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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

Sparse attention reduces the quadratic complexity of full self-attention but faces two challenges: (1) an attention gap, where applying sparse attention to full-attention-trained models causes performance degradation due to train-inference…

Computation and Language · Computer Science 2026-02-02 Zhenyi Shen , Junru Lu , Lin Gui , Jiazheng Li , Yulan He , Di Yin , Xing Sun

Sparse autoencoders (SAEs) have become a central tool for interpreting language models. However, two key SAE analyses that remain difficult to scale are (1) matching semantically similar features across multi-layers and (2) compressing…

Machine Learning · Computer Science 2026-05-28 Tue M. Cao , Nguyen Do , My T. Thai

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

Sparse autoencoders (SAEs) model the activations of a neural network as linear combinations of sparsely occurring directions of variation (latents). The ability of SAEs to reconstruct activations follows scaling laws w.r.t. the number of…

Machine Learning · Computer Science 2025-09-05 Eric J. Michaud , Liv Gorton , Tom McGrath

Attention mechanisms have become ubiquitous in NLP. Recent architectures, notably the Transformer, learn powerful context-aware word representations through layered, multi-headed attention. The multiple heads learn diverse types of word…

Computation and Language · Computer Science 2019-09-09 Gonçalo M. Correia , Vlad Niculae , André F. T. Martins

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 proven useful in disentangling the opaque activations of neural networks, primarily large language models, into sets of interpretable features. However, adapting them to domains beyond language, such as…

Machine Learning · Computer Science 2025-11-13 Ege Erdogan , Ana Lucic

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

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…

One of the roadblocks to a better understanding of neural networks' internals is \textit{polysemanticity}, where neurons appear to activate in multiple, semantically distinct contexts. Polysemanticity prevents us from identifying concise,…

Machine Learning · Computer Science 2023-10-05 Hoagy Cunningham , Aidan Ewart , Logan Riggs , Robert Huben , Lee Sharkey

While the self-attention mechanism has been widely used in a wide variety of tasks, it has the unfortunate property of a quadratic cost with respect to the input length, which makes it difficult to deal with long inputs. In this paper, we…

Computation and Language · Computer Science 2020-09-30 Xiaoya Li , Yuxian Meng , Mingxin Zhou , Qinghong Han , Fei Wu , Jiwei Li

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 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

The Transformer architecture model, based on self-attention and multi-head attention, has achieved remarkable success in offline end-to-end Automatic Speech Recognition (ASR). However, self-attention and multi-head attention cannot be…

Computation and Language · Computer Science 2022-10-03 Chendong Zhao , Jianzong Wang , Wen qi Wei , Xiaoyang Qu , Haoqian Wang , Jing Xiao

Analyzing large-scale text corpora is a core challenge in machine learning, crucial for tasks like identifying undesirable model behaviors or biases in training data. Current methods often rely on costly LLM-based techniques (e.g.…

Artificial Intelligence · Computer Science 2025-12-12 Nick Jiang , Xiaoqing Sun , Lisa Dunlap , Lewis Smith , Neel Nanda

Sparse autoencoders are a promising new approach for decomposing language model activations for interpretation and control. They have been applied successfully to vision transformer image encoders and to small-scale diffusion models.…

Machine Learning · Computer Science 2025-07-14 Stepan Shabalin , Ayush Panda , Dmitrii Kharlapenko , Abdur Raheem Ali , Yixiong Hao , Arthur Conmy

Many current state-of-the-art models for sequential recommendations are based on transformer architectures. Interpretation and explanation of such black box models is an important research question, as a better understanding of their…

Information Retrieval · Computer Science 2026-02-18 Anton Klenitskiy , Konstantin Polev , Daria Denisova , Alexey Vasilev , Dmitry Simakov , Gleb Gusev

The Transformer architecture, despite its widespread success, struggles with long-context scenarios due to quadratic computation and linear memory growth. While various linear attention variants mitigate these efficiency constraints by…

Machine Learning · Computer Science 2025-10-02 Yuqi Pan , Yongqi An , Zheng Li , Yuhong Chou , Ruijie Zhu , Xiaohui Wang , Mingxuan Wang , Jinqiao Wang , Guoqi Li

Sparse autoencoders (SAEs) provide a powerful mechanism for decomposing the dense representations produced by Large Language Models (LLMs) into interpretable latent features. We posit that SAEs constitute a natural foundation for Learned…

Machine Learning · Computer Science 2026-03-17 Thibault Formal , Maxime Louis , Hervé Dejean , Stéphane Clinchant
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