PointJEM: Self-supervised Point Cloud Understanding for Reducing Feature Redundancy via Joint Entropy Maximization

Most deep learning-based point cloud processing methods are supervised and require large scale of labeled data. However, manual labeling of point cloud data is laborious and time-consuming. Self-supervised representation learning can address the aforementioned issue by learning robust and generalized representations from unlabeled datasets. Nevertheless, the embedded features obtained by representation learning usually contain redundant information, and most current methods reduce feature redundancy by linear correlation constraints. In this paper, we propose PointJEM, a self-supervised representation learning method applied to the point cloud field. PointJEM comprises an embedding scheme and a loss function based on joint entropy. The embedding scheme divides the embedding vector into different parts, each part can learn a distinctive feature. To reduce redundant information in the features, PointJEM maximizes the joint entropy between the different parts, thereby rendering the learned feature variables pairwise independent. To validate the effectiveness of our method, we conducted experiments on multiple datasets. The results demonstrate that our method can significantly reduce feature redundancy beyond linear correlation. Furthermore, PointJEM achieves competitive performance in downstream tasks such as classification and segmentation.

Boosting Dermatoscopic Lesion Segmentation via Diffusion Models with Visual and Textual Prompts

Image synthesis approaches, e.g., generative adversarial networks, have been popular as a form of data augmentation in medical image analysis tasks. It is primarily beneficial to overcome the shortage of publicly accessible data and associated quality annotations. However, the current techniques often lack control over the detailed contents in generated images, e.g., the type of disease patterns, the location of lesions, and attributes of the diagnosis. In this work, we adapt the latest advance in the generative model, i.e., the diffusion model, with the added control flow using lesion-specific visual and textual prompts for generating dermatoscopic images. We further demonstrate the advantage of our diffusion model-based framework over the classical generation models in both the image quality and boosting the segmentation performance on skin lesions. It can achieve a 9% increase in the SSIM image quality measure and an over 5% increase in Dice coefficients over the prior arts.

JAX-LOB: A GPU-Accelerated limit order book simulator to unlock large scale reinforcement learning for trading

Financial exchanges across the world use limit order books (LOBs) to process orders and match trades. For research purposes it is important to have large scale efficient simulators of LOB dynamics. LOB simulators have previously been implemented in the context of agent-based models (ABMs), reinforcement learning (RL) environments, and generative models, processing order flows from historical data sets and hand-crafted agents alike. For many applications, there is a requirement for processing multiple books, either for the calibration of ABMs or for the training of RL agents. We showcase the first GPU-enabled LOB simulator designed to process thousands of books in parallel, with a notably reduced per-message processing time. The implementation of our simulator - JAX-LOB - is based on design choices that aim to best exploit the powers of JAX without compromising on the realism of LOB-related mechanisms. We integrate JAX-LOB with other JAX packages, to provide an example of how one may address an optimal execution problem with reinforcement learning, and to share some preliminary results from end-to-end RL training on GPUs.

Generative AI for End-to-End Limit Order Book Modelling: A Token-Level Autoregressive Generative Model of Message Flow Using a Deep State Space Network

Developing a generative model of realistic order flow in financial markets is a challenging open problem, with numerous applications for market participants. Addressing this, we propose the first end-to-end autoregressive generative model that generates tokenized limit order book (LOB) messages. These messages are interpreted by a Jax-LOB simulator, which updates the LOB state. To handle long sequences efficiently, the model employs simplified structured state-space layers to process sequences of order book states and tokenized messages. Using LOBSTER data of NASDAQ equity LOBs, we develop a custom tokenizer for message data, converting groups of successive digits to tokens, similar to tokenization in large language models. Out-of-sample results show promising performance in approximating the data distribution, as evidenced by low model perplexity. Furthermore, the mid-price returns calculated from the generated order flow exhibit a significant correlation with the data, indicating impressive conditional forecast performance. Due to the granularity of generated data, and the accuracy of the model, it offers new application areas for future work beyond forecasting, e.g. acting as a world model in high-frequency financial reinforcement learning applications. Overall, our results invite the use and extension of the model in the direction of autoregressive large financial models for the generation of high-frequency financial data and we commit to open-sourcing our code to facilitate future research.

DMCVR: Morphology-Guided Diffusion Model for 3D Cardiac Volume Reconstruction

Accurate 3D cardiac reconstruction from cine magnetic resonance imaging (cMRI) is crucial for improved cardiovascular disease diagnosis and understanding of the heart's motion. However, current cardiac MRI-based reconstruction technology used in clinical settings is 2D with limited through-plane resolution, resulting in low-quality reconstructed cardiac volumes. To better reconstruct 3D cardiac volumes from sparse 2D image stacks, we propose a morphology-guided diffusion model for 3D cardiac volume reconstruction, DMCVR, that synthesizes high-resolution 2D images and corresponding 3D reconstructed volumes. Our method outperforms previous approaches by conditioning the cardiac morphology on the generative model, eliminating the time-consuming iterative optimization process of the latent code, and improving generation quality. The learned latent spaces provide global semantics, local cardiac morphology and details of each 2D cMRI slice with highly interpretable value to reconstruct 3D cardiac shape. Our experiments show that DMCVR is highly effective in several aspects, such as 2D generation and 3D reconstruction performance. With DMCVR, we can produce high-resolution 3D cardiac MRI reconstructions, surpassing current techniques. Our proposed framework has great potential for improving the accuracy of cardiac disease diagnosis and treatment planning. Code can be accessed at https://github.com/hexiaoxiao-cs/DMCVR.

Deep learning-based estimation of whole-body kinematics from multi-view images

It is necessary to analyze the whole-body kinematics (including joint locations and joint angles) to assess risks of fatal and musculoskeletal injuries in occupational tasks. Human pose estimation has gotten more attention in recent years as a method to minimize the errors in determining joint locations. However, the joint angles are not often estimated, nor is the quality of joint angle estimation assessed. In this paper, we presented an end-to-end approach on direct joint angle estimation from multi-view images. Our method leveraged the volumetric pose representation and mapped the rotation representation to a continuous space where each rotation was uniquely represented. We also presented a new kinematic dataset in the domain of residential roofing with a data processing pipeline to generate necessary annotations for the supervised training procedure on direct joint angle estimation. We achieved a mean angle error of $7.19^\circ$ on the new Roofing dataset and $8.41^\circ$ on the Human3.6M dataset, paving the way for employment of on-site kinematic analysis using multi-view images.

MedLSAM: Localize and Segment Anything Model for 3D Medical Images

The Segment Anything Model (SAM) has recently emerged as a groundbreaking model in the field of image segmentation. Nevertheless, both the original SAM and its medical adaptations necessitate slice-by-slice annotations, which directly increase the annotation workload with the size of the dataset. We propose MedLSAM to address this issue, ensuring a constant annotation workload irrespective of dataset size and thereby simplifying the annotation process. Our model introduces a few-shot localization framework capable of localizing any target anatomical part within the body. To achieve this, we develop a Localize Anything Model for 3D Medical Images (MedLAM), utilizing two self-supervision tasks: relative distance regression (RDR) and multi-scale similarity (MSS) across a comprehensive dataset of 14,012 CT scans. We then establish a methodology for accurate segmentation by integrating MedLAM with SAM. By annotating only six extreme points across three directions on a few templates, our model can autonomously identify the target anatomical region on all data scheduled for annotation. This allows our framework to generate a 2D bounding box for every slice of the image, which are then leveraged by SAM to carry out segmentations. We conducted experiments on two 3D datasets covering 38 organs and found that MedLSAM matches the performance of SAM and its medical adaptations while requiring only minimal extreme point annotations for the entire dataset. Furthermore, MedLAM has the potential to be seamlessly integrated with future 3D SAM models, paving the way for enhanced performance. Our code is public at https://github.com/openmedlab/MedLSAM.

MIS-FM: 3D Medical Image Segmentation using Foundation Models Pretrained on a Large-Scale Unannotated Dataset

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.

Masked conditional variational autoencoders for chromosome straightening

Karyotyping is of importance for detecting chromosomal aberrations in human disease. However, chromosomes easily appear curved in microscopic images, which prevents cytogeneticists from analyzing chromosome types. To address this issue, we propose a framework for chromosome straightening, which comprises a preliminary processing algorithm and a generative model called masked conditional variational autoencoders (MC-VAE). The processing method utilizes patch rearrangement to address the difficulty in erasing low degrees of curvature, providing reasonable preliminary results for the MC-VAE. The MC-VAE further straightens the results by leveraging chromosome patches conditioned on their curvatures to learn the mapping between banding patterns and conditions. During model training, we apply a masking strategy with a high masking ratio to train the MC-VAE with eliminated redundancy. This yields a non-trivial reconstruction task, allowing the model to effectively preserve chromosome banding patterns and structure details in the reconstructed results. Extensive experiments on three public datasets with two stain styles show that our framework surpasses the performance of state-of-the-art methods in retaining banding patterns and structure details. Compared to using real-world bent chromosomes, the use of high-quality straightened chromosomes generated by our proposed method can improve the performance of various deep learning models for chromosome classification by a large margin. Such a straightening approach has the potential to be combined with other karyotyping systems to assist cytogeneticists in chromosome analysis.