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Large Language Models (LLMs) have rapidly become important tools in Biomedical and Health Informatics (BHI), enabling new ways to analyze data, treat patients, and conduct research. This bibliometric review aims to provide a panoramic view of how LLMs have been used in BHI by examining research articles and collaboration networks from 2022 to 2023. It further explores how LLMs can improve Natural Language Processing (NLP) applications in various BHI areas like medical diagnosis, patient engagement, electronic health record management, and personalized medicine. To do this, our bibliometric review identifies key trends, maps out research networks, and highlights major developments in this fast-moving field. Lastly, it discusses the ethical concerns and practical challenges of using LLMs in BHI, such as data privacy and reliable medical recommendations. Looking ahead, we consider how LLMs could further transform biomedical research as well as healthcare delivery and patient outcomes. This bibliometric review serves as a resource for stakeholders in healthcare, including researchers, clinicians, and policymakers, to understand the current state and future potential of LLMs in BHI.

3D simulated environments play a critical role in Embodied AI, but their creation requires expertise and extensive manual effort, restricting their diversity and scope. To mitigate this limitation, we present Holodeck, a system that generates 3D environments to match a user-supplied prompt fully automatedly. Holodeck can generate diverse scenes, e.g., arcades, spas, and museums, adjust the designs for styles, and can capture the semantics of complex queries such as "apartment for a researcher with a cat" and "office of a professor who is a fan of Star Wars". Holodeck leverages a large language model (i.e., GPT-4) for common sense knowledge about what the scene might look like and uses a large collection of 3D assets from Objaverse to populate the scene with diverse objects. To address the challenge of positioning objects correctly, we prompt GPT-4 to generate spatial relational constraints between objects and then optimize the layout to satisfy those constraints. Our large-scale human evaluation shows that annotators prefer Holodeck over manually designed procedural baselines in residential scenes and that Holodeck can produce high-quality outputs for diverse scene types. We also demonstrate an exciting application of Holodeck in Embodied AI, training agents to navigate in novel scenes like music rooms and daycares without human-constructed data, which is a significant step forward in developing general-purpose embodied agents.

Retrieval-Augmented Generation (RAG) demonstrates great value in alleviating outdated knowledge or hallucination by supplying LLMs with updated and relevant knowledge. However, there are still several difficulties for RAG in understanding complex multi-hop query and retrieving relevant documents, which require LLMs to perform reasoning and retrieve step by step. Inspired by human's reasoning process in which they gradually search for the required information, it is natural to ask whether the LLMs could notice the missing information in each reasoning step. In this work, we first experimentally verified the ability of LLMs to extract information as well as to know the missing. Based on the above discovery, we propose a Missing Information Guided Retrieve-Extraction-Solving paradigm (MIGRES), where we leverage the identification of missing information to generate a targeted query that steers the subsequent knowledge retrieval. Besides, we design a sentence-level re-ranking filtering approach to filter the irrelevant content out from document, along with the information extraction capability of LLMs to extract useful information from cleaned-up documents, which in turn to bolster the overall efficacy of RAG. Extensive experiments conducted on multiple public datasets reveal the superiority of the proposed MIGRES method, and analytical experiments demonstrate the effectiveness of our proposed modules.

This article presents Persistence Administered Collective Navigation (PACNav) as an approach for achieving decentralized collective navigation of Unmanned Aerial Vehicle (UAV) swarms. The technique is inspired by the flocking and collective navigation behavior observed in natural swarms, such as cattle herds, bird flocks, and even large groups of humans. PACNav relies solely on local observations of relative positions of UAVs, making it suitable for large swarms deprived of communication capabilities and external localization systems. We introduce the novel concepts of path persistence and path similarity, which allow each swarm member to analyze the motion of others. PACNav is grounded on two main principles: (1) UAVs with little variation in motion direction exhibit high path persistence and are considered reliable leaders by other UAVs; (2) groups of UAVs that move in a similar direction demonstrate high path similarity, and such groups are assumed to contain a reliable leader. The proposed approach also incorporates a reactive collision avoidance mechanism to prevent collisions with swarm members and environmental obstacles. The method is validated through simulated and real-world experiments conducted in a natural forest.

Teleportation, a widely-used locomotion technique in Virtual Reality (VR), allows instantaneous movement within VR environments. Enhanced hand tracking in modern VR headsets has popularized hands-only teleportation methods, which eliminate the need for physical controllers. However, these techniques have not fully explored the potential of bi-manual input, where each hand plays a distinct role in teleportation: one controls the teleportation point and the other confirms selections. Additionally, the influence of users' posture, whether sitting or standing, on these techniques remains unexplored. Furthermore, previous teleportation evaluations lacked assessments based on established human motor models such as Fitts' Law. To address these gaps, we conducted a user study (N=20) to evaluate bi-manual pointing performance in VR teleportation tasks, considering both sitting and standing postures. We proposed a variation of the Fitts' Law model to accurately assess users' teleportation performance. We designed and evaluated various bi-manual teleportation techniques, comparing them to uni-manual and dwell-based techniques. Results showed that bi-manual techniques, particularly when the dominant hand is used for pointing and the non-dominant hand for selection, enable faster teleportation compared to other methods. Furthermore, bi-manual and dwell techniques proved significantly more accurate than uni-manual teleportation. Moreover, our proposed Fitts' Law variation more accurately predicted users' teleportation performance compared to existing models. Finally, we developed a set of guidelines for designers to enhance VR teleportation experiences and optimize user interactions.

The Frozen Section (FS) technique is a rapid and efficient method, taking only 15-30 minutes to prepare slides for pathologists' evaluation during surgery, enabling immediate decisions on further surgical interventions. However, FS process often introduces artifacts and distortions like folds and ice-crystal effects. In contrast, these artifacts and distortions are absent in the higher-quality formalin-fixed paraffin-embedded (FFPE) slides, which require 2-3 days to prepare. While Generative Adversarial Network (GAN)-based methods have been used to translate FS to FFPE images (F2F), they may leave morphological inaccuracies with remaining FS artifacts or introduce new artifacts, reducing the quality of these translations for clinical assessments. In this study, we benchmark recent generative models, focusing on GANs and Latent Diffusion Models (LDMs), to overcome these limitations. We introduce a novel approach that combines LDMs with Histopathology Pre-Trained Embeddings to enhance restoration of FS images. Our framework leverages LDMs conditioned by both text and pre-trained embeddings to learn meaningful features of FS and FFPE histopathology images. Through diffusion and denoising techniques, our approach not only preserves essential diagnostic attributes like color staining and tissue morphology but also proposes an embedding translation mechanism to better predict the targeted FFPE representation of input FS images. As a result, this work achieves a significant improvement in classification performance, with the Area Under the Curve rising from 81.99% to 94.64%, accompanied by an advantageous CaseFD. This work establishes a new benchmark for FS to FFPE image translation quality, promising enhanced reliability and accuracy in histopathology FS image analysis. Our work is available at //minhmanho.github.io/f2f_ldm/.

We present the Evolving Graph Fourier Transform (EFT), the first invertible spectral transform that captures evolving representations on temporal graphs. We motivate our work by the inadequacy of existing methods for capturing the evolving graph spectra, which are also computationally expensive due to the temporal aspect along with the graph vertex domain. We view the problem as an optimization over the Laplacian of the continuous time dynamic graph. Additionally, we propose pseudo-spectrum relaxations that decompose the transformation process, making it highly computationally efficient. The EFT method adeptly captures the evolving graph's structural and positional properties, making it effective for downstream tasks on evolving graphs. Hence, as a reference implementation, we develop a simple neural model induced with EFT for capturing evolving graph spectra. We empirically validate our theoretical findings on a number of large-scale and standard temporal graph benchmarks and demonstrate that our model achieves state-of-the-art performance.

Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.

The problem of Multiple Object Tracking (MOT) consists in following the trajectory of different objects in a sequence, usually a video. In recent years, with the rise of Deep Learning, the algorithms that provide a solution to this problem have benefited from the representational power of deep models. This paper provides a comprehensive survey on works that employ Deep Learning models to solve the task of MOT on single-camera videos. Four main steps in MOT algorithms are identified, and an in-depth review of how Deep Learning was employed in each one of these stages is presented. A complete experimental comparison of the presented works on the three MOTChallenge datasets is also provided, identifying a number of similarities among the top-performing methods and presenting some possible future research directions.

State-of-the-art Convolutional Neural Network (CNN) benefits a lot from multi-task learning (MTL), which learns multiple related tasks simultaneously to obtain shared or mutually related representations for different tasks. The most widely-used MTL CNN structure is based on an empirical or heuristic split on a specific layer (e.g., the last convolutional layer) to minimize different task-specific losses. However, this heuristic sharing/splitting strategy may be harmful to the final performance of one or multiple tasks. In this paper, we propose a novel CNN structure for MTL, which enables automatic feature fusing at every layer. Specifically, we first concatenate features from different tasks according to their channel dimension, and then formulate the feature fusing problem as discriminative dimensionality reduction. We show that this discriminative dimensionality reduction can be done by 1x1 Convolution, Batch Normalization, and Weight Decay in one CNN, which we refer to as Neural Discriminative Dimensionality Reduction (NDDR). We perform ablation analysis in details for different configurations in training the network. The experiments carried out on different network structures and different task sets demonstrate the promising performance and desirable generalizability of our proposed method.