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Transformer models have become state-of-the-art in decoding stimuli and behavior from neural activity, significantly advancing neuroscience research. Yet greater transparency in their decision-making processes would substantially enhance…

Quantitative Methods · Quantitative Biology 2025-06-18 Laurence Freeman , Philip Shamash , Vinam Arora , Caswell Barry , Tiago Branco , Eva Dyer

Sparse Autoencoders (SAEs) have recently emerged as powerful tools for interpreting and steering the internal representations of large language models (LLMs). However, conventional approaches to analyzing SAEs typically rely solely on…

Machine Learning · Computer Science 2025-09-24 Dong Shu , Xuansheng Wu , Haiyan Zhao , Mengnan Du , Ninghao Liu

Latent steering exploits internal representations of Large Language Models (LLMs) to guide generation, yet interventions on dense states can entangle distinct semantic features. In this paper, we investigate attention query activations as a…

Machine Learning · Computer Science 2026-05-25 Sumanta Bhattacharyya , Pedram Rooshenas

While sparse autoencoders (SAEs) have generated significant excitement, a series of negative results have added to skepticism about their usefulness. Here, we establish a conceptual distinction that reconciles competing narratives…

Machine Learning · Computer Science 2025-07-01 Kenny Peng , Rajiv Movva , Jon Kleinberg , Emma Pierson , Nikhil Garg

Mechanistic interpretability of large language models (LLMs) aims to uncover the internal processes of information propagation and reasoning. Sparse autoencoders (SAEs) have demonstrated promise in this domain by extracting interpretable…

Machine Learning · Computer Science 2025-05-26 Wei Shi , Sihang Li , Tao Liang , Mingyang Wan , Guojun Ma , Xiang Wang , Xiangnan He

RFdiffusion is a popular and well-established model for generation of protein structures. However, this generative process offers limited insight into its internal representations and how they contribute to the final protein structure.…

Quantitative Methods · Quantitative Biology 2025-12-01 Wojciech Zarzecki , Paulina Szymczak , Ewa Szczurek , Kamil Deja

A key challenge in interpretability is to decompose model activations into meaningful features. Sparse autoencoders (SAEs) have emerged as a promising tool for this task. However, a central problem in evaluating the quality of SAEs is the…

Machine Learning · Computer Science 2024-10-11 Constantin Venhoff , Anisoara Calinescu , Philip Torr , Christian Schroeder de Witt

Sparse Autoencoders (SAEs) are a prominent tool in mechanistic interpretability (MI) for decomposing neural network activations into interpretable features. However, the aspiration to identify a canonical set of features is challenged by…

Machine Learning · Computer Science 2025-05-27 Xiangchen Song , Aashiq Muhamed , Yujia Zheng , Lingjing Kong , Zeyu Tang , Mona T. Diab , Virginia Smith , Kun Zhang

Standard Sparse Autoencoders (SAEs) excel at discovering a dictionary of a model's learned features, offering a powerful observational lens. However, the ambiguous and ungrounded nature of these features makes them unreliable instruments…

Machine Learning · Computer Science 2025-09-29 Jianrong Ding , Muxi Chen , Chenchen Zhao , Qiang Xu

Disentangling model activations into meaningful features is a central problem in interpretability. However, the absence of ground-truth for these features in realistic scenarios makes validating recent approaches, such as sparse dictionary…

Machine Learning · Computer Science 2024-05-21 Aleksandar Makelov , George Lange , Neel Nanda

Sparse autoencoders (SAEs) are widely used to extract interpretable features from neural network representations, often under the implicit assumption that concepts correspond to independent linear directions. However, a growing body of…

Sparse autoencoders (SAEs) are useful for detecting and steering interpretable features in neural networks, with particular potential for understanding complex multimodal representations. Given their ability to uncover interpretable…

Computer Vision and Pattern Recognition · Computer Science 2025-05-29 Vladimir Zaigrajew , Hubert Baniecki , Przemyslaw Biecek

Sparse Autoencoder (SAE) has emerged as a powerful tool for mechanistic interpretability of large language models. Recent works apply SAE to protein language models (PLMs), aiming to extract and analyze biologically meaningful features from…

Quantitative Methods · Quantitative Biology 2026-01-21 Xiangyu Liu , Haodi Lei , Yi Liu , Yang Liu , Wei Hu

Radiological services are experiencing unprecedented demand, leading to increased interest in automating radiology report generation. Existing Vision-Language Models (VLMs) suffer from hallucinations, lack interpretability, and require…

Computer Vision and Pattern Recognition · Computer Science 2024-10-07 Ahmed Abdulaal , Hugo Fry , Nina Montaña-Brown , Ayodeji Ijishakin , Jack Gao , Stephanie Hyland , Daniel C. Alexander , Daniel C. Castro

Sparse autoencoders (SAEs) decompose large language model (LLM) activations into latent features that reveal mechanistic structure. Conventional SAEs train on broad data distributions, forcing a fixed latent budget to capture only…

Machine Learning · Computer Science 2025-08-14 Charles O'Neill , Mudith Jayasekara , Max Kirkby

While large language models provide strong compositional reasoning, existing reasoning segmentation pipelines fail to transparently connect this reasoning to visual perception. Current methods, such as latent query alignment, are end-to-end…

Computer Vision and Pattern Recognition · Computer Science 2026-05-22 Zhenyu Lu , Liupeng Li , Jinpeng Wang , Haoqian Kang , Yan Feng , Ke Chen , Yaowei Wang

Sparse autoencoders (SAEs) enable interpretability research by decomposing entangled model activations into monosemantic features. However, under what circumstances SAEs derive most fine-grained latent features for safety, a low-frequency…

Machine Learning · Computer Science 2026-04-15 Jiaqi Weng , Han Zheng , Hanyu Zhang , Ej Zhou , Qinqin He , Jialing Tao , Hui Xue , Zhixuan Chu , Xiting Wang

Sparse Autoencoders (SAEs) have emerged as a powerful framework for machine learning interpretability, enabling the unsupervised decomposition of model representations into a dictionary of abstract, human-interpretable concepts. However, we…

Computer Vision and Pattern Recognition · Computer Science 2025-05-27 Thomas Fel , Ekdeep Singh Lubana , Jacob S. Prince , Matthew Kowal , Victor Boutin , Isabel Papadimitriou , Binxu Wang , Martin Wattenberg , Demba Ba , Talia Konkle

Modern LLMs face inference efficiency challenges due to their scale. To address this, many compression methods have been proposed, such as pruning and quantization. However, the effect of compression on a model's interpretability remains…

Machine Learning · Computer Science 2025-07-23 Suchit Gupte , Vishnu Kabir Chhabra , Mohammad Mahdi Khalili

Sparse Autoencoders (SAEs) have shown promise in improving the interpretability of neural network activations, but can learn features that are not features of the input, limiting their effectiveness. We propose \textsc{Mutual Feature…

Machine Learning · Computer Science 2024-11-07 Luke Marks , Alasdair Paren , David Krueger , Fazl Barez