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Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based…

Machine Learning · Computer Science 2025-08-12 Xuefeng Liu , Songhao Jiang , Chih-chan Tien , Jinbo Xu , Rick Stevens

Randomly masking and predicting word tokens has been a successful approach in pre-training language models for a variety of downstream tasks. In this work, we observe that the same idea also applies naturally to sequential decision-making,…

While music generation models have evolved to handle complex multimodal inputs mixing text, lyrics, and reference audio, evaluation mechanisms have lagged behind. In this paper, we bridge this critical gap by establishing a comprehensive…

Structural priming is a cognitive phenomenon where exposure to a particular syntactic structure increases the likelihood of producing the same structure in subsequent utterances. While humans consistently demonstrate structural priming…

Computation and Language · Computer Science 2025-10-20 Bushi Xiao , Michael Bennie , Jayetri Bardhan , Daisy Zhe Wang

Despite significant progress in diffusion-based image generation, subject-driven generation and instruction-based editing remain challenging. Existing methods typically treat them separately, struggling with limited high-quality data and…

Computer Vision and Pattern Recognition · Computer Science 2025-07-29 Xueyun Tian , Wei Li , Bingbing Xu , Yige Yuan , Yuanzhuo Wang , Huawei Shen

Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC,…

Machine Learning · Computer Science 2025-10-29 Minghao Yang , Pengteng Li , Yan Liang , Qianyi Cai , Zhihang Zheng , Shichen Zhang , Pengfei Zhang , Zhi-An Huang , Hui Xiong

Designing RNA molecules that interact with specific proteins is a critical challenge in experimental and computational biology. Existing computational approaches require a substantial amount of previously known interacting RNA sequences for…

Machine Learning · Computer Science 2026-04-17 Roman Klypa , Alberto Bietti , Sergei Grudinin

Multimodal entity linking (MEL) task, which aims at resolving ambiguous mentions to a multimodal knowledge graph, has attracted wide attention in recent years. Though large efforts have been made to explore the complementary effect among…

Artificial Intelligence · Computer Science 2023-07-20 Pengfei Luo , Tong Xu , Shiwei Wu , Chen Zhu , Linli Xu , Enhong Chen

Multimodal embedding models aim to yield informative unified representations that empower diverse cross-modal tasks. Despite promising developments in the evolution from CLIP-based dual-tower architectures to large vision-language models,…

In vision-language pre-training (VLP), masked image modeling (MIM) has recently been introduced for fine-grained cross-modal alignment. However, in most existing methods, the reconstruction targets for MIM lack high-level semantics, and…

Computer Vision and Pattern Recognition · Computer Science 2024-03-04 Haowei Liu , Yaya Shi , Haiyang Xu , Chunfeng Yuan , Qinghao Ye , Chenliang Li , Ming Yan , Ji Zhang , Fei Huang , Bing Li , Weiming Hu

Multimodal deep learning has shown strong potential in medical applications by integrating heterogeneous data sources such as medical images and structured clinical variables. However, most existing approaches implicitly assume complete…

Machine Learning · Computer Science 2026-05-13 Camillo Maria Caruso , Valerio Guarrasi , Paolo Soda

Self-supervised learning has proved effective for skeleton-based human action understanding. However, previous works either rely on contrastive learning that suffers false negative problems or are based on reconstruction that learns too…

Computer Vision and Pattern Recognition · Computer Science 2024-09-17 Lehong Wu , Lilang Lin , Jiahang Zhang , Yiyang Ma , Jiaying Liu

Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…

Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent…

Machine Learning · Computer Science 2024-09-16 Xiaohua Lu , Liangxu Xie , Lei Xu , Rongzhi Mao , Shan Chang , Xiaojun Xu

Unified multimodal models aim to jointly enable visual understanding and generation, yet current benchmarks rarely examine their true integration. Existing evaluations either treat the two abilities in isolation or overlook tasks that…

Computer Vision and Pattern Recognition · Computer Science 2026-04-21 Kai Zou , Ziqi Huang , Yuhao Dong , Shulin Tian , Dian Zheng , Hongbo Liu , Jingwen He , Bin Liu , Yu Qiao , Ziwei Liu

The clinical trial is a pivotal and costly process, often spanning multiple years and requiring substantial financial resources. Therefore, the development of clinical trial outcome prediction models aims to exclude drugs likely to fail and…

Machine Learning · Computer Science 2025-01-29 Wenhao Zheng , Liaoyaqi Wang , Dongshen Peng , Hongxia Xu , Yun Li , Hongtu Zhu , Tianfan Fu , Huaxiu Yao

Cognitive neuroscience is fragmented into specialized models, each tailored to specific experimental paradigms, hence preventing a unified model of cognition in the human brain. Here, we introduce TRIBE v2, a tri-modal (video, audio and…

Foundation models are transforming neuroscience but are often prohibitively large, data-hungry, and difficult to deploy. Here, we introduce BrainSymphony, a lightweight and parameter-efficient foundation model with plug-and-play integration…

Quantitative Methods · Quantitative Biology 2026-02-13 Moein Khajehnejad , Forough Habibollahi , Devon Stoliker , Adeel Razi

In this paper, we present Modality-Importance-Guided Reasoning (MIGR), a framework designed to improve the reliability of reasoning-based multimodal emotion understanding in multimodal large language models. Although existing methods have…

Artificial Intelligence · Computer Science 2025-12-03 Hyeongseop Rha , Jeong Hun Yeo , Junil Won , Se Jin Park , Yong Man Ro

Generative models have revolutionized Artificial Intelligence (AI), particularly in multimodal applications. However, adapting these models to the medical domain poses unique challenges due to the complexity of medical data and the…

Computer Vision and Pattern Recognition · Computer Science 2026-02-16 Daniele Molino , Francesco di Feola , Linlin Shen , Paolo Soda , Valerio Guarrasi