CPath-Omni: A Unified Multimodal Foundation Model for Patch and Whole Slide Image Analysis in Computational Pathology

The emergence of large multimodal models (LMMs) has brought significant advancements to pathology. Previous research has primarily focused on separately training patch-level and whole-slide image (WSI)-level models, limiting the integration of learned knowledge across patches and WSIs, and resulting in redundant models. In this work, we introduce CPath-Omni, the first 15-billion-parameter LMM designed to unify both patch and WSI level image analysis, consolidating a variety of tasks at both levels, including classification, visual question answering, captioning, and visual referring prompting. Extensive experiments demonstrate that CPath-Omni achieves state-of-the-art (SOTA) performance across seven diverse tasks on 39 out of 42 datasets, outperforming or matching task-specific models trained for individual tasks. Additionally, we develop a specialized pathology CLIP-based visual processor for CPath-Omni, CPath-CLIP, which, for the first time, integrates different vision models and incorporates a large language model as a text encoder to build a more powerful CLIP model, which achieves SOTA performance on nine zero-shot and four few-shot datasets. Our findings highlight CPath-Omni's ability to unify diverse pathology tasks, demonstrating its potential to streamline and advance the field of foundation model in pathology.

Health AI Developer Foundations

Robust medical Machine Learning (ML) models have the potential to revolutionize healthcare by accelerating clinical research, improving workflows and outcomes, and producing novel insights or capabilities. Developing such ML models from scratch is cost prohibitive and requires substantial compute, data, and time (e.g., expert labeling). To address these challenges, we introduce Health AI Developer Foundations (HAI-DEF), a suite of pre-trained, domain-specific foundation models, tools, and recipes to accelerate building ML for health applications. The models cover various modalities and domains, including radiology (X-rays and computed tomography), histopathology, dermatological imaging, and audio. These models provide domain specific embeddings that facilitate AI development with less labeled data, shorter training times, and reduced computational costs compared to traditional approaches. In addition, we utilize a common interface and style across these models, and prioritize usability to enable developers to integrate HAI-DEF efficiently. We present model evaluations across various tasks and conclude with a discussion of their application and evaluation, covering the importance of ensuring efficacy, fairness, and equity. Finally, while HAI-DEF and specifically the foundation models lower the barrier to entry for ML in healthcare, we emphasize the importance of validation with problem- and population-specific data for each desired usage setting. This technical report will be updated over time as more modalities and features are added.

Panther: Illuminate the Sight of Multimodal LLMs with Instruction-Guided Visual Prompts

Multimodal large language models (MLLMs) are closing the gap to human visual perception capability rapidly, while, still lag behind on attending to subtle images details or locating small objects precisely, etc. Common schemes to tackle these issues include deploying multiple vision encoders or operating on original high-resolution images. Few studies have concentrated on taking the textual instruction into improving visual representation, resulting in losing focus in some vision-centric tasks, a phenomenon we herein termed as Amblyopia. In this work, we introduce Panther, a MLLM that closely adheres to user instruction and locates targets of interests precisely, with the finesse of a black panther. Specifically, Panther comprises three integral components: Panther-VE, Panther-Bridge, and Panther-Decoder. Panther-VE integrates user instruction information at the early stages of the vision encoder, thereby extracting the most relevant and useful visual representations. The Panther-Bridge module, equipped with powerful filtering capabilities, significantly reduces redundant visual information, leading to a substantial savings in training costs. The Panther-Decoder is versatile and can be employed with any decoder-only architecture of LLMs without discrimination. Experimental results, particularly on vision-centric benchmarks, have demonstrated the effectiveness of Panther.

Path Planning in Complex Environments with Superquadrics and Voronoi-Based Orientation

Path planning in narrow passages is a challenging problem in various applications. Traditional planning algorithms often face challenges in complex environments like mazes and traps, where narrow entrances require special orientation control for successful navigation. In this work, we present a novel approach that combines superquadrics (SQ) representation and Voronoi diagrams to solve the narrow passage problem in both 2D and 3D environment. Our method utilizes the SQ formulation to expand obstacles, eliminating impassable passages, while Voronoi hyperplane ensures maximum clearance path. Additionally, the hyperplane provides a natural reference for robot orientation, aligning its long axis with the passage direction. We validate our framework through a 2D object retrieval task and 3D drone simulation, demonstrating that our approach outperforms classical planners and a cutting-edge drone planner by ensuring passable trajectories with maximum clearance.

Planning for quasi-static manipulation tasks via an intrinsic haptic metric

Contact-rich manipulation often requires strategic interactions with objects, such as pushing to accomplish specific tasks. We propose a novel scenario where a robot inserts a book into a crowded shelf by pushing aside neighboring books to create space before slotting the new book into place. Classical planning algorithms fail in this context due to limited space and their tendency to avoid contact. Additionally, they do not handle indirectly manipulable objects or consider force interactions. Our key contributions are: i) re-framing quasi-static manipulation as a planning problem on an implicit manifold derived from equilibrium conditions; ii) utilizing an intrinsic haptic metric instead of ad-hoc cost functions; and iii) proposing an adaptive algorithm that simultaneously updates robot states, object positions, contact points, and haptic distances. We evaluate our method on such crowded bookshelf insertion task but it is a general formulation to rigid bodies manipulation tasks. We propose proxies to capture contact point and force, with superellipse to represent objects. This simplified model guarantee the differentiablity. Our framework autonomously discovers strategic wedging-in policies while our simplified contact model achieves behavior similar to real world scenarios. We also vary the stiffness and initial positions to analysis our framework comprehensively. The video can be found at https://youtu.be/eab8umZ3AQ0.

Rethinking Transformer for Long Contextual Histopathology Whole Slide Image Analysis

Histopathology Whole Slide Image (WSI) analysis serves as the gold standard for clinical cancer diagnosis in the daily routines of doctors. To develop computer-aided diagnosis model for WSIs, previous methods typically employ Multi-Instance Learning to enable slide-level prediction given only slide-level labels. Among these models, vanilla attention mechanisms without pairwise interactions have traditionally been employed but are unable to model contextual information. More recently, self-attention models have been utilized to address this issue. To alleviate the computational complexity of long sequences in large WSIs, methods like HIPT use region-slicing, and TransMIL employs approximation of full self-attention. Both approaches suffer from suboptimal performance due to the loss of key information. Moreover, their use of absolute positional embedding struggles to effectively handle long contextual dependencies in shape-varying WSIs. In this paper, we first analyze how the low-rank nature of the long-sequence attention matrix constrains the representation ability of WSI modelling. Then, we demonstrate that the rank of attention matrix can be improved by focusing on local interactions via a local attention mask. Our analysis shows that the local mask aligns with the attention patterns in the lower layers of the Transformer. Furthermore, the local attention mask can be implemented during chunked attention calculation, reducing the quadratic computational complexity to linear with a small local bandwidth. Building on this, we propose a local-global hybrid Transformer for both computational acceleration and local-global information interactions modelling. Our method, Long-contextual MIL (LongMIL), is evaluated through extensive experiments on various WSI tasks to validate its superiority. Our code will be available at github.com/invoker-LL/Long-MIL.

Hierarchical Structured Neural Network for Retrieval

Embedding Based Retrieval (EBR) is a crucial component of the retrieval stage in (Ads) Recommendation System that utilizes Two Tower or Siamese Networks to learn embeddings for both users and items (ads). It then employs an Approximate Nearest Neighbor Search (ANN) to efficiently retrieve the most relevant ads for a specific user. Despite the recent rise to popularity in the industry, they have a couple of limitations. Firstly, Two Tower model architecture uses a single dot product interaction which despite their efficiency fail to capture the data distribution in practice. Secondly, the centroid representation and cluster assignment, which are components of ANN, occur after the training process has been completed. As a result, they do not take into account the optimization criteria used for retrieval model. In this paper, we present Hierarchical Structured Neural Network (HSNN), a deployed jointly optimized hierarchical clustering and neural network model that can take advantage of sophisticated interactions and model architectures that are more common in the ranking stages while maintaining a sub-linear inference cost. We achieve 6.5% improvement in offline evaluation and also demonstrate 1.22% online gains through A/B experiments. HSNN has been successfully deployed into the Ads Recommendation system and is currently handling major portion of the traffic. The paper shares our experience in developing this system, dealing with challenges like freshness, volatility, cold start recommendations, cluster collapse and lessons deploying the model in a large scale retrieval production system.

Audit-LLM: Multi-Agent Collaboration for Log-based Insider Threat Detection

Log-based insider threat detection (ITD) detects malicious user activities by auditing log entries. Recently, large language models (LLMs) with strong common sense knowledge have emerged in the domain of ITD. Nevertheless, diverse activity types and overlong log files pose a significant challenge for LLMs in directly discerning malicious ones within myriads of normal activities. Furthermore, the faithfulness hallucination issue from LLMs aggravates its application difficulty in ITD, as the generated conclusion may not align with user commands and activity context. In response to these challenges, we introduce Audit-LLM, a multi-agent log-based insider threat detection framework comprising three collaborative agents: (i) the Decomposer agent, breaking down the complex ITD task into manageable sub-tasks using Chain-of-Thought (COT) reasoning;(ii) the Tool Builder agent, creating reusable tools for sub-tasks to overcome context length limitations in LLMs; and (iii) the Executor agent, generating the final detection conclusion by invoking constructed tools. To enhance conclusion accuracy, we propose a pair-wise Evidence-based Multi-agent Debate (EMAD) mechanism, where two independent Executors iteratively refine their conclusions through reasoning exchange to reach a consensus. Comprehensive experiments conducted on three publicly available ITD datasets-CERT r4.2, CERT r5.2, and PicoDomain-demonstrate the superiority of our method over existing baselines and show that the proposed EMAD significantly improves the faithfulness of explanations generated by LLMs.

Large-scale cervical precancerous screening via AI-assisted cytology whole slide image analysis

Cervical Cancer continues to be the leading gynecological malignancy, posing a persistent threat to women's health on a global scale. Early screening via cytology Whole Slide Image (WSI) diagnosis is critical to prevent this Cancer progression and improve survival rate, but pathologist's single test suffers inevitable false negative due to the immense number of cells that need to be reviewed within a WSI. Though computer-aided automated diagnostic models can serve as strong complement for pathologists, their effectiveness is hampered by the paucity of extensive and detailed annotations, coupled with the limited interpretability and robustness. These factors significantly hinder their practical applicability and reliability in clinical settings. To tackle these challenges, we develop an AI approach, which is a Scalable Technology for Robust and Interpretable Diagnosis built on Extensive data (STRIDE) of cervical cytology. STRIDE addresses the bottleneck of limited annotations by integrating patient-level labels with a small portion of cell-level labels through an end-to-end training strategy, facilitating scalable learning across extensive datasets. To further improve the robustness to real-world domain shifts of cytology slide-making and imaging, STRIDE employs color adversarial samples training that mimic staining and imaging variations. Lastly, to achieve pathologist-level interpretability for the trustworthiness in clinical settings, STRIDE can generate explanatory textual descriptions that simulates pathologists' diagnostic processes by cell image feature and textual description alignment. Conducting extensive experiments and evaluations in 183 medical centers with a dataset of 341,889 WSIs and 0.1 billion cells from cervical cytology patients, STRIDE has demonstrated a remarkable superiority over previous state-of-the-art techniques.

WSI-VQA: Interpreting Whole Slide Images by Generative Visual Question Answering

Whole slide imaging is routinely adopted for carcinoma diagnosis and prognosis. Abundant experience is required for pathologists to achieve accurate and reliable diagnostic results of whole slide images (WSI). The huge size and heterogeneous features of WSIs make the workflow of pathological reading extremely time-consuming. In this paper, we propose a novel framework (WSI-VQA) to interpret WSIs by generative visual question answering. WSI-VQA shows universality by reframing various kinds of slide-level tasks in a question-answering pattern, in which pathologists can achieve immunohistochemical grading, survival prediction, and tumor subtyping following human-machine interaction. Furthermore, we establish a WSI-VQA dataset which contains 8672 slide-level question-answering pairs with 977 WSIs. Besides the ability to deal with different slide-level tasks, our generative model which is named Wsi2Text Transformer (W2T) outperforms existing discriminative models in medical correctness, which reveals the potential of our model to be applied in the clinical scenario. Additionally, we also visualize the co-attention mapping between word embeddings and WSIs as an intuitive explanation for diagnostic results. The dataset and related code are available at https://github.com/cpystan/WSI-VQA.