Pengfei Liu

Yimin Yin, Renye Zhang, Pengfei Liu et al.

Finger vein recognition is an emerging biometric recognition technology. Different from the other biometric features on the body surface, the venous vascular tissue of the fingers is buried deep inside the skin. Due to this advantage, finger vein recognition is highly stable and private. They are almost impossible to be stolen and difficult to interfere with by external conditions. Unlike the finger vein recognition methods based on traditional machine learning, the artificial neural network technique, especially deep learning, it without relying on feature engineering and have superior performance. To summarize the development of finger vein recognition based on artificial neural networks, this paper collects 149 related papers. First, we introduce the background of finger vein recognition and the motivation of this survey. Then, the development history of artificial neural networks and the representative networks on finger vein recognition tasks are introduced. The public datasets that are widely used in finger vein recognition are then described. After that, we summarize the related finger vein recognition tasks based on classical neural networks and deep neural networks, respectively. Finally, the challenges and potential development directions in finger vein recognition are discussed. To our best knowledge, this paper is the first comprehensive survey focusing on finger vein recognition based on artificial neural networks.

Yiqing Xie, Alex Xie, Divyanshu Sheth et al.

To adequately test modern code generation systems, evaluation benchmarks must execute and test the code generated by the system. However, these execution and testing requirements have largely limited benchmarks to settings where code is easily executable or has human-written tests. To facilitate evaluation of code generation systems across diverse scenarios, we present CodeBenchGen, a framework to create scalable execution-based benchmarks from naturally occurring code sources. Specifically, we leverage a large language model (LLM) to sandbox arbitrary pieces of code into evaluation examples, including test cases for execution-based evaluation. We illustrate the usefulness of our framework by creating a dataset, Exec-CSN, which includes 1,931 examples involving 293 libraries converted from code in 367 GitHub repositories taken from the Code- SearchNet dataset. To demonstrate the solvability of examples in Exec-CSN, we present a human study demonstrating that 81.3% of the examples can be solved by humans and 61% are rated as "requires effort to solve". We conduct code generation experiments on open-source and proprietary models and analyze the performance of both humans and models. We provide code and data at: https://github.com/yiqingxyq/CodeBenchGen.

Matthew Neeley, Guantong Qi, Guanchu Wang et al.

Rare diseases are challenging to diagnose due to limited patient data and genetic diversity. Despite advances in variant prioritization, many cases remain undiagnosed. While large language models (LLMs) have performed well in medical exams, their effectiveness in diagnosing rare genetic diseases has not been assessed. To identify causal genes, we benchmarked various LLMs for gene prioritization. Using multi-agent and Human Phenotype Ontology (HPO) classification, we categorized patients based on phenotypes and solvability levels. As gene set size increased, LLM performance deteriorated, so we used a divide-and-conquer strategy to break the task into smaller subsets. At baseline, GPT-4 outperformed other LLMs, achieving near 30% accuracy in ranking causal genes correctly. The multi-agent and HPO approaches helped distinguish confidently solved cases from challenging ones, highlighting the importance of known gene-phenotype associations and phenotype specificity. We found that cases with specific phenotypes or clear associations were more accurately solved. However, we observed biases toward well-studied genes and input order sensitivity, which hindered gene prioritization. Our divide-and-conquer strategy improved accuracy by overcoming these biases. By utilizing HPO classification, novel multi-agent techniques, and our LLM strategy, we improved causal gene identification accuracy compared to our baseline evaluation. This approach streamlines rare disease diagnosis, facilitates reanalysis of unsolved cases, and accelerates gene discovery, supporting the development of targeted diagnostics and therapies.

Thomas Y. Hou, Pengfei Liu

This paper addresses a multi-scale finite element method for second order linear elliptic equations with arbitrarily rough coefficient. We propose a local oversampling method to construct basis functions that have optimal local approximation property. Our methodology is based on the compactness of the solution operator restricted on local regions of the spatial domain, and does not depend on any scale-separation or periodicity assumption of the coefficient. We focus on a special type of basis functions that are harmonic on each element and have optimal approximation property. We first reduce our problem to approximating the trace of the solution space on each edge of the underlying mesh, and then achieve this goal through the singular value decomposition of an oversampling operator. Rigorous error estimates can be obtained through thresholding in constructing the basis functions. Numerical results for several problems with multiple spatial scales and high contrast inclusions are presented to demonstrate the compactness of the local solution space and the capacity of our method in identifying and exploiting this compact structure to achieve computational savings.