Fine-tuning and adaptation

LoRA, PEFT, instruction tuning and domain adaptation — adapting a pretrained model without paying to train one.

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arXiv Machine Learning
Jun 5

An accurate nucleic acid-small molecule docking framework via geometric deep learning with large-scale pretraining

arXiv:2606. 05198v1 Announce Type: cross Abstract: Nucleic acids are increasingly recognized as therapeutic targets beyond conventional protein-centered drug discovery, yet accurate and efficient docking of small molecules to nucleic acid structures remains challenging.

By Shi Li (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Xujun Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Mingquan Liu (Faculty of Health Sciences, University of Macau, Macau SAR, China), Hui Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Shuoying Jia (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Yu Kang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Tingjun Hou (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China), Peichen Pan (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China)
arXiv Machine Learning
Jun 5

Surrogate Neural Architecture Codesign Package (SNAC-Pack)

arXiv:2605. 16138v2 Announce Type: replace Abstract: Neural architecture search (NAS) is a powerful approach for automating model design, but existing methods often optimize for accuracy alone or rely on proxy metrics such as bit operations (BOPs) that correlate poorly with hardware cost.

By Jason Weitz, Dmitri Demler, Benjamin Hawks, Aaron Wang, Nhan Tran, Javier Duarte
arXiv Machine Learning
Jun 5

Binary Gaussian Copula Synthesis: an LLM-powered data augmentation framework for early dialysis prediction in chronic kidney disease

arXiv:2403. 00965v2 Announce Type: replace-cross Abstract: Only a small fraction of patients with chronic kidney disease (CKD) progress to dialysis, creating severe class imbalance that limits the performance of machine learning models for early dialysis prediction.

By Hamed Khosravi, Milad Khanchi, Mobina Noori, Srinjoy Das, Abdullah Al-Mamun, Imtiaz Ahmed
arXiv Machine Learning
Jun 5

PI-JEPA: Label-Free Surrogate Pretraining for Coupled Multiphysics Simulation via Operator-Split Latent Prediction

arXiv:2604. 01349v4 Announce Type: replace Abstract: Reservoir simulation workflows face a fundamental data asymmetry: input parameter fields (geostatistical permeability realizations, porosity distributions) are free to generate in arbitrary quantities, yet existing neural operator surrogates require large corpora of expensive labeled simulation trajectories and cannot exploit this unlabeled structure.

By Brandon Yee, Pairie Koh
arXiv Machine Learning
Jun 5

MolE-RAG: Molecular Structure-Enhanced Retrieval-Augmented Generation for Chemistry

arXiv:2606. 05693v1 Announce Type: new Abstract: Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained.

By Joey Chan, Wonbin Kweon, Ashley Shin, Niharika Bhattacharjee, Pengcheng Jiang, Yue Guo, Jiawei Han
arXiv Machine Learning
Jun 5

Is Diversity All You Need for Scalable Robotic Manipulation?

arXiv:2507. 06219v2 Announce Type: replace-cross Abstract: Data scaling has driven remarkable success in foundation models for Natural Language Processing (NLP) and Computer Vision (CV), yet the principles of effective data scaling in robotic manipulation remain insufficiently understood.

By Modi Shi, Li Chen, Jin Chen, Yuxiang Lu, Chiming Liu, Guanghui Ren, Ping Luo, Di Huang, Maoqing Yao, Hongyang Li
arXiv Machine Learning
Jun 5

Masks Can Be Distracting: On Context Comprehension in Diffusion Language Models

arXiv:2511. 21338v2 Announce Type: replace Abstract: Masked Diffusion Language Models (MDLMs) have recently emerged as a promising alternative to Autoregressive Language Models (ARLMs), leveraging a denoising objective that, in principle, should enable more uniform context utilisation.

By Julianna Piskorz, Cristina Pinneri, Alvaro Correia, Motasem Alfarra, Risheek Garrepalli, Christos Louizos
arXiv Machine Learning
Jun 5

In-Training Defenses against Emergent Misalignment in Language Models

arXiv:2508. 06249v3 Announce Type: replace Abstract: Fine-tuning lets practitioners repurpose aligned large language models (LLMs) for new domains, yet recent work reveals emergent misalignment (EM): Even a small, domain-specific fine-tune can induce harmful behaviors far outside the target domain.

By David Kacz\'er, Magnus J{\o}rgenv{\aa}g, Clemens Vetter, Esha Afzal, Robin Haselhorst, Lucie Flek, Florian Mai
arXiv Machine Learning
Jun 5

Dominant-Layer ZO: A Single Layer Dominates Zeroth-Order Fine-Tuning of LLMs

arXiv:2606. 05516v1 Announce Type: new Abstract: Zeroth-order (ZO) optimization enables memory-efficient fine-tuning of large language models (LLMs) using only forward passes, but it remains unclear how useful adaptation is distributed across layers.

By Wanhao Yu, Ziyan Wang, Zheng Wang, Abeer Matar Almalky, Yihang Zuo, Shuteng Niu, Sen Lin, Adnan Siraj Rakin, Deliang Fan, Li Yang
arXiv Machine Learning
Jun 5

State commitment learning: training language models to distinguish computation from memory

arXiv:2606. 05201v1 Announce Type: new Abstract: Reasoning language models do not distinguish tokens used for computation from tokens that constitute persistent state: once generated, all hidden thoughts remain in context and influence future predictions.

By Fei Ding, Yongkang Zhang, Runhao Liu, Yuhao Liao, Zijian Zeng, Huiming Yang