches are limited to generating static slides or text summaries, our method advances beyond these limitations by producing fully synchronized visual and spoken content that closely mimics human-style presentations. To achieve this integration, PresentAgent employs a modular pipeline that systematically segments the input document, plans and renders slide-style visual frames, generates contextual spoken narration with large language models and Text-to-Speech models, and seamlessly composes the final video with precise audio-visual alignment. Given the complexity of evaluating such multimodal outputs, we introduce PresentEval, a unified assessment framework powered by Vision-Language Models that comprehensively scores videos across three critical dimensions: content fidelity, visual clarity, and audience comprehension through prompt-based evaluation. Our experimental validation on a curated dataset of 30 document-presentation pairs demonstrates that PresentAgent approaches human-level quality across all evaluation metrics. These results highlight the significant potential of controllable multimodal agents in transforming static textual materials into dynamic, effective, and accessible presentation formats. Code will be available at https://github.com/AIGeeksGroup/PresentAgent.

  • 7 authors
·
Jul 5 1

Physically Embodied Gaussian Splatting: A Realtime Correctable World Model for Robotics

For robots to robustly understand and interact with the physical world, it is highly beneficial to have a comprehensive representation - modelling geometry, physics, and visual observations - that informs perception, planning, and control algorithms. We propose a novel dual Gaussian-Particle representation that models the physical world while (i) enabling predictive simulation of future states and (ii) allowing online correction from visual observations in a dynamic world. Our representation comprises particles that capture the geometrical aspect of objects in the world and can be used alongside a particle-based physics system to anticipate physically plausible future states. Attached to these particles are 3D Gaussians that render images from any viewpoint through a splatting process thus capturing the visual state. By comparing the predicted and observed images, our approach generates visual forces that correct the particle positions while respecting known physical constraints. By integrating predictive physical modelling with continuous visually-derived corrections, our unified representation reasons about the present and future while synchronizing with reality. Our system runs in realtime at 30Hz using only 3 cameras. We validate our approach on 2D and 3D tracking tasks as well as photometric reconstruction quality. Videos are found at https://embodied-gaussians.github.io/.

  • 4 authors
·
Jun 15, 2024

Differentiable Blocks World: Qualitative 3D Decomposition by Rendering Primitives

Given a set of calibrated images of a scene, we present an approach that produces a simple, compact, and actionable 3D world representation by means of 3D primitives. While many approaches focus on recovering high-fidelity 3D scenes, we focus on parsing a scene into mid-level 3D representations made of a small set of textured primitives. Such representations are interpretable, easy to manipulate and suited for physics-based simulations. Moreover, unlike existing primitive decomposition methods that rely on 3D input data, our approach operates directly on images through differentiable rendering. Specifically, we model primitives as textured superquadric meshes and optimize their parameters from scratch with an image rendering loss. We highlight the importance of modeling transparency for each primitive, which is critical for optimization and also enables handling varying numbers of primitives. We show that the resulting textured primitives faithfully reconstruct the input images and accurately model the visible 3D points, while providing amodal shape completions of unseen object regions. We compare our approach to the state of the art on diverse scenes from DTU, and demonstrate its robustness on real-life captures from BlendedMVS and Nerfstudio. We also showcase how our results can be used to effortlessly edit a scene or perform physical simulations. Code and video results are available at https://www.tmonnier.com/DBW .

  • 5 authors
·
Jul 11, 2023

ReSpace: Text-Driven 3D Scene Synthesis and Editing with Preference Alignment

Scene synthesis and editing has emerged as a promising direction in computer graphics. Current trained approaches for 3D indoor scenes either oversimplify object semantics through one-hot class encodings (e.g., 'chair' or 'table'), require masked diffusion for editing, ignore room boundaries, or rely on floor plan renderings that fail to capture complex layouts. In contrast, LLM-based methods enable richer semantics via natural language (e.g., 'modern studio with light wood furniture') but do not support editing, remain limited to rectangular layouts or rely on weak spatial reasoning from implicit world models. We introduce ReSpace, a generative framework for text-driven 3D indoor scene synthesis and editing using autoregressive language models. Our approach features a compact structured scene representation with explicit room boundaries that frames scene editing as a next-token prediction task. We leverage a dual-stage training approach combining supervised fine-tuning and preference alignment, enabling a specially trained language model for object addition that accounts for user instructions, spatial geometry, object semantics, and scene-level composition. For scene editing, we employ a zero-shot LLM to handle object removal and prompts for addition. We further introduce a novel voxelization-based evaluation that captures fine-grained geometry beyond 3D bounding boxes. Experimental results surpass state-of-the-art on object addition while maintaining competitive results on full scene synthesis.

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

PathGen-1.6M: 1.6 Million Pathology Image-text Pairs Generation through Multi-agent Collaboration

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

  • 10 authors
·
Jun 28, 2024

BLIP-Diffusion: Pre-trained Subject Representation for Controllable Text-to-Image Generation and Editing

Subject-driven text-to-image generation models create novel renditions of an input subject based on text prompts. Existing models suffer from lengthy fine-tuning and difficulties preserving the subject fidelity. To overcome these limitations, we introduce BLIP-Diffusion, a new subject-driven image generation model that supports multimodal control which consumes inputs of subject images and text prompts. Unlike other subject-driven generation models, BLIP-Diffusion introduces a new multimodal encoder which is pre-trained to provide subject representation. We first pre-train the multimodal encoder following BLIP-2 to produce visual representation aligned with the text. Then we design a subject representation learning task which enables a diffusion model to leverage such visual representation and generates new subject renditions. Compared with previous methods such as DreamBooth, our model enables zero-shot subject-driven generation, and efficient fine-tuning for customized subject with up to 20x speedup. We also demonstrate that BLIP-Diffusion can be flexibly combined with existing techniques such as ControlNet and prompt-to-prompt to enable novel subject-driven generation and editing applications. Code and models will be released at https://github.com/salesforce/LAVIS/tree/main/projects/blip-diffusion. Project page at https://dxli94.github.io/BLIP-Diffusion-website/.

  • 3 authors
·
May 24, 2023

ConSlide: Asynchronous Hierarchical Interaction Transformer with Breakup-Reorganize Rehearsal for Continual Whole Slide Image Analysis

Whole slide image (WSI) analysis has become increasingly important in the medical imaging community, enabling automated and objective diagnosis, prognosis, and therapeutic-response prediction. However, in clinical practice, the ever-evolving environment hamper the utility of WSI analysis models. In this paper, we propose the FIRST continual learning framework for WSI analysis, named ConSlide, to tackle the challenges of enormous image size, utilization of hierarchical structure, and catastrophic forgetting by progressive model updating on multiple sequential datasets. Our framework contains three key components. The Hierarchical Interaction Transformer (HIT) is proposed to model and utilize the hierarchical structural knowledge of WSI. The Breakup-Reorganize (BuRo) rehearsal method is developed for WSI data replay with efficient region storing buffer and WSI reorganizing operation. The asynchronous updating mechanism is devised to encourage the network to learn generic and specific knowledge respectively during the replay stage, based on a nested cross-scale similarity learning (CSSL) module. We evaluated the proposed ConSlide on four public WSI datasets from TCGA projects. It performs best over other state-of-the-art methods with a fair WSI-based continual learning setting and achieves a better trade-off of the overall performance and forgetting on previous task

  • 6 authors
·
Aug 25, 2023

Matryoshka Representation Learning

Learned representations are a central component in modern ML systems, serving a multitude of downstream tasks. When training such representations, it is often the case that computational and statistical constraints for each downstream task are unknown. In this context rigid, fixed capacity representations can be either over or under-accommodating to the task at hand. This leads us to ask: can we design a flexible representation that can adapt to multiple downstream tasks with varying computational resources? Our main contribution is Matryoshka Representation Learning (MRL) which encodes information at different granularities and allows a single embedding to adapt to the computational constraints of downstream tasks. MRL minimally modifies existing representation learning pipelines and imposes no additional cost during inference and deployment. MRL learns coarse-to-fine representations that are at least as accurate and rich as independently trained low-dimensional representations. The flexibility within the learned Matryoshka Representations offer: (a) up to 14x smaller embedding size for ImageNet-1K classification at the same level of accuracy; (b) up to 14x real-world speed-ups for large-scale retrieval on ImageNet-1K and 4K; and (c) up to 2% accuracy improvements for long-tail few-shot classification, all while being as robust as the original representations. Finally, we show that MRL extends seamlessly to web-scale datasets (ImageNet, JFT) across various modalities -- vision (ViT, ResNet), vision + language (ALIGN) and language (BERT). MRL code and pretrained models are open-sourced at https://github.com/RAIVNLab/MRL.

  • 11 authors
·
May 26, 2022

LiteReality: Graphics-Ready 3D Scene Reconstruction from RGB-D Scans

We propose LiteReality, a novel pipeline that converts RGB-D scans of indoor environments into compact, realistic, and interactive 3D virtual replicas. LiteReality not only reconstructs scenes that visually resemble reality but also supports key features essential for graphics pipelines -- such as object individuality, articulation, high-quality physically based rendering materials, and physically based interaction. At its core, LiteReality first performs scene understanding and parses the results into a coherent 3D layout and objects with the help of a structured scene graph. It then reconstructs the scene by retrieving the most visually similar 3D artist-crafted models from a curated asset database. Next, the Material Painting module enhances realism by recovering high-quality, spatially varying materials. Finally, the reconstructed scene is integrated into a simulation engine with basic physical properties to enable interactive behavior. The resulting scenes are compact, editable, and fully compatible with standard graphics pipelines, making them suitable for applications in AR/VR, gaming, robotics, and digital twins. In addition, LiteReality introduces a training-free object retrieval module that achieves state-of-the-art similarity performance on the Scan2CAD benchmark, along with a robust material painting module capable of transferring appearances from images of any style to 3D assets -- even under severe misalignment, occlusion, and poor lighting. We demonstrate the effectiveness of LiteReality on both real-life scans and public datasets. Project page: https://litereality.github.io; Video: https://www.youtube.com/watch?v=ecK9m3LXg2c

  • 6 authors
·
Jul 3

Controllable Latent Space Augmentation for Digital Pathology

Whole slide image (WSI) analysis in digital pathology presents unique challenges due to the gigapixel resolution of WSIs and the scarcity of dense supervision signals. While Multiple Instance Learning (MIL) is a natural fit for slide-level tasks, training robust models requires large and diverse datasets. Even though image augmentation techniques could be utilized to increase data variability and reduce overfitting, implementing them effectively is not a trivial task. Traditional patch-level augmentation is prohibitively expensive due to the large number of patches extracted from each WSI, and existing feature-level augmentation methods lack control over transformation semantics. We introduce HistAug, a fast and efficient generative model for controllable augmentations in the latent space for digital pathology. By conditioning on explicit patch-level transformations (e.g., hue, erosion), HistAug generates realistic augmented embeddings while preserving initial semantic information. Our method allows the processing of a large number of patches in a single forward pass efficiently, while at the same time consistently improving MIL model performance. Experiments across multiple slide-level tasks and diverse organs show that HistAug outperforms existing methods, particularly in low-data regimes. Ablation studies confirm the benefits of learned transformations over noise-based perturbations and highlight the importance of uniform WSI-wise augmentation. Code is available at https://github.com/MICS-Lab/HistAug.

  • 6 authors
·
Aug 20

Compositional Visual Generation with Composable Diffusion Models

Large text-guided diffusion models, such as DALLE-2, are able to generate stunning photorealistic images given natural language descriptions. While such models are highly flexible, they struggle to understand the composition of certain concepts, such as confusing the attributes of different objects or relations between objects. In this paper, we propose an alternative structured approach for compositional generation using diffusion models. An image is generated by composing a set of diffusion models, with each of them modeling a certain component of the image. To do this, we interpret diffusion models as energy-based models in which the data distributions defined by the energy functions may be explicitly combined. The proposed method can generate scenes at test time that are substantially more complex than those seen in training, composing sentence descriptions, object relations, human facial attributes, and even generalizing to new combinations that are rarely seen in the real world. We further illustrate how our approach may be used to compose pre-trained text-guided diffusion models and generate photorealistic images containing all the details described in the input descriptions, including the binding of certain object attributes that have been shown difficult for DALLE-2. These results point to the effectiveness of the proposed method in promoting structured generalization for visual generation. Project page: https://energy-based-model.github.io/Compositional-Visual-Generation-with-Composable-Diffusion-Models/

  • 5 authors
·
Jun 3, 2022

TopNet: Transformer-based Object Placement Network for Image Compositing

We investigate the problem of automatically placing an object into a background image for image compositing. Given a background image and a segmented object, the goal is to train a model to predict plausible placements (location and scale) of the object for compositing. The quality of the composite image highly depends on the predicted location/scale. Existing works either generate candidate bounding boxes or apply sliding-window search using global representations from background and object images, which fail to model local information in background images. However, local clues in background images are important to determine the compatibility of placing the objects with certain locations/scales. In this paper, we propose to learn the correlation between object features and all local background features with a transformer module so that detailed information can be provided on all possible location/scale configurations. A sparse contrastive loss is further proposed to train our model with sparse supervision. Our new formulation generates a 3D heatmap indicating the plausibility of all location/scale combinations in one network forward pass, which is over 10 times faster than the previous sliding-window method. It also supports interactive search when users provide a pre-defined location or scale. The proposed method can be trained with explicit annotation or in a self-supervised manner using an off-the-shelf inpainting model, and it outperforms state-of-the-art methods significantly. The user study shows that the trained model generalizes well to real-world images with diverse challenging scenes and object categories.

  • 6 authors
·
Apr 6, 2023

Kinetic Typography Diffusion Model

This paper introduces a method for realistic kinetic typography that generates user-preferred animatable 'text content'. We draw on recent advances in guided video diffusion models to achieve visually-pleasing text appearances. To do this, we first construct a kinetic typography dataset, comprising about 600K videos. Our dataset is made from a variety of combinations in 584 templates designed by professional motion graphics designers and involves changing each letter's position, glyph, and size (i.e., flying, glitches, chromatic aberration, reflecting effects, etc.). Next, we propose a video diffusion model for kinetic typography. For this, there are three requirements: aesthetic appearances, motion effects, and readable letters. This paper identifies the requirements. For this, we present static and dynamic captions used as spatial and temporal guidance of a video diffusion model, respectively. The static caption describes the overall appearance of the video, such as colors, texture and glyph which represent a shape of each letter. The dynamic caption accounts for the movements of letters and backgrounds. We add one more guidance with zero convolution to determine which text content should be visible in the video. We apply the zero convolution to the text content, and impose it on the diffusion model. Lastly, our glyph loss, only minimizing a difference between the predicted word and its ground-truth, is proposed to make the prediction letters readable. Experiments show that our model generates kinetic typography videos with legible and artistic letter motions based on text prompts.

  • 4 authors
·
Jul 15, 2024 1