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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

The ImageNet hierarchy provides a structured taxonomy of object categories, offering a valuable lens through which to analyze the representations learned by deep vision models. In this work, we conduct a comprehensive analysis of how vision…

Computer Vision and Pattern Recognition · Computer Science 2025-05-23 Matthew Lyle Olson , Musashi Hinck , Neale Ratzlaff , Changbai Li , Phillip Howard , Vasudev Lal , Shao-Yen Tseng

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

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 emerged as a popular tool for interpreting the hidden states of large language models (LLMs). By learning to reconstruct activations from a sparse bottleneck layer, SAEs discover interpretable features from…

Computer Vision and Pattern Recognition · Computer Science 2025-09-19 Matthew Lyle Olson , Musashi Hinck , Neale Ratzlaff , Changbai Li , Phillip Howard , Vasudev Lal , Shao-Yen Tseng

Sparse Autoencoders (SAEs) are widely used to interpret neural networks by identifying meaningful concepts from their representations. However, do SAEs truly uncover all concepts a model relies on, or are they inherently biased toward…

Machine Learning · Computer Science 2025-12-03 Sai Sumedh R. Hindupur , Ekdeep Singh Lubana , Thomas Fel , Demba Ba

Sparse Autoencoders (SAEs) have proven to be powerful tools for interpreting neural networks by decomposing hidden representations into disentangled, interpretable features via sparsity constraints. However, conventional SAEs are…

We present Universal Sparse Autoencoders (USAEs), a framework for uncovering and aligning interpretable concepts spanning multiple pretrained deep neural networks. Unlike existing concept-based interpretability methods, which focus on a…

Computer Vision and Pattern Recognition · Computer Science 2026-03-20 Harrish Thasarathan , Julian Forsyth , Thomas Fel , Matthew Kowal , Konstantinos G. Derpanis

Sparse autoencoders (SAEs) have shown promise in extracting interpretable features from complex neural networks. We present one of the first applications of SAEs to dense text embeddings from large language models, demonstrating their…

Machine Learning · Computer Science 2024-08-06 Charles O'Neill , Christine Ye , Kartheik Iyer , John F. Wu

Sparse autoencoders (SAEs) have emerged as a powerful tool for uncovering interpretable features in large language models (LLMs) through the sparse directions they learn. However, the sheer number of extracted directions makes comprehensive…

Computation and Language · Computer Science 2025-11-11 Xinyuan Yan , Shusen Liu , Kowshik Thopalli , Bei Wang

Sparse Autoencoders (SAEs) are a powerful dictionary learning technique for decomposing neural network activations, translating the hidden state into human ideas with high semantic value despite no external intervention or guidance.…

Machine Learning · Computer Science 2025-12-17 Albert Miao , Chenliang Zhou , Jiawei Zhou , Cengiz Oztireli

Brain MRI foundation models learn rich representations of anatomy, but interpreting what clinical information they encode remains an open problem. Standard sparse autoencoders (SAEs) suffer from severe feature collapse in deep transformer…

Computer Vision and Pattern Recognition · Computer Science 2026-05-05 Favour Nerrise , Lucy Yin , Mohammad H. Abbasi , Kilian M. Pohl , Ehsan Adeli

Decomposing model activations into interpretable components is a key open problem in mechanistic interpretability. Sparse autoencoders (SAEs) are a popular method for decomposing the internal activations of trained transformers into sparse,…

Machine Learning · Computer Science 2024-06-26 Connor Kissane , Robert Krzyzanowski , Joseph Isaac Bloom , Arthur Conmy , Neel Nanda

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

Sparse Autoencoders (SAEs) are powerful tools for interpreting neural representations, yet their use in audio remains underexplored. We train SAEs across all encoder layers of Whisper and HuBERT, provide an extensive evaluation of their…

A recent line of work has shown promise in using sparse autoencoders (SAEs) to uncover interpretable features in neural network representations. However, the simple linear-nonlinear encoding mechanism in SAEs limits their ability to perform…

Machine Learning · Computer Science 2025-01-31 Charles O'Neill , Alim Gumran , David Klindt

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

Sparse Autoencoders (SAEs) are a promising approach for extracting neural network representations by learning a sparse and overcomplete decomposition of the network's internal activations. However, SAEs are traditionally trained considering…

Machine Learning · Computer Science 2025-04-02 Jeffrey Olmo , Jared Wilson , Max Forsey , Bryce Hepner , Thomas Vin Howe , David Wingate

Sparse autoencoders (SAEs) have been used widely to decompose and interpret neural network activations, especially those of transformer language models. One key issue with SAEs is their inability to directly model multidimensional features.…

Machine Learning · Computer Science 2026-05-12 Collin Francel

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