Using Structural Similarity and Kolmogorov-Arnold Networks for Anatomical Embedding of 3-hinge Gyrus

The 3-hinge gyrus (3HG) is a newly defined folding pattern, which is the conjunction of gyri coming from three directions in cortical folding. Many studies demonstrated that 3HGs can be reliable nodes when constructing brain networks or connectome since they simultaneously possess commonality and individuality across different individual brains and populations. However, 3HGs are identified and validated within individual spaces, making it difficult to directly serve as the brain network nodes due to the absence of cross-subject correspondence. The 3HG correspondences represent the intrinsic regulation of brain organizational architecture, traditional image-based registration methods tend to fail because individual anatomical properties need to be fully respected. To address this challenge, we propose a novel self-supervised framework for anatomical feature embedding of the 3HGs to build the correspondences among different brains. The core component of this framework is to construct a structural similarity-enhanced multi-hop feature encoding strategy based on the recently developed Kolmogorov-Arnold network (KAN) for anatomical feature embedding. Extensive experiments suggest that our approach can effectively establish robust cross-subject correspondences when no one-to-one mapping exists.

Evaluation of OpenAI o1: Opportunities and Challenges of AGI

This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.

GP-GPT: Large Language Model for Gene-Phenotype Mapping

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

Introducing Learning Rate Adaptation CMA-ES into Rigid 2D/3D Registration for Robotic Navigation in Spine Surgery

The covariance matrix adaptive evolution strategy (CMA-ES) has been widely used in the field of 2D/3D registration in recent years. This optimization method exhibits exceptional robustness and usability for complex surgical scenarios. However, due to the inherent ill-posed nature of the 2D/3D registration task and the presence of numerous local minima in the landscape of similarity measures. Evolution strategies often require a larger population size in each generation in each generation to ensure the stability of registration and the globality and effectiveness of search, which makes the entire process computationally expensive. In this paper, we build a 2D/3D registration framework based on a learning rate adaptation CMA-ES manner. The framework employs a fixed and small population size, leading to minimized runtime and optimal utilization of computing resources. We conduct experimental comparisons between the proposed framework and other intensity-based baselines using a substantial volume of synthetic data. The results suggests that our method demonstrates superiority in both registration accuracy and running time. Code is available at github.com/m1nhengChen/CMAES-reg.

An Optimization-based Baseline for Rigid 2D/3D Registration Applied to Spine Surgical Navigation Using CMA-ES

A robust and efficient optimization-based 2D/3D registration framework is crucial for the navigation system of orthopedic surgical robots. It can provide precise position information of surgical instruments and implants during surgery. While artificial intelligence technology has advanced rapidly in recent years, traditional optimization-based registration methods remain indispensable in the field of 2D/3D registration.he exceptional precision of this method enables it to be considered as a post-processing step of the learning-based methods, thereby offering a reliable assurance for registration. In this paper, we present a coarse-to-fine registration framework based on the CMA-ES algorithm. We conducted intensive testing of our method using data from different parts of the spine. The results shows the effectiveness of the proposed framework on real orthopedic spine surgery clinical data. This work can be viewed as an additional extension that complements the optimization-based methods employed in our previous studies.

Fully Differentiable Correlation-driven 2D/3D Registration for X-ray to CT Image Fusion

Image-based rigid 2D/3D registration is a critical technique for fluoroscopic guided surgical interventions. In recent years, some learning-based fully differentiable methods have produced beneficial outcomes while the process of feature extraction and gradient flow transmission still lack controllability and interpretability. To alleviate these problems, in this work, we propose a novel fully differentiable correlation-driven network using a dual-branch CNN-transformer encoder which enables the network to extract and separate low-frequency global features from high-frequency local features. A correlation-driven loss is further proposed for low-frequency feature and high-frequency feature decomposition based on embedded information. Besides, a training strategy that learns to approximate a convex-shape similarity function is applied in our work. We test our approach on a in-house datasetand show that it outperforms both existing fully differentiable learning-based registration approaches and the conventional optimization-based baseline.

SpineCLUE: Automatic Vertebrae Identification Using Contrastive Learning and Uncertainty Estimation

Vertebrae identification in arbitrary fields-of-view plays a crucial role in diagnosing spine disease. Most spine CT contain only local regions, such as the neck, chest, and abdomen. Therefore, identification should not depend on specific vertebrae or a particular number of vertebrae being visible. Existing methods at the spine-level are unable to meet this challenge. In this paper, we propose a three-stage method to address the challenges in 3D CT vertebrae identification at vertebrae-level. By sequentially performing the tasks of vertebrae localization, segmentation, and identification, the anatomical prior information of the vertebrae is effectively utilized throughout the process. Specifically, we introduce a dual-factor density clustering algorithm to acquire localization information for individual vertebra, thereby facilitating subsequent segmentation and identification processes. In addition, to tackle the issue of interclass similarity and intra-class variability, we pre-train our identification network by using a supervised contrastive learning method. To further optimize the identification results, we estimated the uncertainty of the classification network and utilized the message fusion module to combine the uncertainty scores, while aggregating global information about the spine. Our method achieves state-of-the-art results on the VerSe19 and VerSe20 challenge benchmarks. Additionally, our approach demonstrates outstanding generalization performance on an collected dataset containing a wide range of abnormal cases.

Embedded Feature Similarity Optimization with Specific Parameter Initialization for 2D/3D Registration

We present a novel deep learning-based framework: Embedded Feature Similarity Optimization with Specific Parameter Initialization (SOPI) for 2D/3D registration which is a most challenging problem due to the difficulty such as dimensional mismatch, heavy computation load and lack of golden evaluating standard. The framework we designed includes a parameter specification module to efficiently choose initialization pose parameter and a fine-registration network to align images. The proposed framework takes extracting multi-scale features into consideration using a novel composite connection encoder with special training techniques. The method is compared with both learning-based methods and optimization-based methods to further evaluate the performance. Our experiments demonstrate that the method in this paper has improved the registration performance, and thereby outperforms the existing methods in terms of accuracy and running time. We also show the potential of the proposed method as an initial pose estimator.