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.

PertEval: Unveiling Real Knowledge Capacity of LLMs with Knowledge-Invariant Perturbations

Expert-designed close-ended benchmarks serve as vital tools in assessing the knowledge capacity of large language models (LLMs). Despite their widespread use, concerns have mounted regarding their reliability due to limited test scenarios and an unavoidable risk of data contamination. To rectify this, we present PertEval, a toolkit devised for in-depth probing of LLMs' knowledge capacity through knowledge-invariant perturbations. These perturbations employ human-like restatement techniques to generate on-the-fly test samples from static benchmarks, meticulously retaining knowledge-critical content while altering irrelevant details. Our toolkit further includes a suite of transition analyses that compare performance on raw vs. perturbed test sets to precisely assess LLMs' genuine knowledge capacity. Six state-of-the-art LLMs are re-evaluated using PertEval. Results reveal significantly inflated performance of the LLMs on raw benchmarks, including an absolute 21% overestimation for GPT-4. Additionally, through a nuanced response pattern analysis, we discover that PertEval retains LLMs' uncertainty to specious knowledge, potentially being resolved through rote memorization and leading to inflated performance. We also find that the detailed transition analyses by PertEval could illuminate weaknesses in existing LLMs' knowledge mastery and guide the development of refinement. Given these insights, we posit that PertEval can act as an essential tool that, when applied alongside any close-ended benchmark, unveils the true knowledge capacity of LLMs, marking a significant step toward more trustworthy LLM evaluation.

MRISegmentator-Abdomen: A Fully Automated Multi-Organ and Structure Segmentation Tool for T1-weighted Abdominal MRI

Background: Segmentation of organs and structures in abdominal MRI is useful for many clinical applications, such as disease diagnosis and radiotherapy. Current approaches have focused on delineating a limited set of abdominal structures (13 types). To date, there is no publicly available abdominal MRI dataset with voxel-level annotations of multiple organs and structures. Consequently, a segmentation tool for multi-structure segmentation is also unavailable. Methods: We curated a T1-weighted abdominal MRI dataset consisting of 195 patients who underwent imaging at National Institutes of Health (NIH) Clinical Center. The dataset comprises of axial pre-contrast T1, arterial, venous, and delayed phases for each patient, thereby amounting to a total of 780 series (69,248 2D slices). Each series contains voxel-level annotations of 62 abdominal organs and structures. A 3D nnUNet model, dubbed as MRISegmentator-Abdomen (MRISegmentator in short), was trained on this dataset, and evaluation was conducted on an internal test set and two large external datasets: AMOS22 and Duke Liver. The predicted segmentations were compared against the ground-truth using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD). Findings: MRISegmentator achieved an average DSC of 0.861$\pm$0.170 and a NSD of 0.924$\pm$0.163 in the internal test set. On the AMOS22 dataset, MRISegmentator attained an average DSC of 0.829$\pm$0.133 and a NSD of 0.908$\pm$0.067. For the Duke Liver dataset, an average DSC of 0.933$\pm$0.015 and a NSD of 0.929$\pm$0.021 was obtained. Interpretation: The proposed MRISegmentator provides automatic, accurate, and robust segmentations of 62 organs and structures in T1-weighted abdominal MRI sequences. The tool has the potential to accelerate research on various clinical topics, such as abnormality detection, radiotherapy, disease classification among others.

Survey of Computerized Adaptive Testing: A Machine Learning Perspective

Computerized Adaptive Testing (CAT) provides an efficient and tailored method for assessing the proficiency of examinees, by dynamically adjusting test questions based on their performance. Widely adopted across diverse fields like education, healthcare, sports, and sociology, CAT has revolutionized testing practices. While traditional methods rely on psychometrics and statistics, the increasing complexity of large-scale testing has spurred the integration of machine learning techniques. This paper aims to provide a machine learning-focused survey on CAT, presenting a fresh perspective on this adaptive testing method. By examining the test question selection algorithm at the heart of CAT's adaptivity, we shed light on its functionality. Furthermore, we delve into cognitive diagnosis models, question bank construction, and test control within CAT, exploring how machine learning can optimize these components. Through an analysis of current methods, strengths, limitations, and challenges, we strive to develop robust, fair, and efficient CAT systems. By bridging psychometric-driven CAT research with machine learning, this survey advocates for a more inclusive and interdisciplinary approach to the future of adaptive testing.

Linear optimal transport subspaces for point set classification

Learning from point sets is an essential component in many computer vision and machine learning applications. Native, unordered, and permutation invariant set structure space is challenging to model, particularly for point set classification under spatial deformations. Here we propose a framework for classifying point sets experiencing certain types of spatial deformations, with a particular emphasis on datasets featuring affine deformations. Our approach employs the Linear Optimal Transport (LOT) transform to obtain a linear embedding of set-structured data. Utilizing the mathematical properties of the LOT transform, we demonstrate its capacity to accommodate variations in point sets by constructing a convex data space, effectively simplifying point set classification problems. Our method, which employs a nearest-subspace algorithm in the LOT space, demonstrates label efficiency, non-iterative behavior, and requires no hyper-parameter tuning. It achieves competitive accuracies compared to state-of-the-art methods across various point set classification tasks. Furthermore, our approach exhibits robustness in out-of-distribution scenarios where training and test distributions vary in terms of deformation magnitudes.

Semantic Image Synthesis for Abdominal CT

As a new emerging and promising type of generative models, diffusion models have proven to outperform Generative Adversarial Networks (GANs) in multiple tasks, including image synthesis. In this work, we explore semantic image synthesis for abdominal CT using conditional diffusion models, which can be used for downstream applications such as data augmentation. We systematically evaluated the performance of three diffusion models, as well as to other state-of-the-art GAN-based approaches, and studied the different conditioning scenarios for the semantic mask. Experimental results demonstrated that diffusion models were able to synthesize abdominal CT images with better quality. Additionally, encoding the mask and the input separately is more effective than na\"ive concatenating.

ECLM: Efficient Edge-Cloud Collaborative Learning with Continuous Environment Adaptation

Pervasive mobile AI applications primarily employ one of the two learning paradigms: cloud-based learning (with powerful large models) or on-device learning (with lightweight small models). Despite their own advantages, neither paradigm can effectively handle dynamic edge environments with frequent data distribution shifts and on-device resource fluctuations, inevitably suffering from performance degradation. In this paper, we propose ECLM, an edge-cloud collaborative learning framework for rapid model adaptation for dynamic edge environments. We first propose a novel block-level model decomposition design to decompose the original large cloud model into multiple combinable modules. By flexibly combining a subset of the modules, this design enables the derivation of compact, task-specific sub-models for heterogeneous edge devices from the large cloud model, and the seamless integration of new knowledge learned on these devices into the cloud model periodically. As such, ECLM ensures that the cloud model always provides up-to-date sub-models for edge devices. We further propose an end-to-end learning framework that incorporates the modular model design into an efficient model adaptation pipeline including an offline on-cloud model prototyping and training stage, and an online edge-cloud collaborative adaptation stage. Extensive experiments over various datasets demonstrate that ECLM significantly improves model performance (e.g., 18.89% accuracy increase) and resource efficiency (e.g., 7.12x communication cost reduction) in adapting models to dynamic edge environments by efficiently collaborating the edge and the cloud models.

Efficiently Measuring the Cognitive Ability of LLMs: An Adaptive Testing Perspective

Large language models (LLMs), like ChatGPT, have shown some human-like cognitive abilities. For comparing these abilities of different models, several benchmarks (i.e. sets of standard test questions) from different fields (e.g., Literature, Biology and Psychology) are often adopted and the test results under traditional metrics such as accuracy, recall and F1, are reported. However, such way for evaluating LLMs can be inefficient and inaccurate from the cognitive science perspective. Inspired by Computerized Adaptive Testing (CAT) used in psychometrics, we propose an adaptive testing framework for LLM evaluation. Rather than using a standard test set and simply reporting accuracy, this approach dynamically adjusts the characteristics of the test questions, such as difficulty, based on the model's performance. This allows for a more accurate estimation of the model's abilities, using fewer questions. More importantly, it allows LLMs to be compared with humans easily, which is essential for NLP models that aim for human-level ability. Our diagnostic reports have found that ChatGPT often behaves like a ``careless student'', prone to slip and occasionally guessing the questions. We conduct a fine-grained diagnosis and rank the latest 6 instruction-tuned LLMs from three aspects of Subject Knowledge, Mathematical Reasoning, and Programming, where GPT4 can outperform other models significantly and reach the cognitive ability of middle-level students. Different tests for different models using efficient adaptive testing -- we believe this has the potential to become a new norm in evaluating large language models.