Publication Library
PyPulse A Python Library for Biosignal Imputation
Description: See: https://github.com/rehg-lab/pulseimpute. We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data transmission loss. PyPulse's framework provides a modular and extendable framework with high ease-of-use for a broad userbase, including non-machine-learning bioresearchers. Specifically, its new capabilities include using pre-trained imputation methods out-of-the-box on custom datasets, running the full workflow of training or testing a baseline method with a single line of code, and comparing baseline methods in an interactive visualization tool. We released PyPulse under the MIT License on Github and PyPI.
Created At: 13 December 2024
Updated At: 13 December 2024
Liner Shipping Network Design with Reinforcement Learning
Description: This paper proposes a novel reinforcement learning framework to address the Liner Shipping Network Design Problem (LSNDP), a challenging combinatorial optimization problem focused on designing cost-efficient maritime shipping routes. Traditional methods for solving the LSNDP typically involve decomposing the problem into sub-problems, such as network design and multi-commodity flow, which are then tackled using approximate heuristics or large neighborhood search (LNS) techniques. In contrast, our approach employs a model-free reinforcement learning algorithm on the network design, integrated with a heuristic-based multi-commodity flow solver, to produce competitive results on the publicly available LINERLIB benchmark. Additionally, our method also demonstrates generalization capabilities by producing competitive solutions on the benchmark instances after training on perturbed instances.
Created At: 13 December 2024
Updated At: 13 December 2024
TopoCellGen Generating Histopathology Cell Topology with a Diffusion Model
Description: Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue environments, enhances downstream tasks by augmenting training data, aligns more closely with pathologists' domain knowledge, and offers new opportunities for controlling and generalizing the tumor microenvironment. In this paper, we propose a novel approach that integrates topological constraints into a diffusion model to improve the generation of realistic, contextually accurate cell topologies. Our method refines the simulation of cell distributions and interactions, increasing the precision and interpretability of results in downstream tasks such as cell detection and classification. To assess the topological fidelity of generated layouts, we introduce a new metric, Topological Frechet Distance (TopoFD), which overcomes the limitations of traditional metrics like FID in evaluating topological structure. Experimental results demonstrate the effectiveness of our approach in generating multi-class cell layouts that capture intricate topological relationships.
Created At: 13 December 2024
Updated At: 13 December 2024
Real-time volumetric free-hand ultrasound imaging for large-sized organs A study of imaging the whole spine
Description: Three-dimensional (3D) ultrasound imaging can overcome the limitations of conventional two dimensional (2D) ultrasound imaging in structural observation and measurement. However, conducting volumetric ultrasound imaging for large-sized organs still faces difficulties including long acquisition time, inevitable patient movement, and 3D feature recognition. In this study, we proposed a real-time volumetric free-hand ultrasound imaging system optimized for the above issues and applied it to the clinical diagnosis of scoliosis. This study employed an incremental imaging method coupled with algorithmic acceleration to enable real-time processing and visualization of the large amounts of data generated when scanning large-sized organs. Furthermore, to deal with the difficulty of image feature recognition, we proposed two tissue segmentation algorithms to reconstruct and visualize the spinal anatomy in 3D space by approximating the depth at which the bone structures are located and segmenting the ultrasound images at different depths. We validated the adaptability of our system by deploying it to multiple models of ultra-sound equipment and conducting experiments using different types of ultrasound probes. We also conducted experiments on 6 scoliosis patients and 10 normal volunteers to evaluate the performance of our proposed method. Ultrasound imaging of a volunteer spine from shoulder to crotch (more than 500 mm) was performed in 2 minutes, and the 3D imaging results displayed in real-time were compared with the corresponding X-ray images with a correlation coefficient of 0.96 in spinal curvature. Our proposed volumetric ultrasound imaging system might hold the potential to be clinically applied to other large-sized organs.
Created At: 13 December 2024
Updated At: 13 December 2024
Path-RAG Knowledge-Guided Key Region Retrieval for Open-ended Pathology Visual Question Answering
Description: See: https://github.com/embedded-robotics/path-rag. Accurate diagnosis and prognosis assisted by pathology images are essential for cancer treatment selection and planning. Despite the recent trend of adopting deep-learning approaches for analyzing complex pathology images, they fall short as they often overlook the domain-expert understanding of tissue structure and cell composition. In this work, we focus on a challenging Open-ended Pathology VQA (PathVQA-Open) task and propose a novel framework named Path-RAG, which leverages HistoCartography to retrieve relevant domain knowledge from pathology images and significantly improves performance on PathVQA-Open. Admitting the complexity of pathology image analysis, Path-RAG adopts a human-centered AI approach by retrieving domain knowledge using HistoCartography to select the relevant patches from pathology images. Our experiments suggest that domain guidance can significantly boost the accuracy of LLaVA-Med from 38% to 47%, with a notable gain of 28% for H&E-stained pathology images in the PathVQA-Open dataset. For longer-form question and answer pairs, our model consistently achieves significant improvements of 32.5% in ARCH-Open PubMed and 30.6% in ARCH-Open Books on H\&E images.
Created At: 13 December 2024
Updated At: 13 December 2024