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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

Sparse autoencoders (SAEs) have recently emerged as a powerful tool for interpreting the features learned by large language models (LLMs). By reconstructing features with sparsely activated networks, SAEs aim to recover complex superposed…

Machine Learning · Computer Science 2026-03-05 Jingyi Cui , Qi Zhang , Yifei Wang , Yisen Wang

Sparse autoencoders (SAEs) are a promising technique for decomposing language model activations into interpretable linear features. However, current SAEs fall short of completely explaining model performance, resulting in "dark matter":…

Machine Learning · Computer Science 2025-03-26 Joshua Engels , Logan Riggs , Max Tegmark

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

The mechanisms behind multilingual capabilities in Large Language Models (LLMs) have been examined using neuron-based or internal-activation-based methods. However, these methods often face challenges such as superposition and layer-wise…

Computation and Language · Computer Science 2025-05-28 Boyi Deng , Yu Wan , Yidan Zhang , Baosong Yang , Fuli Feng

Large Language Models (LLMs) have transformed natural language processing, yet their internal mechanisms remain largely opaque. Recently, mechanistic interpretability has attracted significant attention from the research community as a…

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

A common goal of mechanistic interpretability is to decompose the activations of neural networks into features: interpretable properties of the input computed by the model. Sparse autoencoders (SAEs) are a popular method for finding these…

Machine Learning · Computer Science 2025-02-10 Patrick Leask , Bart Bussmann , Michael Pearce , Joseph Bloom , Curt Tigges , Noura Al Moubayed , Lee Sharkey , Neel Nanda

Understanding the internal representations of large language models (LLMs) remains a central challenge for interpretability research. Sparse autoencoders (SAEs) offer a promising solution by decomposing activations into interpretable…

Machine Learning · Computer Science 2025-10-10 Yifei Yao , Mengnan Du

We study the challenge of achieving theoretically grounded feature recovery using Sparse Autoencoders (SAEs) for the interpretation of Large Language Models. Existing SAE training algorithms often lack rigorous mathematical guarantees and…

Machine Learning · Computer Science 2025-06-18 Siyu Chen , Heejune Sheen , Xuyuan Xiong , Tianhao Wang , Zhuoran Yang

Motivated by the hypothesis that neural network representations encode abstract, interpretable features as linearly accessible, approximately orthogonal directions, sparse autoencoders (SAEs) have become a popular tool in interpretability.…

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

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

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

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

Identifying the features learned by neural networks is a core challenge in mechanistic interpretability. Sparse autoencoders (SAEs), which learn a sparse, overcomplete dictionary that reconstructs a network's internal activations, have been…

Machine Learning · Computer Science 2024-05-27 Dan Braun , Jordan Taylor , Nicholas Goldowsky-Dill , Lee Sharkey

Sparse autoencoders (SAEs) are used to analyze embeddings, but their role and practical value are debated. We propose a new perspective on SAEs by demonstrating that they can be naturally understood as topic models. We propose a continuous…

Computer Vision and Pattern Recognition · Computer Science 2026-05-19 Leander Girrbach , Zeynep Akata

Sparse autoencoders (SAEs) trained on large language model activations output thousands of features that enable mapping to human-interpretable concepts. The current practice for analyzing these features primarily relies on inspecting…

Computation and Language · Computer Science 2026-03-26 Wilson E. Marcílio-Jr , Danilo M. Eler

We extend variational autoencoders (VAEs) to collaborative filtering for implicit feedback. This non-linear probabilistic model enables us to go beyond the limited modeling capacity of linear factor models which still largely dominate…

Machine Learning · Statistics 2018-02-19 Dawen Liang , Rahul G. Krishnan , Matthew D. Hoffman , Tony Jebara

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) have emerged as a promising approach for interpreting neural network representations by learning sparse, human-interpretable features from dense activations. We investigate whether incorporating variational…

Machine Learning · Computer Science 2025-10-03 Zachary Baker , Yuxiao Li

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
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