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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) that can accurately reconstruct their input (minimizing distortion) by making efficient use of few features (minimizing the rate) often fail to learn monosemantic representations (highly interpretable), limiting…

Machine Learning · Computer Science 2026-05-15 Tommaso Mencattini , Francesco Montagna , Francesco Locatello

Understanding and mitigating the potential risks associated with foundation models (FMs) hinges on developing effective interpretability methods. Sparse Autoencoders (SAEs) have emerged as a promising tool for disentangling FM…

Machine Learning · Computer Science 2024-11-04 Aashiq Muhamed , Mona Diab , Virginia Smith

Sparse autoencoders (SAEs) interpret neural network representations by decomposing activations into sparse combinations of dictionary atoms. However, SAEs assume features combine additively through linear reconstruction, an assumption that…

Machine Learning · Computer Science 2026-05-26 Panagiotis Koromilas , Andreas D. Demou , James Oldfield , Yannis Panagakis , Mihalis Nicolaou

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

Sparse Autoencoder (SAE) features have become essential tools for mechanistic interpretability research. SAE features are typically characterized by examining their activating examples, which are often "monosemantic" and align with human…

Artificial Intelligence · Computer Science 2025-09-30 Claire Tian , Katherine Tian , Nathan Hu

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) 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) are a prominent tool in mechanistic interpretability (MI) for decomposing neural network activations into interpretable features. However, the aspiration to identify a canonical set of features is challenged by…

Machine Learning · Computer Science 2025-05-27 Xiangchen Song , Aashiq Muhamed , Yujia Zheng , Lingjing Kong , Zeyu Tang , Mona T. Diab , Virginia Smith , Kun Zhang

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

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) have emerged as powerful techniques for interpretability of large language models (LLMs), aiming to decompose hidden states into meaningful semantic features. While several SAE variants have been proposed, there…

Machine Learning · Computer Science 2025-10-03 Xudong Zhu , Mohammad Mahdi Khalili , Zhihui Zhu

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

Sparse autoencoders (SAEs) have emerged as a powerful technique for extracting human-interpretable features from neural networks activations. Previous works compared different models based on SAE-derived features but those comparisons have…

Computer Vision and Pattern Recognition · Computer Science 2025-07-25 Clément Cornet , Romaric Besançon , Hervé Le Borgne

Sparse autoencoders (SAEs) \citep{bricken2023monosemanticity,gao2024scalingevaluatingsparseautoencoders} rely on dictionary learning to extract interpretable features from neural networks at scale in an unsupervised manner, with…

Machine Learning · Computer Science 2025-05-02 Hans Peter , Anders Søgaard

Sparse autoencoders (SAEs) have emerged as a promising approach for learning interpretable features from neural network activations. However, the optimization landscape for SAE training can be challenging due to correlations in the input…

Machine Learning · Computer Science 2025-11-19 Ashwin Saraswatula , David Klindt

The rapid advancements in transformer-based language models have revolutionized natural language processing, yet understanding the internal mechanisms of these models remains a significant challenge. This paper explores the application of…

Machine Learning · Computer Science 2025-02-14 Edith Natalia Villegas Garcia , Alessio Ansuini

Determining company similarity is a vital task in finance, underpinning risk management, hedging, and portfolio diversification. Practitioners often rely on sector and industry classifications such as SIC and GICS codes to gauge similarity,…

Sparse autoencoders (SAEs) enable feature-level mechanistic interpretability and activation steering in large language models (LLMs), but SAE-based language control remains unreliable in multilingual settings: most SAEs are trained on…

Computation and Language · Computer Science 2026-05-25 Yusser Al Ghussin , Daniil Gurgurov , Tanja Baeumel , Josef van Genabith , Patrick Schramowski , Simon Ostermann

Deep learning, particularly with the advancement of Large Language Models, has transformed biomolecular modeling, with protein language models such as ESM inspiring emerging RNA language models such as RiNALMo. Recent work has begun…

Biomolecules · Quantitative Biology 2026-05-18 Taehan Kim , Sangdae Nam
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