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.

Eye-gaze Guided Multi-modal Alignment Framework for Radiology

In multi-modal frameworks, the alignment of cross-modal features presents a significant challenge. The predominant approach in multi-modal pre-training emphasizes either global or local alignment between modalities, utilizing extensive datasets. This bottom-up driven method often suffers from a lack of interpretability, a critical concern in radiology. Previous studies have integrated high-level labels in medical images or text, but these still rely on manual annotation, a costly and labor-intensive process. Our work introduces a novel approach by using eye-gaze data, collected synchronously by radiologists during diagnostic evaluations. This data, indicating radiologists' focus areas, naturally links chest X-rays to diagnostic texts. We propose the Eye-gaze Guided Multi-modal Alignment (EGMA) framework to harness eye-gaze data for better alignment of image and text features, aiming to reduce reliance on manual annotations and thus cut training costs. Our model demonstrates robust performance, outperforming other state-of-the-art methods in zero-shot classification and retrieval tasks. The incorporation of easily-obtained eye-gaze data during routine radiological diagnoses signifies a step towards minimizing manual annotation dependency. Additionally, we explore the impact of varying amounts of eye-gaze data on model performance, highlighting the feasibility and utility of integrating this auxiliary data into multi-modal pre-training.

InterLUDE: Interactions between Labeled and Unlabeled Data to Enhance Semi-Supervised Learning

Semi-supervised learning (SSL) seeks to enhance task performance by training on both labeled and unlabeled data. Mainstream SSL image classification methods mostly optimize a loss that additively combines a supervised classification objective with a regularization term derived solely from unlabeled data. This formulation neglects the potential for interaction between labeled and unlabeled images. In this paper, we introduce InterLUDE, a new approach to enhance SSL made of two parts that each benefit from labeled-unlabeled interaction. The first part, embedding fusion, interpolates between labeled and unlabeled embeddings to improve representation learning. The second part is a new loss, grounded in the principle of consistency regularization, that aims to minimize discrepancies in the model's predictions between labeled versus unlabeled inputs. Experiments on standard closed-set SSL benchmarks and a medical SSL task with an uncurated unlabeled set show clear benefits to our approach. On the STL-10 dataset with only 40 labels, InterLUDE achieves 3.2% error rate, while the best previous method reports 14.9%.

Semi-Supervised Multimodal Multi-Instance Learning for Aortic Stenosis Diagnosis

Automated interpretation of ultrasound imaging of the heart (echocardiograms) could improve the detection and treatment of aortic stenosis (AS), a deadly heart disease. However, existing deep learning pipelines for assessing AS from echocardiograms have two key limitations. First, most methods rely on limited 2D cineloops, thereby ignoring widely available Doppler imaging that contains important complementary information about pressure gradients and blood flow abnormalities associated with AS. Second, obtaining labeled data is difficult. There are often far more unlabeled echocardiogram recordings available, but these remain underutilized by existing methods. To overcome these limitations, we introduce Semi-supervised Multimodal Multiple-Instance Learning (SMMIL), a new deep learning framework for automatic interpretation for structural heart diseases like AS. When deployed, SMMIL can combine information from two input modalities, spectral Dopplers and 2D cineloops, to produce a study-level AS diagnosis. During training, SMMIL can combine a smaller labeled set and an abundant unlabeled set of both modalities to improve its classifier. Experiments demonstrate that SMMIL outperforms recent alternatives at 3-level AS severity classification as well as several clinically relevant AS detection tasks.

Exploring the Influence of Information Entropy Change in Learning Systems

In this work, we explore the influence of entropy change in deep learning systems by adding noise to the inputs/latent features. The applications in this paper focus on deep learning tasks within computer vision, but the proposed theory can be further applied to other fields. Noise is conventionally viewed as a harmful perturbation in various deep learning architectures, such as convolutional neural networks (CNNs) and vision transformers (ViTs), as well as different learning tasks like image classification and transfer learning. However, this paper aims to rethink whether the conventional proposition always holds. We demonstrate that specific noise can boost the performance of various deep architectures under certain conditions. We theoretically prove the enhancement gained from positive noise by reducing the task complexity defined by information entropy and experimentally show the significant performance gain in large image datasets, such as the ImageNet. Herein, we use the information entropy to define the complexity of the task. We categorize the noise into two types, positive noise (PN) and harmful noise (HN), based on whether the noise can help reduce the complexity of the task. Extensive experiments of CNNs and ViTs have shown performance improvements by proactively injecting positive noise, where we achieved an unprecedented top 1 accuracy of over 95% on ImageNet. Both theoretical analysis and empirical evidence have confirmed that the presence of positive noise can benefit the learning process, while the traditionally perceived harmful noise indeed impairs deep learning models. The different roles of noise offer new explanations for deep models on specific tasks and provide a new paradigm for improving model performance. Moreover, it reminds us that we can influence the performance of learning systems via information entropy change.

Hierarchical Semantic Tree Concept Whitening for Interpretable Image Classification

With the popularity of deep neural networks (DNNs), model interpretability is becoming a critical concern. Many approaches have been developed to tackle the problem through post-hoc analysis, such as explaining how predictions are made or understanding the meaning of neurons in middle layers. Nevertheless, these methods can only discover the patterns or rules that naturally exist in models. In this work, rather than relying on post-hoc schemes, we proactively instill knowledge to alter the representation of human-understandable concepts in hidden layers. Specifically, we use a hierarchical tree of semantic concepts to store the knowledge, which is leveraged to regularize the representations of image data instances while training deep models. The axes of the latent space are aligned with the semantic concepts, where the hierarchical relations between concepts are also preserved. Experiments on real-world image datasets show that our method improves model interpretability, showing better disentanglement of semantic concepts, without negatively affecting model classification performance.

Segment Anything Model (SAM) for Radiation Oncology

In this study, we evaluate the performance of the Segment Anything Model (SAM) in clinical radiotherapy. Our results indicate that SAM's 'segment anything' mode can achieve clinically acceptable segmentation results in most organs-at-risk (OARs) with Dice scores higher than 0.7. SAM's 'box prompt' mode further improves the Dice scores by 0.1 to 0.5. Considering the size of the organ and the clarity of its boundary, SAM displays better performance for large organs with clear boundaries but performs worse for smaller organs with unclear boundaries. Given that SAM, a model pre-trained purely on natural images, can handle the delineation of OARs from medical images with clinically acceptable accuracy, these results highlight SAM's robust generalization capabilities with consistent accuracy in automatic segmentation for radiotherapy. In other words, SAM can achieve delineation of different OARs at different sites using a generic automatic segmentation model. SAM's generalization capabilities across different disease sites suggest that it is technically feasible to develop a generic model for automatic segmentation in radiotherapy.

Instruction-ViT: Multi-Modal Prompts for Instruction Learning in ViT

Prompts have been proven to play a crucial role in large language models, and in recent years, vision models have also been using prompts to improve scalability for multiple downstream tasks. In this paper, we focus on adapting prompt design based on instruction tuning into a visual transformer model for image classification which we called Instruction-ViT. The key idea is to implement multi-modal prompts (text or image prompt) related to category information to guide the fine-tuning of the model. Based on the experiments of several image captionining tasks, the performance and domain adaptability were improved. Our work provided an innovative strategy to fuse multi-modal prompts with better performance and faster adaptability for visual classification models.