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Sparse autoencoders (SAEs) are designed to extract interpretable features from language models by enforcing a sparsity constraint. Ideally, training an SAE would yield latents that are both sparse and semantically meaningful. However, many…

Machine Learning · Computer Science 2025-11-06 Xiaoqing Sun , Alessandro Stolfo , Joshua Engels , Ben Wu , Senthooran Rajamanoharan , Mrinmaya Sachan , Max Tegmark

Sparse autoencoders (SAEs) have recently emerged as a powerful tool for language model steering. Prior work has explored top-k SAE latents for steering, but we observe that many dimensions among the top-k latents capture non-semantic…

Computation and Language · Computer Science 2025-10-03 Jiaqing Xie

Mechanistic interpretability aims to decompose neural networks into interpretable features and map their connecting circuits. The standard approach trains sparse autoencoders (SAEs) on each layer's activations. However, SAEs trained in…

Machine Learning · Computer Science 2025-11-12 Sean P. Fillingham , Andrew Gordon , Peter Lai , Xavier Poncini , David Quarel , Stefan Heimersheim

Protein language models have revolutionized structure prediction, but their nonlinear nature obscures how sequence representations inform structure prediction. While sparse autoencoders (SAEs) offer a path to interpretability here by…

Biomolecules · Quantitative Biology 2025-03-13 Nithin Parsan , David J. Yang , John J. Yang

Sparse Autoencoders (SAEs) have been successfully used to probe Large Language Models (LLMs) and extract interpretable concepts from their internal representations. These concepts are linear combinations of neuron activations that…

Computation and Language · Computer Science 2026-02-23 Mathis Le Bail , Jérémie Dentan , Davide Buscaldi , Sonia Vanier

Understanding the internal machinations of deep Transformer-based NLP models is more crucial than ever as these models see widespread use in various domains that affect the public at large, such as industry, academia, finance, health. While…

Computation and Language · Computer Science 2026-05-13 Dan Pluth , Zachary Nicholas Houghton , Yu Zhou , Vijay K. Gurbani

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

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

Artificial Neural Networks form the basis of very powerful learning methods. It has been observed that a naive application of fully connected neural networks to data with many irrelevant variables often leads to overfitting. In an attempt…

Machine Learning · Computer Science 2020-02-12 Gitesh Dawer , Yangzi Guo , Sida Liu , Adrian Barbu

Sparse autoencoders (SAEs) are a popular technique for interpreting language model activations, and there is extensive recent work on improving SAE effectiveness. However, most prior work evaluates progress using unsupervised proxy metrics…

Sparse autoencoders (SAEs) have been widely used for interpretability of neural networks, but their learned features often vary across seeds and hyperparameter settings. We introduce Ordered Sparse Autoencoders (OSAE), which extend…

Machine Learning · Computer Science 2025-12-03 Sophie L. Wang , Alex Quach , Nithin Parsan , John J. Yang

We investigate whether sparse autoencoders (SAEs) can be used to remove knowledge from language models. We use the biology subset of the Weapons of Mass Destruction Proxy dataset and test on the gemma-2b-it and gemma-2-2b-it language…

Machine Learning · Computer Science 2024-11-05 Eoin Farrell , Yeu-Tong Lau , Arthur Conmy

We present SAE-BrainMap, a novel framework that directly aligns deep learning visual model representations with voxel-level fMRI responses using sparse autoencoders (SAEs). First, we train layer-wise SAEs on model activations and compute…

Neurons and Cognition · Quantitative Biology 2025-06-16 Ziming Mao , Jia Xu , Zeqi Zheng , Haofang Zheng , Dabing Sheng , Yaochu Jin , Guoyuan Yang

EEG foundation models achieve state-of-the-art clinical performance, yet the internal computations driving their predictions remain opaque: a barrier to clinical trust. We apply TopK Sparse Autoencoders (SAEs) across three architecturally…

Sparse Autoencoders (SAEs) are increasingly used to interpret foundation models, but their role as an actionable intervention space remains less understood, especially in vision. We study whether sparse visual features can be used not only…

Computer Vision and Pattern Recognition · Computer Science 2026-05-28 Gerasimos Chatzoudis , Zhuowei Li , Gemma E. Moran , Hao Wang , Dimitris N. Metaxas

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) 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

Sparse autoencoders (SAEs) decompose neural activations into interpretable features. A widely adopted variant, the TopK SAE, reconstructs each token from its K most active latents. However, this approach is inefficient, as some tokens carry…

Machine Learning · Computer Science 2025-09-01 Narmeen Oozeer , Nirmalendu Prakash , Michael Lan , Alice Rigg , Amirali Abdullah

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) 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