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Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…

Genomics · Quantitative Biology 2026-03-23 Carlos Albors , Jianan Canal Li , Gonzalo Benegas , Chengzhong Ye , Yun S. Song

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE),…

Neural and Evolutionary Computing · Computer Science 2024-07-18 Clint Morris , Michael Jurado , Jason Zutty

Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…

Large language models (LLMs) can already identify patterns and reason effectively, yet their variable accuracy hampers adoption in high-stakes decision-making applications. In this paper, we study this issue from a venture capital…

Artificial Intelligence · Computer Science 2025-10-28 Rick Chen , Joseph Ternasky , Aaron Ontoyin Yin , Xianling Mu , Fuat Alican , Yigit Ihlamur

In the wake of relentless digital transformation, data-driven solutions are emerging as powerful tools to address multifarious industrial tasks such as forecasting, anomaly detection, planning, and even complex decision-making. Although…

Artificial Intelligence · Computer Science 2023-10-18 Xu Yang , Xiao Yang , Weiqing Liu , Jinhui Li , Peng Yu , Zeqi Ye , Jiang Bian

The representation of feature space is a crucial environment where data points get vectorized and embedded for subsequent modeling. Thus the efficacy of machine learning (ML) algorithms is closely related to the quality of feature…

Machine Learning · Computer Science 2026-01-12 Xinhao Zhang , Jinghan Zhang , Banafsheh Rekabdar , Yuanchun Zhou , Pengfei Wang , Kunpeng Liu

Designing controllers for complex industrial electronic systems is challenging due to nonlinearities and parameter uncertainties, and traditional methods are often slow and costly. To address this, we propose a novel autonomous design…

Systems and Control · Electrical Eng. & Systems 2025-07-23 Chenggang Cui , Jiaming Liu , Peifeng Hui , Pengfeng Lin , Chuanlin Zhang

Foundational models (FMs), pretrained on extensive datasets using self-supervised techniques, are capable of learning generalized patterns from large amounts of data. This reduces the need for extensive labeled datasets for each new task,…

Machine Learning · Computer Science 2024-06-19 Quan M. Tran , Suong N. Hoang , Lam M. Nguyen , Dzung Phan , Hoang Thanh Lam

Recent Vision-based Large Language Models~(VisionLLMs) for autonomous driving have seen rapid advancements. However, such promotion is extremely dependent on large-scale high-quality annotated data, which is costly and labor-intensive. To…

Computer Vision and Pattern Recognition · Computer Science 2025-03-18 Chaoqun Wang , Jie Yang , Xiaobin Hong , Ruimao Zhang

Accurately diagnosing bearing faults is crucial for maintaining the efficient operation of rotating machinery. However, traditional diagnosis methods face challenges due to the diversification of application environments, including…

Signal Processing · Electrical Eng. & Systems 2024-11-06 Laifa Tao , Haifei Liu , Guoao Ning , Wenyan Cao , Bohao Huang , Chen Lu

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a…

Computation and Language · Computer Science 2025-10-21 Ming Hu , Chenglong Ma , Wei Li , Wanghan Xu , Jiamin Wu , Jucheng Hu , Tianbin Li , Guohang Zhuang , Jiaqi Liu , Yingzhou Lu , Ying Chen , Chaoyang Zhang , Cheng Tan , Jie Ying , Guocheng Wu , Shujian Gao , Pengcheng Chen , Jiashi Lin , Haitao Wu , Lulu Chen , Fengxiang Wang , Yuanyuan Zhang , Xiangyu Zhao , Feilong Tang , Encheng Su , Junzhi Ning , Xinyao Liu , Ye Du , Changkai Ji , Pengfei Jiang , Cheng Tang , Ziyan Huang , Jiyao Liu , Jiaqi Wei , Yuejin Yang , Xiang Zhang , Guangshuai Wang , Yue Yang , Huihui Xu , Ziyang Chen , Yizhou Wang , Chen Tang , Jianyu Wu , Yuchen Ren , Siyuan Yan , Zhonghua Wang , Zhongxing Xu , Shiyan Su , Shangquan Sun , Runkai Zhao , Zhisheng Zhang , Dingkang Yang , Jinjie Wei , Jiaqi Wang , Jiahao Xu , Jiangtao Yan , Wenhao Tang , Hongze Zhu , Yu Liu , Fudi Wang , Yiqing Shen , Yuanfeng Ji , Yanzhou Su , Tong Xie , Hongming Shan , Chun-Mei Feng , Zhi Hou , Diping Song , Lihao Liu , Yanyan Huang , Lequan Yu , Bin Fu , Shujun Wang , Xiaomeng Li , Xiaowei Hu , Yun Gu , Ben Fei , Benyou Wang , Yuewen Cao , Minjie Shen , Jie Xu , Haodong Duan , Fang Yan , Hongxia Hao , Jielan Li , Jiajun Du , Yanbo Wang , Imran Razzak , Zhongying Deng , Chi Zhang , Lijun Wu , Conghui He , Zhaohui Lu , Jinhai Huang , Wenqi Shao , Yihao Liu , Siqi Luo , Yi Xin , Xiaohong Liu , Fenghua Ling , Yuqiang Li , Aoran Wang , Siqi Sun , Qihao Zheng , Nanqing Dong , Tianfan Fu , Dongzhan Zhou , Yan Lu , Wenlong Zhang , Jin Ye , Jianfei Cai , Yirong Chen , Wanli Ouyang , Yu Qiao , Zongyuan Ge , Shixiang Tang , Junjun He , Chunfeng Song , Lei Bai , Bowen Zhou

The advent of Large Language Models (LLMs) has opened new frontiers in automated algorithm design, giving rise to numerous powerful methods. However, these approaches retain critical limitations: they require extensive evaluation of the…

Neural and Evolutionary Computing · Computer Science 2026-02-05 Haoran Yin , Shuaiqun Pan , Zhao Wei , Jian Cheng Wong , Yew-Soon Ong , Anna V. Kononova , Thomas Bäck , Niki van Stein

In recent years, data science agents powered by Large Language Models (LLMs), known as "data agents," have shown significant potential to transform the traditional data analysis paradigm. This survey provides an overview of the evolution,…

Artificial Intelligence · Computer Science 2025-12-01 Maojun Sun , Ruijian Han , Binyan Jiang , Houduo Qi , Defeng Sun , Yancheng Yuan , Jian Huang

Although Large Language Models (LLMs) exhibit remarkable adaptability across domains, these models often fall short in structured knowledge extraction tasks such as named entity recognition (NER). This paper explores an innovative,…

Computation and Language · Computer Science 2024-06-11 Yuzhao Heng , Chunyuan Deng , Yitong Li , Yue Yu , Yinghao Li , Rongzhi Zhang , Chao Zhang

In today's visually dominated social media landscape, predicting the perceived credibility of visual content and understanding what drives human judgment are crucial for countering misinformation. However, these tasks are challenging due to…

Computer Vision and Pattern Recognition · Computer Science 2025-04-16 Yilang Peng , Sijia Qian , Yingdan Lu , Cuihua Shen

Large language models (LLMs) have greatly accelerated the automation of algorithm generation and optimization. However, current methods such as EoH and FunSearch mainly rely on predefined templates and expert-specified functions that focus…

Software Engineering · Computer Science 2025-03-17 Zhe Zhao , Haibin Wen , Pengkun Wang , Ye Wei , Zaixi Zhang , Xi Lin , Fei Liu , Bo An , Hui Xiong , Yang Wang , Qingfu Zhang

The automatic development of phenotype algorithms from Electronic Health Record data with machine learning (ML) techniques is of great interest given the current practice is very time-consuming and resource intensive. The extraction of…

Current multimodal survival prediction methods typically rely on pathology images (WSIs) and genomic data, both of which are high-dimensional and redundant, making it difficult to extract discriminative features from them and align…

Computer Vision and Pattern Recognition · Computer Science 2025-12-17 Chenyu Zhao , Yingxue Xu , Fengtao Zhou , Yihui Wang , Hao Chen

Although traditional statistical techniques and machine learning methods have contributed significantly to genetics and, in particular, inherited disease diagnosis, they often struggle with complex, high-dimensional data, a challenge now…

Machine Learning · Computer Science 2025-08-29 Anton Changalidis , Yury Barbitoff , Yulia Nasykhova , Andrey Glotov

The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…

Computation and Language · Computer Science 2024-10-21 Magdalena Wysocka , Oskar Wysocki , Maxime Delmas , Vincent Mutel , Andre Freitas