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Sparse autoencoders (SAEs) have lately been used to uncover interpretable latent features in large language models. By projecting dense embeddings into a much higher-dimensional and sparse space, learned features become disentangled and…

Machine Learning · Computer Science 2025-07-30 Viktoria Schuster

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

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

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 a mechanistic interpretability technique that have been used to provide insight into learned concepts within large protein language models. Here, we employ TopK and Ordered SAEs to investigate autoregressive…

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

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

Sparse autoencoders (SAEs) are a useful tool for uncovering human-interpretable features in the activations of large language models (LLMs). While some expect SAEs to find the true underlying features used by a model, our research shows…

Machine Learning · Computer Science 2025-01-31 Gonçalo Paulo , Nora Belrose

Sparse Autoencoders (SAEs) provide potentials for uncovering structured, human-interpretable representations in Large Language Models (LLMs), making them a crucial tool for transparent and controllable AI systems. We systematically analyze…

Machine Learning · Computer Science 2026-02-03 Jack Gallifant , Shan Chen , Kuleen Sasse , Hugo Aerts , Thomas Hartvigsen , Danielle S. Bitterman

Translating the internal representations and computations of models into concepts that humans can understand is a key goal of interpretability. While recent dictionary learning methods such as Sparse Autoencoders (SAEs) provide a promising…

Computation and Language · Computer Science 2026-02-27 Usha Bhalla , Alex Oesterling , Claudio Mayrink Verdun , Himabindu Lakkaraju , Flavio P. Calmon

Vision foundation models (FMs) achieve state-of-the-art performance in medical imaging. However, they encode information in abstract latent representations that clinicians cannot interrogate or verify. The goal of this study is to…

Computer Vision and Pattern Recognition · Computer Science 2026-03-26 Philipp Wesp , Robbie Holland , Vasiliki Sideri-Lampretsa , Sergios Gatidis

Is there really much more to say about sparse autoencoders (SAEs)? Autoencoders in general, and SAEs in particular, represent deep architectures that are capable of modeling low-dimensional latent structure in data. Such structure could…

Machine Learning · Computer Science 2025-06-09 Yin Lu , Xuening Zhu , Tong He , David Wipf

Mechanistic interpretability of large language models (LLMs) aims to uncover the internal processes of information propagation and reasoning. Sparse autoencoders (SAEs) have demonstrated promise in this domain by extracting interpretable…

Machine Learning · Computer Science 2025-05-26 Wei Shi , Sihang Li , Tao Liang , Mingyang Wan , Guojun Ma , Xiang Wang , Xiangnan He

Audio pretrained models are widely employed to solve various tasks in speech processing, sound event detection, or music information retrieval. However, the representations learned by these models are unclear, and their analysis mainly…

Sparse autoencoders (SAEs) are a popular method for interpreting concepts represented in large language model (LLM) activations. However, there is a lack of evidence regarding the validity of their interpretations due to the lack of a…

Machine Learning · Computer Science 2025-02-25 Subhash Kantamneni , Joshua Engels , Senthooran Rajamanoharan , Max Tegmark , Neel Nanda

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

To truly understand vision models, we must not only interpret their learned features but also validate these interpretations through controlled experiments. While earlier work offers either rich semantics or direct control, few post-hoc…

Computer Vision and Pattern Recognition · Computer Science 2025-11-25 Samuel Stevens , Wei-Lun Chao , Tanya Berger-Wolf , Yu Su

Understanding the multilingual mechanisms of large language models (LLMs) provides insight into how they process different languages, yet this remains challenging. Existing studies often focus on individual neurons, but their polysemantic…

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

Pathology plays an important role in disease diagnosis, treatment decision-making and drug development. Previous works on interpretability for machine learning models on pathology images have revolved around methods such as attention value…

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