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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 Autoencoders (SAEs) have been proposed as an unsupervised approach to learn a decomposition of a model's latent space. This enables useful applications such as steering - influencing the output of a model towards a desired concept -…

Machine Learning · Computer Science 2025-12-23 Dana Arad , Aaron Mueller , Yonatan Belinkov

Leveraging the framework of Optimal Transport, we introduce a new family of generative autoencoders with a learnable prior, called Symmetric Wasserstein Autoencoders (SWAEs). We propose to symmetrically match the joint distributions of the…

Machine Learning · Computer Science 2021-06-25 Sun Sun , Hongyu Guo

A rekindled the interest in auto-encoder algorithms has been spurred by recent work on deep learning. Current efforts have been directed towards effective training of auto-encoder architectures with a large number of coding units. Here, we…

Machine Learning · Computer Science 2014-04-18 Luis G. Sanchez Giraldo , Jose C. Principe

This letter introduces a new denoiser that modifies the structure of denoising autoencoder (DAE), namely noise learning based DAE (nlDAE). The proposed nlDAE learns the noise of the input data. Then, the denoising is performed by…

Machine Learning · Computer Science 2022-01-24 Woong-Hee Lee , Mustafa Ozger , Ursula Challita , Ki Won Sung

Autoencoders are certainly among the most studied and used Deep Learning models: the idea behind them is to train a model in order to reconstruct the same input data. The peculiarity of these models is to compress the information through a…

Machine Learning · Computer Science 2023-09-06 Gabriele Martino , Davide Moroni , Massimo Martinelli

Non-parallel text style transfer has attracted increasing research interests in recent years. Despite successes in transferring the style based on the encoder-decoder framework, current approaches still lack the ability to preserve the…

Computation and Language · Computer Science 2021-02-02 Yukai Shi , Sen Zhang , Chenxing Zhou , Xiaodan Liang , Xiaojun Yang , Liang Lin

Variational Autoencoders (VAEs) provide a theoretically-backed and popular framework for deep generative models. However, learning a VAE from data poses still unanswered theoretical questions and considerable practical challenges. In this…

Machine Learning · Computer Science 2020-06-01 Partha Ghosh , Mehdi S. M. Sajjadi , Antonio Vergari , Michael Black , Bernhard Schölkopf

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

Variational autoencoders learn unsupervised data representations, but these models frequently converge to minima that fail to preserve meaningful semantic information. For example, variational autoencoders with autoregressive decoders often…

Machine Learning · Computer Science 2019-05-21 Bryan Seybold , Emily Fertig , Alex Alemi , Ian Fischer

Masked graph autoencoder (MGAE) has emerged as a promising self-supervised graph pre-training (SGP) paradigm due to its simplicity and effectiveness. However, existing efforts perform the mask-then-reconstruct operation in the raw data…

Machine Learning · Computer Science 2023-04-07 Wenxuan Tu , Qing Liao , Sihang Zhou , Xin Peng , Chuan Ma , Zhe Liu , Xinwang Liu , Zhiping Cai

Recent state-of-the-art autoencoder based generative models have an encoder-decoder structure and learn a latent representation with a pre-defined distribution that can be sampled from. Implementing the encoder networks of these models in a…

Machine Learning · Computer Science 2020-05-11 D. T. Braithwaite , M. O'Connor , W. B. Kleijn

A popular new method in mechanistic interpretability is to train high-dimensional sparse autoencoders (SAEs) on neuron activations and use SAE features as the atomic units of analysis. However, the body of evidence on whether SAE feature…

Machine Learning · Computer Science 2024-09-10 Maheep Chaudhary , Atticus Geiger

Stacked Auto-Encoder (SAE) is a kind of deep learning algorithm for unsupervised learning. Which has multi layers that project the vector representation of input data into a lower vector space. These projection vectors are dense…

Computer Vision and Pattern Recognition · Computer Science 2016-10-11 Fei Hu , Changjiu Pu , Haowei Gao , Mengzi Tang , Li Li

This paper investigates a novel algorithmic approach to data representation based on kernel methods. Assuming that the observations lie in a Hilbert space X, the introduced Kernel Autoencoder (KAE) is the composition of mappings from…

Machine Learning · Statistics 2020-12-03 Pierre Laforgue , Stephan Clémençon , Florence d'Alché-Buc

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 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

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

Text-to-image diffusion models generate images through an iterative denoising process, so internal neural layers produce trajectories of activations rather than single static representations. Sparse autoencoders (SAEs) have recently been…

Computer Vision and Pattern Recognition · Computer Science 2026-05-28 Calvin Yeung , Prathyush Poduval , Ali Zakeri , Zhuowen Zou , Mohsen Imani

Sparse autoencoders (SAEs) have been successfully used to discover sparse and human-interpretable representations of the latent activations of LLMs. However, we would ultimately like to understand the computations performed by LLMs and not…

Machine Learning · Computer Science 2025-06-09 Lucy Farnik , Tim Lawson , Conor Houghton , Laurence Aitchison