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Sparse auto-encoders (SAEs) have re-emerged as a prominent method for mechanistic interpretability, yet they face two significant challenges: the non-smoothness of the $L_1$ penalty, which hinders reconstruction and scalability, and a lack…

Artificial Intelligence · Computer Science 2026-05-19 Ouns El Harzli , Hugo Wallner , Yoonsoo Nam , Haixuan Xavier Tao

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

In this paper we propose Structuring AutoEncoders (SAE). SAEs are neural networks which learn a low dimensional representation of data which are additionally enriched with a desired structure in this low dimensional space. While traditional…

Machine Learning · Computer Science 2019-08-20 Marco Rudolph , Bastian Wandt , Bodo Rosenhahn

Sparse autoencoders (SAEs) have recently become central tools for interpretability, leveraging dictionary learning principles to extract sparse, interpretable features from neural representations whose underlying structure is typically…

Machine Learning · Computer Science 2025-11-05 Valérie Costa , Thomas Fel , Ekdeep Singh Lubana , Bahareh Tolooshams , Demba Ba

Sparse autoencoders (SAEs) are a mechanistic interpretability technique that have been used to provide insight into learned concepts within large protein language models. Here, we employ TopK and Ordered SAEs to investigate autoregressive…

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in…

Computer Vision and Pattern Recognition · Computer Science 2025-11-25 Samuel Stevens , Jacob Beattie , Tanya Berger-Wolf , Yu Su

Intermediate layers of large language models (LLMs) best predict human brain responses to language, one of the most robust findings in computational neurolinguistics, yet why remains mechanistically unexplained. We address this gap by…

Computation and Language · Computer Science 2026-05-25 Dongxin Guo , Jikun Wu , Siu Ming Yiu

Recent work shows that Sparse Autoencoders (SAE) applied to large language model (LLM) layers have neurons corresponding to interpretable concepts. These SAE neurons can be modified to align generated outputs, but only towards…

Computation and Language · Computer Science 2025-07-01 Ananya Joshi , Celia Cintas , Skyler Speakman

Sparse auto-encoders (SAEs) have become a prevalent tool for interpreting language models' inner workings. However, it is unknown how tightly SAE features correspond to computationally important directions in the model. This work…

Machine Learning · Computer Science 2025-02-25 Thomas Dooms , Daniel Wilhelm

Sparse Autoencoders (SAEs) have become an important tool in mechanistic interpretability, helping to analyze internal representations in both Large Language Models (LLMs) and Vision Transformers (ViTs). By decomposing polysemantic…

Machine Learning · Computer Science 2026-05-11 Jakub Stępień , Marcin Mazur , Jacek Tabor , Przemysław Spurek

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 widely employed for mechanistic interpretability and model steering. Within this context, steering is by design performed by means of decoding altered SAE intermediate representations. This procedure…

Machine Learning · Computer Science 2025-12-08 Antonio Bărbălau , Cristian Daniel Păduraru , Teodor Poncu , Alexandru Tifrea , Elena Burceanu

We introduce sparse autoencoder neural operators (SAE-NOs), a new class of sparse autoencoders that operate in function spaces rather than fixed-dimensional Euclidean representations. We formalize the functional representation hypothesis,…

Machine Learning · Computer Science 2026-05-11 Bahareh Tolooshams , Ailsa Shen , Anima Anandkumar

Sparse autoencoders (SAEs) are a core interpretability tool for large language models, and progress on SAE architectures depends on benchmarks that reliably distinguish better SAEs from worse ones. We audit the SAE quality metrics in…

Machine Learning · Computer Science 2026-05-19 David Chanin

The Linear Representation Hypothesis asserts that the embeddings learned by neural networks can be understood as linear combinations of features corresponding to high-level concepts. Based on this ansatz, sparse autoencoders (SAEs) have…

Machine Learning · Computer Science 2026-01-29 Chiraag Kaushik , Davis Barch , Andrea Fanelli

Sparse autoencoders (SAEs) have been applied to large language models and protein language models, but not systematically to electronic health record (EHR) foundation models. We train TopK SAEs on FlatASCEND, a 14.5-million-parameter…

Machine Learning · Computer Science 2026-05-07 Chris Sainsbury , Feng Dong , Andreas Karwath

Autoencoders have been used for finding interpretable and disentangled features underlying neural network representations in both image and text domains. While the efficacy and pitfalls of such methods are well-studied in vision, there is a…

Machine Learning · Computer Science 2025-02-06 Abhinav Menon , Manish Shrivastava , David Krueger , Ekdeep Singh Lubana

As black box models and pretrained models gain traction in time series applications, understanding and explaining their predictions becomes increasingly vital, especially in high-stakes domains where interpretability and trust are…

Machine Learning · Computer Science 2026-01-16 Khalid Oublal , Quentin Bouniot , Qi Gan , Stephan Clémençon , Zeynep Akata

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

Sparse Autoencoders (SAEs) have demonstrated significant promise in interpreting the hidden states of language models by decomposing them into interpretable latent directions. However, training and interpreting SAEs at scale remains…

Machine Learning · Computer Science 2025-12-23 Vadim Kurochkin , Yaroslav Aksenov , Daniil Laptev , Daniil Gavrilov , Nikita Balagansky