Cost-effective Instruction Learning for Pathology Vision and Language Analysis

The advent of vision-language models fosters the interactive conversations between AI-enabled models and humans. Yet applying these models into clinics must deal with daunting challenges around large-scale training data, financial, and computational resources. Here we propose a cost-effective instruction learning framework for conversational pathology named as CLOVER. CLOVER only trains a lightweight module and uses instruction tuning while freezing the parameters of the large language model. Instead of using costly GPT-4, we propose well-designed prompts on GPT-3.5 for building generation-based instructions, emphasizing the utility of pathological knowledge derived from the Internet source. To augment the use of instructions, we construct a high-quality set of template-based instructions in the context of digital pathology. From two benchmark datasets, our findings reveal the strength of hybrid-form instructions in the visual question-answer in pathology. Extensive results show the cost-effectiveness of CLOVER in answering both open-ended and closed-ended questions, where CLOVER outperforms strong baselines that possess 37 times more training parameters and use instruction data generated from GPT-4. Through the instruction tuning, CLOVER exhibits robustness of few-shot learning in the external clinical dataset. These findings demonstrate that cost-effective modeling of CLOVER could accelerate the adoption of rapid conversational applications in the landscape of digital pathology.

Aligning Human Knowledge with Visual Concepts Towards Explainable Medical Image Classification

Although explainability is essential in the clinical diagnosis, most deep learning models still function as black boxes without elucidating their decision-making process. In this study, we investigate the explainable model development that can mimic the decision-making process of human experts by fusing the domain knowledge of explicit diagnostic criteria. We introduce a simple yet effective framework, Explicd, towards Explainable language-informed criteria-based diagnosis. Explicd initiates its process by querying domain knowledge from either large language models (LLMs) or human experts to establish diagnostic criteria across various concept axes (e.g., color, shape, texture, or specific patterns of diseases). By leveraging a pretrained vision-language model, Explicd injects these criteria into the embedding space as knowledge anchors, thereby facilitating the learning of corresponding visual concepts within medical images. The final diagnostic outcome is determined based on the similarity scores between the encoded visual concepts and the textual criteria embeddings. Through extensive evaluation of five medical image classification benchmarks, Explicd has demonstrated its inherent explainability and extends to improve classification performance compared to traditional black-box models.

Data-Centric Foundation Models in Computational Healthcare: A Survey

The advent of foundation models (FMs) as an emerging suite of AI techniques has struck a wave of opportunities in computational healthcare. The interactive nature of these models, guided by pre-training data and human instructions, has ignited a data-centric AI paradigm that emphasizes better data characterization, quality, and scale. In healthcare AI, obtaining and processing high-quality clinical data records has been a longstanding challenge, ranging from data quantity, annotation, patient privacy, and ethics. In this survey, we investigate a wide range of data-centric approaches in the FM era (from model pre-training to inference) towards improving the healthcare workflow. We discuss key perspectives in AI security, assessment, and alignment with human values. Finally, we offer a promising outlook of FM-based analytics to enhance the performance of patient outcome and clinical workflow in the evolving landscape of healthcare and medicine. We provide an up-to-date list of healthcare-related foundation models and datasets at https://github.com/Yunkun-Zhang/Data-Centric-FM-Healthcare .

Acceleration Estimation of Signal Propagation Path Length Changes for Wireless Sensing

As indoor applications grow in diversity, wireless sensing, vital in areas like localization and activity recognition, is attracting renewed interest. Indoor wireless sensing relies on signal processing, particularly channel state information (CSI) based signal parameter estimation. Nonetheless, regarding reflected signals induced by dynamic human targets, no satisfactory algorithm yet exists for estimating the acceleration of dynamic path length change (DPLC), which is crucial for various sensing tasks in this context. Hence, this paper proposes DP-AcE, a CSI-based DPLC acceleration estimation algorithm. We first model the relationship between the phase difference of adjacent CSI measurements and the DPLC's acceleration. Unlike existing works assuming constant velocity, DP-AcE considers both velocity and acceleration, yielding a more accurate and objective representation. Using this relationship, an algorithm combining scaling with Fourier transform is proposed to realize acceleration estimation. We evaluate DP-AcE via the acceleration estimation and acceleration-based fall detection with the collected CSI. Experimental results reveal that, using distance as the metric, DP-AcE achieves a median acceleration estimation percentage error of 4.38%. Furthermore, in multi-target scenarios, the fall detection achieves an average true positive rate of 89.56% and a false positive rate of 11.78%, demonstrating its importance in enhancing indoor wireless sensing capabilities.

SegRap2023: A Benchmark of Organs-at-Risk and Gross Tumor Volume Segmentation for Radiotherapy Planning of Nasopharyngeal Carcinoma

Radiation therapy is a primary and effective NasoPharyngeal Carcinoma (NPC) treatment strategy. The precise delineation of Gross Tumor Volumes (GTVs) and Organs-At-Risk (OARs) is crucial in radiation treatment, directly impacting patient prognosis. Previously, the delineation of GTVs and OARs was performed by experienced radiation oncologists. Recently, deep learning has achieved promising results in many medical image segmentation tasks. However, for NPC OARs and GTVs segmentation, few public datasets are available for model development and evaluation. To alleviate this problem, the SegRap2023 challenge was organized in conjunction with MICCAI2023 and presented a large-scale benchmark for OAR and GTV segmentation with 400 Computed Tomography (CT) scans from 200 NPC patients, each with a pair of pre-aligned non-contrast and contrast-enhanced CT scans. The challenge's goal was to segment 45 OARs and 2 GTVs from the paired CT scans. In this paper, we detail the challenge and analyze the solutions of all participants. The average Dice similarity coefficient scores for all submissions ranged from 76.68\% to 86.70\%, and 70.42\% to 73.44\% for OARs and GTVs, respectively. We conclude that the segmentation of large-size OARs is well-addressed, and more efforts are needed for GTVs and small-size or thin-structure OARs. The benchmark will remain publicly available here: https://segrap2023.grand-challenge.org

Text-guided Foundation Model Adaptation for Pathological Image Classification

The recent surge of foundation models in computer vision and natural language processing opens up perspectives in utilizing multi-modal clinical data to train large models with strong generalizability. Yet pathological image datasets often lack biomedical text annotation and enrichment. Guiding data-efficient image diagnosis from the use of biomedical text knowledge becomes a substantial interest. In this paper, we propose to Connect Image and Text Embeddings (CITE) to enhance pathological image classification. CITE injects text insights gained from language models pre-trained with a broad range of biomedical texts, leading to adapt foundation models towards pathological image understanding. Through extensive experiments on the PatchGastric stomach tumor pathological image dataset, we demonstrate that CITE achieves leading performance compared with various baselines especially when training data is scarce. CITE offers insights into leveraging in-domain text knowledge to reinforce data-efficient pathological image classification. Code is available at https://github.com/Yunkun-Zhang/CITE.

Pathology-and-genomics Multimodal Transformer for Survival Outcome Prediction

Survival outcome assessment is challenging and inherently associated with multiple clinical factors (e.g., imaging and genomics biomarkers) in cancer. Enabling multimodal analytics promises to reveal novel predictive patterns of patient outcomes. In this study, we propose a multimodal transformer (PathOmics) integrating pathology and genomics insights into colon-related cancer survival prediction. We emphasize the unsupervised pretraining to capture the intrinsic interaction between tissue microenvironments in gigapixel whole slide images (WSIs) and a wide range of genomics data (e.g., mRNA-sequence, copy number variant, and methylation). After the multimodal knowledge aggregation in pretraining, our task-specific model finetuning could expand the scope of data utility applicable to both multi- and single-modal data (e.g., image- or genomics-only). We evaluate our approach on both TCGA colon and rectum cancer cohorts, showing that the proposed approach is competitive and outperforms state-of-the-art studies. Finally, our approach is desirable to utilize the limited number of finetuned samples towards data-efficient analytics for survival outcome prediction. The code is available at https://github.com/Cassie07/PathOmics.

AmadeusGPT: a natural language interface for interactive animal behavioral analysis

The process of quantifying and analyzing animal behavior involves translating the naturally occurring descriptive language of their actions into machine-readable code. Yet, codifying behavior analysis is often challenging without deep understanding of animal behavior and technical machine learning knowledge. To limit this gap, we introduce AmadeusGPT: a natural language interface that turns natural language descriptions of behaviors into machine-executable code. Large-language models (LLMs) such as GPT3.5 and GPT4 allow for interactive language-based queries that are potentially well suited for making interactive behavior analysis. However, the comprehension capability of these LLMs is limited by the context window size, which prevents it from remembering distant conversations. To overcome the context window limitation, we implement a novel dual-memory mechanism to allow communication between short-term and long-term memory using symbols as context pointers for retrieval and saving. Concretely, users directly use language-based definitions of behavior and our augmented GPT develops code based on the core AmadeusGPT API, which contains machine learning, computer vision, spatio-temporal reasoning, and visualization modules. Users then can interactively refine results, and seamlessly add new behavioral modules as needed. We benchmark AmadeusGPT and show we can produce state-of-the-art performance on the MABE 2022 behavior challenge tasks. Note, an end-user would not need to write any code to achieve this. Thus, collectively AmadeusGPT presents a novel way to merge deep biological knowledge, large-language models, and core computer vision modules into a more naturally intelligent system. Code and demos can be found at: https://github.com/AdaptiveMotorControlLab/AmadeusGPT.

Rethinking pose estimation in crowds: overcoming the detection information-bottleneck and ambiguity

Frequent interactions between individuals are a fundamental challenge for pose estimation algorithms. Current pipelines either use an object detector together with a pose estimator (top-down approach), or localize all body parts first and then link them to predict the pose of individuals (bottom-up). Yet, when individuals closely interact, top-down methods are ill-defined due to overlapping individuals, and bottom-up methods often falsely infer connections to distant body parts. Thus, we propose a novel pipeline called bottom-up conditioned top-down pose estimation (BUCTD) that combines the strengths of bottom-up and top-down methods. Specifically, we propose to use a bottom-up model as the detector, which in addition to an estimated bounding box provides a pose proposal that is fed as condition to an attention-based top-down model. We demonstrate the performance and efficiency of our approach on animal and human pose estimation benchmarks. On CrowdPose and OCHuman, we outperform previous state-of-the-art models by a significant margin. We achieve 78.5 AP on CrowdPose and 47.2 AP on OCHuman, an improvement of 8.6% and 4.9% over the prior art, respectively. Furthermore, we show that our method has excellent performance on non-crowded datasets such as COCO, and strongly improves the performance on multi-animal benchmarks involving mice, fish and monkeys.

Training Like a Medical Resident: Universal Medical Image Segmentation via Context Prior Learning

A major enduring focus of clinical workflows is disease analytics and diagnosis, leading to medical imaging datasets where the modalities and annotations are strongly tied to specific clinical objectives. To date, building task-specific segmentation models is intuitive yet a restrictive approach, lacking insights gained from widespread imaging cohorts. Inspired by the training of medical residents, we explore universal medical image segmentation, whose goal is to learn from diverse medical imaging sources covering a range of clinical targets, body regions, and image modalities. Following this paradigm, we propose Hermes, a context prior learning approach that addresses the challenges related to the heterogeneity on data, modality, and annotations in the proposed universal paradigm. In a collection of seven diverse datasets, we demonstrate the appealing merits of the universal paradigm over the traditional task-specific training paradigm. By leveraging the synergy among various tasks, Hermes shows superior performance and model scalability. Our in-depth investigation on two additional datasets reveals Hermes' strong capabilities for transfer learning, incremental learning, and generalization to different downstream tasks. The code is available: https://github.com/yhygao/universal-medical-image-segmentation.