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Protein representation learning is critical in various tasks in biology, such as drug design and protein structure or function prediction, which has primarily benefited from protein language models and graph neural networks. These models…

Biomolecules · Quantitative Biology 2024-02-16 Bozhen Hu , Zelin Zang , Cheng Tan , Stan Z. Li

Contrastive learning models have demonstrated impressive abilities to capture semantic similarities by aligning representations in the embedding space. However, their performance can be limited by the quality of the training data and its…

Computer Vision and Pattern Recognition · Computer Science 2025-03-27 Amirabbas Afzali , Borna Khodabandeh , Ali Rasekh , Mahyar JafariNodeh , Sepehr kazemi , Simon Gottschalk

Direct Preference Optimization (DPO) has shown promising results in aligning generative outputs with human preferences by distinguishing between chosen and rejected samples. However, a critical limitation of DPO is likelihood displacement,…

Computer Vision and Pattern Recognition · Computer Science 2025-11-25 Ruojun Xu , Yu Kai , Xuhua Ren , Jiaxiang Cheng , Bing Ma , Tianxiang Zheng , Qinhlin Lu

Fairness in Continual Learning for Large Multimodal Models (LMMs) is an emerging yet underexplored challenge, particularly in the presence of imbalanced data distributions that can lead to biased model updates and suboptimal performance…

Machine Learning · Computer Science 2026-03-31 Thanh-Dat Truong , Huu-Thien Tran , Jackson Cothren , Bhiksha Raj , Khoa Luu

Direct Preference Optimization (DPO) is broadly utilized for aligning Large Language Models (LLMs) with human values because of its flexibility. Despite its effectiveness, it has been observed that the capability of DPO to generate…

Machine Learning · Computer Science 2025-05-20 Wenqiao Zhu , Ji Liu , Lulu Wang , Jun Wu , Yulun Zhang

Direct Preference Optimization (DPO) has emerged as a prominent algorithm for the direct and robust alignment of Large Language Models (LLMs) with human preferences, offering a more straightforward alternative to the complex Reinforcement…

Computation and Language · Computer Science 2024-12-10 Junru Lu , Jiazheng Li , Siyu An , Meng Zhao , Yulan He , Di Yin , Xing Sun

Large language models (LLMs) are fine-tuned using human comparison data with Reinforcement Learning from Human Feedback (RLHF) methods to make them better aligned with users' preferences. In contrast to LLMs, human preference learning has…

Computer Vision and Pattern Recognition · Computer Science 2023-11-23 Bram Wallace , Meihua Dang , Rafael Rafailov , Linqi Zhou , Aaron Lou , Senthil Purushwalkam , Stefano Ermon , Caiming Xiong , Shafiq Joty , Nikhil Naik

Fine-tuning pre-trained Large Language Models (LLMs) is essential to align them with human values and intentions. This process often utilizes methods like pairwise comparisons and KL divergence against a reference LLM, focusing on the…

Computation and Language · Computer Science 2024-09-02 Yongcheng Zeng , Guoqing Liu , Weiyu Ma , Ning Yang , Haifeng Zhang , Jun Wang

Direct Preference Optimization (DPO), which derives reward signals directly from pairwise preference data, has shown its effectiveness on aligning Large Language Models (LLMs) with human preferences. Despite its widespread use across…

Computation and Language · Computer Science 2024-04-09 Duanyu Feng , Bowen Qin , Chen Huang , Zheng Zhang , Wenqiang Lei

Generating accurate glyphs for visual text rendering is essential yet challenging. Existing methods typically enhance text rendering by training on a large amount of high-quality scene text images, but the limited coverage of glyph…

Computer Vision and Pattern Recognition · Computer Science 2026-03-17 Xincheng Shuai , Ziye Li , Henghui Ding , Dacheng Tao

Direct Preference Optimization (DPO) is a method for enhancing model performance by directly optimizing for the preferences or rankings of outcomes, instead of traditional loss functions. This approach has proven effective in aligning Large…

Machine Learning · Computer Science 2024-09-18 Ruoyu Wang , Jiachen Sun , Shaowei Hua , Quan Fang

Large Language Models (LLMs) have become increasingly popular due to their ability to process and generate natural language. However, as they are trained on massive datasets of text, LLMs can inherit harmful biases and produce outputs that…

Computation and Language · Computer Science 2025-01-23 Qi Gou , Cam-Tu Nguyen

We study an LLM fine-tuning task for designing reward functions for sequential resource allocation problems in public health, guided by human preferences expressed in natural language. This setting presents a challenging testbed for…

Machine Learning · Computer Science 2025-11-19 Cheol Woo Kim , Shresth Verma , Mauricio Tec , Milind Tambe

Structure-based drug design (SBDD) aims to efficiently discover high-affinity ligands within vast chemical spaces. However, current generative models struggle with objective misalignment and rigid sampling budgets. We present MolFORM, a…

Computational Engineering, Finance, and Science · Computer Science 2026-02-26 Daiheng Zhang , Zhao Zhang

Aligning large language models with human preferences is crucial for their safe deployment. While Direct Preference Optimization (DPO) offers an efficient alternative to reinforcement learning from human feedback, traditional DPO methods…

Artificial Intelligence · Computer Science 2025-07-30 Mengyang Li , Zhong Zhang

Direct Preference Optimization (DPO) has emerged as an important approach for learning from human preferences in aligning large language models (LLMs). However, collecting human preference data is costly and inefficient, motivating methods…

Computation and Language · Computer Science 2025-12-01 Jiacheng Guo , Zihao Li , Jiahao Qiu , Yue Wu , Mengdi Wang

Despite considerable progress, ab initio protein structure prediction remains suboptimal. A crowdsourcing approach is the online puzzle video game Foldit, that provided several useful results that matched or even outperformed…

Biomolecules · Quantitative Biology 2020-11-09 Dimitra N. Panou , Martin Reczko

Direct Preference Optimization (DPO) has emerged as an effective approach for aligning large language models (LLMs) with human preferences. However, its performance is highly dependent on the quality of the underlying human preference data.…

Machine Learning · Computer Science 2026-03-10 Zixuan Huang , Yikun Ban , Lean Fu , Xiaojie Li , Zhongxiang Dai , Jianxin Li , Deqing Wang

Post-training alignment of diffusion models relies on simplified signals, such as scalar rewards or binary preferences. This limits alignment with complex human expertise, which is hierarchical and fine-grained. To address this, we first…

Computer Vision and Pattern Recognition · Computer Science 2026-01-09 Chenye Meng , Zejian Li , Zhongni Liu , Yize Li , Changle Xie , Kaixin Jia , Ling Yang , Huanghuang Deng , Shiying Ding , Shengyuan Zhang , Jiayi Li , Lingyun Sun

Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…

Biomolecules · Quantitative Biology 2024-09-17 Boqiao Lai