Online Reasoning Video Segmentation with Just-in-Time Digital Twins

Reasoning segmentation (RS) aims to identify and segment objects of interest based on implicit text queries. As such, RS is a catalyst for embodied AI agents, enabling them to interpret high-level commands without requiring explicit step-by-step guidance. However, current RS approaches rely heavily on the visual perception capabilities of multimodal large language models (LLMs), leading to several major limitations. First, they struggle with queries that require multiple steps of reasoning or those that involve complex spatial/temporal relationships. Second, they necessitate LLM fine-tuning, which may require frequent updates to maintain compatibility with contemporary LLMs and may increase risks of catastrophic forgetting during fine-tuning. Finally, being primarily designed for static images or offline video processing, they scale poorly to online video data. To address these limitations, we propose an agent framework that disentangles perception and reasoning for online video RS without LLM fine-tuning. Our innovation is the introduction of a just-in-time digital twin concept, where -- given an implicit query -- a LLM plans the construction of a low-level scene representation from high-level video using specialist vision models. We refer to this approach to creating a digital twin as "just-in-time" because the LLM planner will anticipate the need for specific information and only request this limited subset instead of always evaluating every specialist model. The LLM then performs reasoning on this digital twin representation to identify target objects. To evaluate our approach, we introduce a new comprehensive video reasoning segmentation benchmark comprising 200 videos with 895 implicit text queries. The benchmark spans three reasoning categories (semantic, spatial, and temporal) with three different reasoning chain complexity.

Operating Room Workflow Analysis via Reasoning Segmentation over Digital Twins

Analyzing operating room (OR) workflows to derive quantitative insights into OR efficiency is important for hospitals to maximize patient care and financial sustainability. Prior work on OR-level workflow analysis has relied on end-to-end deep neural networks. While these approaches work well in constrained settings, they are limited to the conditions specified at development time and do not offer the flexibility necessary to accommodate the OR workflow analysis needs of various OR scenarios (e.g., large academic center vs. rural provider) without data collection, annotation, and retraining. Reasoning segmentation (RS) based on foundation models offers this flexibility by enabling automated analysis of OR workflows from OR video feeds given only an implicit text query related to the objects of interest. Due to the reliance on large language model (LLM) fine-tuning, current RS approaches struggle with reasoning about semantic/spatial relationships and show limited generalization to OR video due to variations in visual characteristics and domain-specific terminology. To address these limitations, we first propose a novel digital twin (DT) representation that preserves both semantic and spatial relationships between the various OR components. Then, building on this foundation, we propose ORDiRS (Operating Room Digital twin representation for Reasoning Segmentation), an LLM-tuning-free RS framework that reformulates RS into a "reason-retrieval-synthesize" paradigm. Finally, we present ORDiRS-Agent, an LLM-based agent that decomposes OR workflow analysis queries into manageable RS sub-queries and generates responses by combining detailed textual explanations with supporting visual evidence from RS. Experimental results on both an in-house and a public OR dataset demonstrate that our ORDiRS achieves a cIoU improvement of 6.12%-9.74% compared to the existing state-of-the-arts.

TSCnet: A Text-driven Semantic-level Controllable Framework for Customized Low-Light Image Enhancement

Deep learning-based image enhancement methods show significant advantages in reducing noise and improving visibility in low-light conditions. These methods are typically based on one-to-one mapping, where the model learns a direct transformation from low light to specific enhanced images. Therefore, these methods are inflexible as they do not allow highly personalized mapping, even though an individual's lighting preferences are inherently personalized. To overcome these limitations, we propose a new light enhancement task and a new framework that provides customized lighting control through prompt-driven, semantic-level, and quantitative brightness adjustments. The framework begins by leveraging a Large Language Model (LLM) to understand natural language prompts, enabling it to identify target objects for brightness adjustments. To localize these target objects, the Retinex-based Reasoning Segment (RRS) module generates precise target localization masks using reflection images. Subsequently, the Text-based Brightness Controllable (TBC) module adjusts brightness levels based on the generated illumination map. Finally, an Adaptive Contextual Compensation (ACC) module integrates multi-modal inputs and controls a conditional diffusion model to adjust the lighting, ensuring seamless and precise enhancements accurately. Experimental results on benchmark datasets demonstrate our framework's superior performance at increasing visibility, maintaining natural color balance, and amplifying fine details without creating artifacts. Furthermore, its robust generalization capabilities enable complex semantic-level lighting adjustments in diverse open-world environments through natural language interactions.

An Intrinsically Explainable Approach to Detecting Vertebral Compression Fractures in CT Scans via Neurosymbolic Modeling

Vertebral compression fractures (VCFs) are a common and potentially serious consequence of osteoporosis. Yet, they often remain undiagnosed. Opportunistic screening, which involves automated analysis of medical imaging data acquired primarily for other purposes, is a cost-effective method to identify undiagnosed VCFs. In high-stakes scenarios like opportunistic medical diagnosis, model interpretability is a key factor for the adoption of AI recommendations. Rule-based methods are inherently explainable and closely align with clinical guidelines, but they are not immediately applicable to high-dimensional data such as CT scans. To address this gap, we introduce a neurosymbolic approach for VCF detection in CT volumes. The proposed model combines deep learning (DL) for vertebral segmentation with a shape-based algorithm (SBA) that analyzes vertebral height distributions in salient anatomical regions. This allows for the definition of a rule set over the height distributions to detect VCFs. Evaluation of VerSe19 dataset shows that our method achieves an accuracy of 96% and a sensitivity of 91% in VCF detection. In comparison, a black box model, DenseNet, achieved an accuracy of 95% and sensitivity of 91% in the same dataset. Our results demonstrate that our intrinsically explainable approach can match or surpass the performance of black box deep neural networks while providing additional insights into why a prediction was made. This transparency can enhance clinician's trust thus, supporting more informed decision-making in VCF diagnosis and treatment planning.

Memorizing SAM: 3D Medical Segment Anything Model with Memorizing Transformer

Segment Anything Models (SAMs) have gained increasing attention in medical image analysis due to their zero-shot generalization capability in segmenting objects of unseen classes and domains when provided with appropriate user prompts. Addressing this performance gap is important to fully leverage the pre-trained weights of SAMs, particularly in the domain of volumetric medical image segmentation, where accuracy is important but well-annotated 3D medical data for fine-tuning is limited. In this work, we investigate whether introducing the memory mechanism as a plug-in, specifically the ability to memorize and recall internal representations of past inputs, can improve the performance of SAM with limited computation cost. To this end, we propose Memorizing SAM, a novel 3D SAM architecture incorporating a memory Transformer as a plug-in. Unlike conventional memorizing Transformers that save the internal representation during training or inference, our Memorizing SAM utilizes existing highly accurate internal representation as the memory source to ensure the quality of memory. We evaluate the performance of Memorizing SAM in 33 categories from the TotalSegmentator dataset, which indicates that Memorizing SAM can outperform state-of-the-art 3D SAM variant i.e., FastSAM3D with an average Dice increase of 11.36% at the cost of only 4.38 millisecond increase in inference time. The source code is publicly available at https://github.com/swedfr/memorizingSAM

DiffuseReg: Denoising Diffusion Model for Obtaining Deformation Fields in Unsupervised Deformable Image Registration

Deformable image registration aims to precisely align medical images from different modalities or times. Traditional deep learning methods, while effective, often lack interpretability, real-time observability and adjustment capacity during registration inference. Denoising diffusion models present an alternative by reformulating registration as iterative image denoising. However, existing diffusion registration approaches do not fully harness capabilities, neglecting the critical sampling phase that enables continuous observability during the inference. Hence, we introduce DiffuseReg, an innovative diffusion-based method that denoises deformation fields instead of images for improved transparency. We also propose a novel denoising network upon Swin Transformer, which better integrates moving and fixed images with diffusion time step throughout the denoising process. Furthermore, we enhance control over the denoising registration process with a novel similarity consistency regularization. Experiments on ACDC datasets demonstrate DiffuseReg outperforms existing diffusion registration methods by 1.32 in Dice score. The sampling process in DiffuseReg enables real-time output observability and adjustment unmatched by previous deep models.

A Survey for Large Language Models in Biomedicine

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering

The structural similarities between protein sequences and natural languages have led to parallel advancements in deep learning across both domains. While large language models (LLMs) have achieved much progress in the domain of natural language processing, their potential in protein engineering remains largely unexplored. Previous approaches have equipped LLMs with protein understanding capabilities by incorporating external protein encoders, but this fails to fully leverage the inherent similarities between protein sequences and natural languages, resulting in sub-optimal performance and increased model complexity. To address this gap, we present TourSynbio-7B, the first multi-modal large model specifically designed for protein engineering tasks without external protein encoders. TourSynbio-7B demonstrates that LLMs can inherently learn to understand proteins as language. The model is post-trained and instruction fine-tuned on InternLM2-7B using ProteinLMDataset, a dataset comprising 17.46 billion tokens of text and protein sequence for self-supervised pretraining and 893K instructions for supervised fine-tuning. TourSynbio-7B outperforms GPT-4 on the ProteinLMBench, a benchmark of 944 manually verified multiple-choice questions, with 62.18% accuracy. Leveraging TourSynbio-7B's enhanced protein sequence understanding capability, we introduce TourSynbio-Agent, an innovative framework capable of performing various protein engineering tasks, including mutation analysis, inverse folding, protein folding, and visualization. TourSynbio-Agent integrates previously disconnected deep learning models in the protein engineering domain, offering a unified conversational user interface for improved usability. Finally, we demonstrate the efficacy of TourSynbio-7B and TourSynbio-Agent through two wet lab case studies on vanilla key enzyme modification and steroid compound catalysis.

Performance and Non-adversarial Robustness of the Segment Anything Model 2 in Surgical Video Segmentation

Fully supervised deep learning (DL) models for surgical video segmentation have been shown to struggle with non-adversarial, real-world corruptions of image quality including smoke, bleeding, and low illumination. Foundation models for image segmentation, such as the segment anything model (SAM) that focuses on interactive prompt-based segmentation, move away from semantic classes and thus can be trained on larger and more diverse data, which offers outstanding zero-shot generalization with appropriate user prompts. Recently, building upon this success, SAM-2 has been proposed to further extend the zero-shot interactive segmentation capabilities from independent frame-by-frame to video segmentation. In this paper, we present a first experimental study evaluating SAM-2's performance on surgical video data. Leveraging the SegSTRONG-C MICCAI EndoVIS 2024 sub-challenge dataset, we assess SAM-2's effectiveness on uncorrupted endoscopic sequences and evaluate its non-adversarial robustness on videos with corrupted image quality simulating smoke, bleeding, and low brightness conditions under various prompt strategies. Our experiments demonstrate that SAM-2, in zero-shot manner, can achieve competitive or even superior performance compared to fully-supervised deep learning models on surgical video data, including under non-adversarial corruptions of image quality. Additionally, SAM-2 consistently outperforms the original SAM and its medical variants across all conditions. Finally, frame-sparse prompting can consistently outperform frame-wise prompting for SAM-2, suggesting that allowing SAM-2 to leverage its temporal modeling capabilities leads to more coherent and accurate segmentation compared to frequent prompting.

AutoM3L: An Automated Multimodal Machine Learning Framework with Large Language Models

Automated Machine Learning (AutoML) offers a promising approach to streamline the training of machine learning models. However, existing AutoML frameworks are often limited to unimodal scenarios and require extensive manual configuration. Recent advancements in Large Language Models (LLMs) have showcased their exceptional abilities in reasoning, interaction, and code generation, presenting an opportunity to develop a more automated and user-friendly framework. To this end, we introduce AutoM3L, an innovative Automated Multimodal Machine Learning framework that leverages LLMs as controllers to automatically construct multimodal training pipelines. AutoM3L comprehends data modalities and selects appropriate models based on user requirements, providing automation and interactivity. By eliminating the need for manual feature engineering and hyperparameter optimization, our framework simplifies user engagement and enables customization through directives, addressing the limitations of previous rule-based AutoML approaches. We evaluate the performance of AutoM3L on six diverse multimodal datasets spanning classification, regression, and retrieval tasks, as well as a comprehensive set of unimodal datasets. The results demonstrate that AutoM3L achieves competitive or superior performance compared to traditional rule-based AutoML methods. Furthermore, a user study highlights the user-friendliness and usability of our framework, compared to the rule-based AutoML methods.