Daily Papers

Neural autoencoders underpin generative models. Practical, large-scale use of neural autoencoders for generative modeling necessitates fast encoding, low latent rates, and a single model across representations. Existing approaches are reconstruction-first: they incur high latent rates, slow encoding, and separate architectures for discrete vs. continuous latents and for different audio channel formats, hindering workflows from preprocessing to inference conditioning. We introduce a generative-first architecture for audio autoencoding that increases temporal downsampling from 2048x to 3360x and supports continuous and discrete representations and common audio channel formats in one model. By balancing compression, quality, and speed, it delivers 10x faster encoding, 1.6x lower rates, and eliminates channel-format-specific variants while maintaining competitive reconstruction quality. This enables applications previously constrained by processing costs: a 60-second mono signal compresses to 788 tokens, making generative modeling more tractable.

Neural audio codecs and autoencoders have emerged as versatile models for audio compression, transmission, feature-extraction, and latent-space generation. However, a key limitation is that most are trained to maximize reconstruction fidelity, often neglecting the specific latent structure necessary for optimal performance in diverse downstream applications. We propose a simple, post-hoc framework to address this by modifying the bottleneck of a pre-trained autoencoder. Our method introduces a "Re-Bottleneck", an inner bottleneck trained exclusively through latent space losses to instill user-defined structure. We demonstrate the framework's effectiveness in three experiments. First, we enforce an ordering on latent channels without sacrificing reconstruction quality. Second, we align latents with semantic embeddings, analyzing the impact on downstream diffusion modeling. Third, we introduce equivariance, ensuring that a filtering operation on the input waveform directly corresponds to a specific transformation in the latent space. Ultimately, our Re-Bottleneck framework offers a flexible and efficient way to tailor representations of neural audio models, enabling them to seamlessly meet the varied demands of different applications with minimal additional training.

Neural audio autoencoders create compact latent representations that preserve perceptually important information, serving as the foundation for both modern audio compression systems and generation approaches like next-token prediction and latent diffusion. Despite their prevalence, most audio processing operations, such as spatial and spectral up-sampling, still inefficiently operate on raw waveforms or spectral representations rather than directly on these compressed representations. We propose a framework that performs audio processing operations entirely within an autoencoder's latent space, eliminating the need to decode to raw audio formats. Our approach dramatically simplifies training by operating solely in the latent domain, with a latent L1 reconstruction term, augmented by a single latent adversarial discriminator. This contrasts sharply with raw-audio methods that typically require complex combinations of multi-scale losses and discriminators. Through experiments in bandwidth extension and mono-to-stereo up-mixing, we demonstrate computational efficiency gains of up to 100x while maintaining quality comparable to post-processing on raw audio. This work establishes a more efficient paradigm for audio processing pipelines that already incorporate autoencoders, enabling significantly faster and more resource-efficient workflows across various audio tasks.

Multi-agent coordination is crucial for reliable multi-robot navigation in shared spaces such as automated warehouses. In regions of dense robot traffic, local coordination methods may fail to find a deadlock-free solution. In these scenarios, it is appropriate to let a central unit generate a global schedule that decides the passing order of robots. However, the runtime of such centralized coordination methods increases significantly with the problem scale. In this paper, we propose to leverage Graph Neural Network Variational Autoencoders (GNN-VAE) to solve the multi-agent coordination problem at scale faster than through centralized optimization. We formulate the coordination problem as a graph problem and collect ground truth data using a Mixed-Integer Linear Program (MILP) solver. During training, our learning framework encodes good quality solutions of the graph problem into a latent space. At inference time, solution samples are decoded from the sampled latent variables, and the lowest-cost sample is selected for coordination. Finally, the feasible proposal with the highest performance index is selected for the deployment. By construction, our GNN-VAE framework returns solutions that always respect the constraints of the considered coordination problem. Numerical results show that our approach trained on small-scale problems can achieve high-quality solutions even for large-scale problems with 250 robots, being much faster than other baselines. Project page: https://mengyuest.github.io/gnn-vae-coord

Characterizing the relationship between neural population activity and behavioral data is a central goal of neuroscience. While latent variable models (LVMs) are successful in describing high-dimensional time-series data, they are typically only designed for a single type of data, making it difficult to identify structure shared across different experimental data modalities. Here, we address this shortcoming by proposing an unsupervised LVM which extracts temporally evolving shared and independent latents for distinct, simultaneously recorded experimental modalities. We do this by combining Gaussian Process Factor Analysis (GPFA), an interpretable LVM for neural spiking data with temporally smooth latent space, with Gaussian Process Variational Autoencoders (GP-VAEs), which similarly use a GP prior to characterize correlations in a latent space, but admit rich expressivity due to a deep neural network mapping to observations. We achieve interpretability in our model by partitioning latent variability into components that are either shared between or independent to each modality. We parameterize the latents of our model in the Fourier domain, and show improved latent identification using this approach over standard GP-VAE methods. We validate our model on simulated multi-modal data consisting of Poisson spike counts and MNIST images that scale and rotate smoothly over time. We show that the multi-modal GP-VAE (MM-GPVAE) is able to not only identify the shared and independent latent structure across modalities accurately, but provides good reconstructions of both images and neural rates on held-out trials. Finally, we demonstrate our framework on two real world multi-modal experimental settings: Drosophila whole-brain calcium imaging alongside tracked limb positions, and Manduca sexta spike train measurements from ten wing muscles as the animal tracks a visual stimulus.

Neural Radiance Fields (NeRFs) have proven to be powerful 3D representations, capable of high quality novel view synthesis of complex scenes. While NeRFs have been applied to graphics, vision, and robotics, problems with slow rendering speed and characteristic visual artifacts prevent adoption in many use cases. In this work, we investigate combining an autoencoder (AE) with a NeRF, in which latent features (instead of colours) are rendered and then convolutionally decoded. The resulting latent-space NeRF can produce novel views with higher quality than standard colour-space NeRFs, as the AE can correct certain visual artifacts, while rendering over three times faster. Our work is orthogonal to other techniques for improving NeRF efficiency. Further, we can control the tradeoff between efficiency and image quality by shrinking the AE architecture, achieving over 13 times faster rendering with only a small drop in performance. We hope that our approach can form the basis of an efficient, yet high-fidelity, 3D scene representation for downstream tasks, especially when retaining differentiability is useful, as in many robotics scenarios requiring continual learning.

Sparse autoencoders are a standard tool for uncovering interpretable latent representations in neural networks. Yet, their interpretation depends on the inputs, making their isolated study incomplete. Polynomials offer a solution; they serve as algebraic primitives that can be analysed without reference to input and can describe structures ranging from linear concepts to complicated manifolds. This work uses bilinear autoencoders to efficiently decompose representations into quadratic polynomials. We discuss improvements that induce importance ordering, clustering, and activation sparsity. This is an initial step toward nonlinear yet analysable latents through their algebraic properties.

We investigate applying audio manipulations using pretrained neural network-based autoencoders as an alternative to traditional signal processing methods, since the former may provide greater semantic or perceptual organization. To establish the potential of this approach, we first establish if representations from these models encode information about manipulations. We carry out experiments and produce visualizations using representations from two different pretrained autoencoders. Our findings indicate that, while some information about audio manipulations is encoded, this information is both limited and encoded in a non-trivial way. This is supported by our attempts to visualize these representations, which demonstrated that trajectories of representations for common manipulations are typically nonlinear and content dependent, even for linear signal manipulations. As a result, it is not yet clear how these pretrained autoencoders can be used to manipulate audio signals, however, our results indicate this may be due to the lack of disentanglement with respect to common audio manipulations.

In recent years, a specific machine learning method called deep learning has gained huge attraction, as it has obtained astonishing results in broad applications such as pattern recognition, speech recognition, computer vision, and natural language processing. Recent research has also been shown that deep learning techniques can be combined with reinforcement learning methods to learn useful representations for the problems with high dimensional raw data input. This chapter reviews the recent advances in deep reinforcement learning with a focus on the most used deep architectures such as autoencoders, convolutional neural networks and recurrent neural networks which have successfully been come together with the reinforcement learning framework.

Autoencoder networks are unsupervised approaches aiming at combining generative and representational properties by learning simultaneously an encoder-generator map. Although studied extensively, the issues of whether they have the same generative power of GANs, or learn disentangled representations, have not been fully addressed. We introduce an autoencoder that tackles these issues jointly, which we call Adversarial Latent Autoencoder (ALAE). It is a general architecture that can leverage recent improvements on GAN training procedures. We designed two autoencoders: one based on a MLP encoder, and another based on a StyleGAN generator, which we call StyleALAE. We verify the disentanglement properties of both architectures. We show that StyleALAE can not only generate 1024x1024 face images with comparable quality of StyleGAN, but at the same resolution can also produce face reconstructions and manipulations based on real images. This makes ALAE the first autoencoder able to compare with, and go beyond the capabilities of a generator-only type of architecture.

Diffusion models have achieved remarkable success in image and video generation. In this work, we demonstrate that diffusion models can also generate high-performing neural network parameters. Our approach is simple, utilizing an autoencoder and a standard latent diffusion model. The autoencoder extracts latent representations of a subset of the trained network parameters. A diffusion model is then trained to synthesize these latent parameter representations from random noise. It then generates new representations that are passed through the autoencoder's decoder, whose outputs are ready to use as new subsets of network parameters. Across various architectures and datasets, our diffusion process consistently generates models of comparable or improved performance over trained networks, with minimal additional cost. Notably, we empirically find that the generated models perform differently with the trained networks. Our results encourage more exploration on the versatile use of diffusion models.

Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.

Sparse Autoencoders (SAEs) have shown promise in improving the interpretability of neural network activations, but can learn features that are not features of the input, limiting their effectiveness. We propose Mutual Feature Regularization (MFR), a regularization technique for improving feature learning by encouraging SAEs trained in parallel to learn similar features. We motivate MFR by showing that features learned by multiple SAEs are more likely to correlate with features of the input. By training on synthetic data with known features of the input, we show that MFR can help SAEs learn those features, as we can directly compare the features learned by the SAE with the input features for the synthetic data. We then scale MFR to SAEs that are trained to denoise electroencephalography (EEG) data and SAEs that are trained to reconstruct GPT-2 Small activations. We show that MFR can improve the reconstruction loss of SAEs by up to 21.21\% on GPT-2 Small, and 6.67\% on EEG data. Our results suggest that the similarity between features learned by different SAEs can be leveraged to improve SAE training, thereby enhancing performance and the usefulness of SAEs for model interpretability.

Neural fields excel in computer vision and robotics due to their ability to understand the 3D visual world such as inferring semantics, geometry, and dynamics. Given the capabilities of neural fields in densely representing a 3D scene from 2D images, we ask the question: Can we scale their self-supervised pretraining, specifically using masked autoencoders, to generate effective 3D representations from posed RGB images. Owing to the astounding success of extending transformers to novel data modalities, we employ standard 3D Vision Transformers to suit the unique formulation of NeRFs. We leverage NeRF's volumetric grid as a dense input to the transformer, contrasting it with other 3D representations such as pointclouds where the information density can be uneven, and the representation is irregular. Due to the difficulty of applying masked autoencoders to an implicit representation, such as NeRF, we opt for extracting an explicit representation that canonicalizes scenes across domains by employing the camera trajectory for sampling. Our goal is made possible by masking random patches from NeRF's radiance and density grid and employing a standard 3D Swin Transformer to reconstruct the masked patches. In doing so, the model can learn the semantic and spatial structure of complete scenes. We pretrain this representation at scale on our proposed curated posed-RGB data, totaling over 1.8 million images. Once pretrained, the encoder is used for effective 3D transfer learning. Our novel self-supervised pretraining for NeRFs, NeRF-MAE, scales remarkably well and improves performance on various challenging 3D tasks. Utilizing unlabeled posed 2D data for pretraining, NeRF-MAE significantly outperforms self-supervised 3D pretraining and NeRF scene understanding baselines on Front3D and ScanNet datasets with an absolute performance improvement of over 20% AP50 and 8% AP25 for 3D object detection.

Generative models in vision have seen rapid progress due to algorithmic improvements and the availability of high-quality image datasets. In this paper, we offer contributions in both these areas to enable similar progress in audio modeling. First, we detail a powerful new WaveNet-style autoencoder model that conditions an autoregressive decoder on temporal codes learned from the raw audio waveform. Second, we introduce NSynth, a large-scale and high-quality dataset of musical notes that is an order of magnitude larger than comparable public datasets. Using NSynth, we demonstrate improved qualitative and quantitative performance of the WaveNet autoencoder over a well-tuned spectral autoencoder baseline. Finally, we show that the model learns a manifold of embeddings that allows for morphing between instruments, meaningfully interpolating in timbre to create new types of sounds that are realistic and expressive.

We propose split-brain autoencoders, a straightforward modification of the traditional autoencoder architecture, for unsupervised representation learning. The method adds a split to the network, resulting in two disjoint sub-networks. Each sub-network is trained to perform a difficult task -- predicting one subset of the data channels from another. Together, the sub-networks extract features from the entire input signal. By forcing the network to solve cross-channel prediction tasks, we induce a representation within the network which transfers well to other, unseen tasks. This method achieves state-of-the-art performance on several large-scale transfer learning benchmarks.

Generative autoencoders offer a promising approach for controllable text generation by leveraging their latent sentence representations. However, current models struggle to maintain coherent latent spaces required to perform meaningful text manipulations via latent vector operations. Specifically, we demonstrate by example that neural encoders do not necessarily map similar sentences to nearby latent vectors. A theoretical explanation for this phenomenon establishes that high capacity autoencoders can learn an arbitrary mapping between sequences and associated latent representations. To remedy this issue, we augment adversarial autoencoders with a denoising objective where original sentences are reconstructed from perturbed versions (referred to as DAAE). We prove that this simple modification guides the latent space geometry of the resulting model by encouraging the encoder to map similar texts to similar latent representations. In empirical comparisons with various types of autoencoders, our model provides the best trade-off between generation quality and reconstruction capacity. Moreover, the improved geometry of the DAAE latent space enables zero-shot text style transfer via simple latent vector arithmetic.

Neural networks transform high-dimensional data into compact, structured representations, often modeled as elements of a lower dimensional latent space. In this paper, we present an alternative interpretation of neural models as dynamical systems acting on the latent manifold. Specifically, we show that autoencoder models implicitly define a latent vector field on the manifold, derived by iteratively applying the encoding-decoding map, without any additional training. We observe that standard training procedures introduce inductive biases that lead to the emergence of attractor points within this vector field. Drawing on this insight, we propose to leverage the vector field as a representation for the network, providing a novel tool to analyze the properties of the model and the data. This representation enables to: (i) analyze the generalization and memorization regimes of neural models, even throughout training; (ii) extract prior knowledge encoded in the network's parameters from the attractors, without requiring any input data; (iii) identify out-of-distribution samples from their trajectories in the vector field. We further validate our approach on vision foundation models, showcasing the applicability and effectiveness of our method in real-world scenarios.

Designing neural networks typically relies on manual trial and error or a neural architecture search (NAS) followed by weight training. The former is time-consuming and labor-intensive, while the latter often discretizes architecture search and weight optimization. In this paper, we propose a fundamentally different approach that simultaneously optimizes both the architecture and the weights of a neural network. Our framework first trains a universal multi-scale autoencoder that embeds both architectural and parametric information into a continuous latent space, where functionally similar neural networks are mapped closer together. Given a dataset, we then randomly initialize a point in the embedding space and update it via gradient descent to obtain the optimal neural network, jointly optimizing its structure and weights. The optimization process incorporates sparsity and compactness penalties to promote efficient models. Experiments on synthetic regression tasks demonstrate that our method effectively discovers sparse and compact neural networks with strong performance.

This paper introduces an efficient and robust method for discovering interpretable circuits in large language models using discrete sparse autoencoders. Our approach addresses key limitations of existing techniques, namely computational complexity and sensitivity to hyperparameters. We propose training sparse autoencoders on carefully designed positive and negative examples, where the model can only correctly predict the next token for the positive examples. We hypothesise that learned representations of attention head outputs will signal when a head is engaged in specific computations. By discretising the learned representations into integer codes and measuring the overlap between codes unique to positive examples for each head, we enable direct identification of attention heads involved in circuits without the need for expensive ablations or architectural modifications. On three well-studied tasks - indirect object identification, greater-than comparisons, and docstring completion - the proposed method achieves higher precision and recall in recovering ground-truth circuits compared to state-of-the-art baselines, while reducing runtime from hours to seconds. Notably, we require only 5-10 text examples for each task to learn robust representations. Our findings highlight the promise of discrete sparse autoencoders for scalable and efficient mechanistic interpretability, offering a new direction for analysing the inner workings of large language models.

In recent years, exploiting the domain-specific underlying structure of data and its generative factors for representation learning has shown success in various use-case agnostic applications. However, the diversity and complexity of tabular data have made it challenging to represent these structures in a latent space through multi-dimensional vectors. We design an autoencoder-based framework for building general purpose embeddings, we assess the performance of different autoencoder architectures, and show simpler models outperform complex ones in embedding highly complex tabular data. We apply our framework to produce plug-and-play, rich, and anonymized embeddings representing AWS customers for usage in any model, saving up to 45% of development time, and observe significant improvements in downstream models. Moreover, we propose a significant improvement to the calculation of reconstruction loss for multi-layer contractive autoencoders (CAE) by calculating the Jacobian of the entire encoder leading to a 15% improvement in reconstruction quality when compared to a stacked CAE.

Deep learning models have revolutionized various domains, with Multi-Layer Perceptrons (MLPs) being a cornerstone for tasks like data regression and image classification. However, a recent study has introduced Kolmogorov-Arnold Networks (KANs) as promising alternatives to MLPs, leveraging activation functions placed on edges rather than nodes. This structural shift aligns KANs closely with the Kolmogorov-Arnold representation theorem, potentially enhancing both model accuracy and interpretability. In this study, we explore the efficacy of KANs in the context of data representation via autoencoders, comparing their performance with traditional Convolutional Neural Networks (CNNs) on the MNIST, SVHN, and CIFAR-10 datasets. Our results demonstrate that KAN-based autoencoders achieve competitive performance in terms of reconstruction accuracy, thereby suggesting their viability as effective tools in data analysis tasks.

Recently, it has been observed that when representations are learnt in a way that encourages sparsity, improved performance is obtained on classification tasks. These methods involve combinations of activation functions, sampling steps and different kinds of penalties. To investigate the effectiveness of sparsity by itself, we propose the k-sparse autoencoder, which is an autoencoder with linear activation function, where in hidden layers only the k highest activities are kept. When applied to the MNIST and NORB datasets, we find that this method achieves better classification results than denoising autoencoders, networks trained with dropout, and RBMs. k-sparse autoencoders are simple to train and the encoding stage is very fast, making them well-suited to large problem sizes, where conventional sparse coding algorithms cannot be applied.

This paper proposes a new type of generative model that is able to quickly learn a latent representation without an encoder. This is achieved using empirical Bayes to calculate the expectation of the posterior, which is implemented by initialising a latent vector with zeros, then using the gradient of the log-likelihood of the data with respect to this zero vector as new latent points. The approach has similar characteristics to autoencoders, but with a simpler architecture, and is demonstrated in a variational autoencoder equivalent that permits sampling. This also allows implicit representation networks to learn a space of implicit functions without requiring a hypernetwork, retaining their representation advantages across datasets. The experiments show that the proposed method converges faster, with significantly lower reconstruction error than autoencoders, while requiring half the parameters.

Deep neural networks are widely used for classification. These deep models often suffer from a lack of interpretability -- they are particularly difficult to understand because of their non-linear nature. As a result, neural networks are often treated as "black box" models, and in the past, have been trained purely to optimize the accuracy of predictions. In this work, we create a novel network architecture for deep learning that naturally explains its own reasoning for each prediction. This architecture contains an autoencoder and a special prototype layer, where each unit of that layer stores a weight vector that resembles an encoded training input. The encoder of the autoencoder allows us to do comparisons within the latent space, while the decoder allows us to visualize the learned prototypes. The training objective has four terms: an accuracy term, a term that encourages every prototype to be similar to at least one encoded input, a term that encourages every encoded input to be close to at least one prototype, and a term that encourages faithful reconstruction by the autoencoder. The distances computed in the prototype layer are used as part of the classification process. Since the prototypes are learned during training, the learned network naturally comes with explanations for each prediction, and the explanations are loyal to what the network actually computes.

This paper studies a conceptually simple extension of Masked Autoencoders (MAE) to spatiotemporal representation learning from videos. We randomly mask out spacetime patches in videos and learn an autoencoder to reconstruct them in pixels. Interestingly, we show that our MAE method can learn strong representations with almost no inductive bias on spacetime (only except for patch and positional embeddings), and spacetime-agnostic random masking performs the best. We observe that the optimal masking ratio is as high as 90% (vs. 75% on images), supporting the hypothesis that this ratio is related to information redundancy of the data. A high masking ratio leads to a large speedup, e.g., > 4x in wall-clock time or even more. We report competitive results on several challenging video datasets using vanilla Vision Transformers. We observe that MAE can outperform supervised pre-training by large margins. We further report encouraging results of training on real-world, uncurated Instagram data. Our study suggests that the general framework of masked autoencoding (BERT, MAE, etc.) can be a unified methodology for representation learning with minimal domain knowledge.

Variational autoencoders provide a principled framework for learning deep latent-variable models and corresponding inference models. In this work, we provide an introduction to variational autoencoders and some important extensions.

Dense retrieval requires high-quality text sequence embeddings to support effective search in the representation space. Autoencoder-based language models are appealing in dense retrieval as they train the encoder to output high-quality embedding that can reconstruct the input texts. However, in this paper, we provide theoretical analyses and show empirically that an autoencoder language model with a low reconstruction loss may not provide good sequence representations because the decoder may take shortcuts by exploiting language patterns. To address this, we propose a new self-learning method that pre-trains the autoencoder using a weak decoder, with restricted capacity and attention flexibility to push the encoder to provide better text representations. Our experiments on web search, news recommendation, and open domain question answering show that our pre-trained model significantly boosts the effectiveness and few-shot ability of dense retrieval models. Our code is available at https://github.com/microsoft/SEED-Encoder/.

Sparse Autoencoders (SAEs) have emerged as a promising tool for interpreting neural networks by decomposing their activations into sparse sets of human-interpretable features. Recent work has introduced multiple SAE variants and successfully scaled them to frontier models. Despite much excitement, a growing number of negative results in downstream tasks casts doubt on whether SAEs recover meaningful features. To directly investigate this, we perform two complementary evaluations. On a synthetic setup with known ground-truth features, we demonstrate that SAEs recover only 9% of true features despite achieving 71% explained variance, showing that they fail at their core task even when reconstruction is strong. To evaluate SAEs on real activations, we introduce three baselines that constrain SAE feature directions or their activation patterns to random values. Through extensive experiments across multiple SAE architectures, we show that our baselines match fully-trained SAEs in interpretability (0.87 vs 0.90), sparse probing (0.69 vs 0.72), and causal editing (0.73 vs 0.72). Together, these results suggest that SAEs in their current state do not reliably decompose models' internal mechanisms.

Sparse Autoencoders (SAEs) have emerged as a useful tool for interpreting the internal representations of neural networks. However, naively optimising SAEs for reconstruction loss and sparsity results in a preference for SAEs that are extremely wide and sparse. We present an information-theoretic framework for interpreting SAEs as lossy compression algorithms for communicating explanations of neural activations. We appeal to the Minimal Description Length (MDL) principle to motivate explanations of activations which are both accurate and concise. We further argue that interpretable SAEs require an additional property, "independent additivity": features should be able to be understood separately. We demonstrate an example of applying our MDL-inspired framework by training SAEs on MNIST handwritten digits and find that SAE features representing significant line segments are optimal, as opposed to SAEs with features for memorised digits from the dataset or small digit fragments. We argue that using MDL rather than sparsity may avoid potential pitfalls with naively maximising sparsity such as undesirable feature splitting and that this framework naturally suggests new hierarchical SAE architectures which provide more concise explanations.

Neural networks achieve remarkable performance through superposition: encoding multiple features as overlapping directions in activation space rather than dedicating individual neurons to each feature. This challenges interpretability, yet we lack principled methods to measure superposition. We present an information-theoretic framework measuring a neural representation's effective degrees of freedom. We apply Shannon entropy to sparse autoencoder activations to compute the number of effective features as the minimum neurons needed for interference-free encoding. Equivalently, this measures how many "virtual neurons" the network simulates through superposition. When networks encode more effective features than actual neurons, they must accept interference as the price of compression. Our metric strongly correlates with ground truth in toy models, detects minimal superposition in algorithmic tasks, and reveals systematic reduction under dropout. Layer-wise patterns mirror intrinsic dimensionality studies on Pythia-70M. The metric also captures developmental dynamics, detecting sharp feature consolidation during grokking. Surprisingly, adversarial training can increase effective features while improving robustness, contradicting the hypothesis that superposition causes vulnerability. Instead, the effect depends on task complexity and network capacity: simple tasks with ample capacity allow feature expansion (abundance regime), while complex tasks or limited capacity force reduction (scarcity regime). By defining superposition as lossy compression, this work enables principled measurement of how neural networks organize information under computational constraints, connecting superposition to adversarial robustness.

Sparse autoencoders (SAEs) are used to decompose neural network activations into human-interpretable features. Typically, features learned by a single SAE are used for downstream applications. However, it has recently been shown that SAEs trained with different initial weights can learn different features, demonstrating that a single SAE captures only a limited subset of features that can be extracted from the activation space. Motivated by this limitation, we propose to ensemble multiple SAEs through naive bagging and boosting. Specifically, SAEs trained with different weight initializations are ensembled in naive bagging, whereas SAEs sequentially trained to minimize the residual error are ensembled in boosting. We evaluate our ensemble approaches with three settings of language models and SAE architectures. Our empirical results demonstrate that ensembling SAEs can improve the reconstruction of language model activations, diversity of features, and SAE stability. Furthermore, ensembling SAEs performs better than applying a single SAE on downstream tasks such as concept detection and spurious correlation removal, showing improved practical utility.

Despite progress in training neural networks for lossy image compression, current approaches fail to maintain both perceptual quality and abstract features at very low bitrates. Encouraged by recent success in learning discrete representations with Vector Quantized Variational Autoencoders (VQ-VAEs), we motivate the use of a hierarchy of VQ-VAEs to attain high factors of compression. We show that the combination of stochastic quantization and hierarchical latent structure aids likelihood-based image compression. This leads us to introduce a novel objective for training hierarchical VQ-VAEs. Our resulting scheme produces a Markovian series of latent variables that reconstruct images of high-perceptual quality which retain semantically meaningful features. We provide qualitative and quantitative evaluations on the CelebA and MNIST datasets.

Representation learning seeks to expose certain aspects of observed data in a learned representation that's amenable to downstream tasks like classification. For instance, a good representation for 2D images might be one that describes only global structure and discards information about detailed texture. In this paper, we present a simple but principled method to learn such global representations by combining Variational Autoencoder (VAE) with neural autoregressive models such as RNN, MADE and PixelRNN/CNN. Our proposed VAE model allows us to have control over what the global latent code can learn and , by designing the architecture accordingly, we can force the global latent code to discard irrelevant information such as texture in 2D images, and hence the VAE only "autoencodes" data in a lossy fashion. In addition, by leveraging autoregressive models as both prior distribution p(z) and decoding distribution p(x|z), we can greatly improve generative modeling performance of VAEs, achieving new state-of-the-art results on MNIST, OMNIGLOT and Caltech-101 Silhouettes density estimation tasks.

Sparse Autoencoders (SAEs) are powerful tools for interpreting neural representations, yet their use in audio remains underexplored. We train SAEs across all encoder layers of Whisper and HuBERT, provide an extensive evaluation of their stability, interpretability, and show their practical utility. Over 50% of the features remain consistent across random seeds, and reconstruction quality is preserved. SAE features capture general acoustic and semantic information as well as specific events, including environmental noises and paralinguistic sounds (e.g. laughter, whispering) and disentangle them effectively, requiring removal of only 19-27% of features to erase a concept. Feature steering reduces Whisper's false speech detections by 70% with negligible WER increase, demonstrating real-world applicability. Finally, we find SAE features correlated with human EEG activity during speech perception, indicating alignment with human neural processing. The code and checkpoints are available at https://github.com/audiosae/audiosae_demo.

Sparse autoencoders (SAEs) are a technique for sparse decomposition of neural network activations into human-interpretable features. However, current SAEs suffer from feature absorption, where specialized features capture instances of general features creating representation holes, and feature composition, where independent features merge into composite representations. In this work, we introduce Orthogonal SAE (OrtSAE), a novel approach aimed to mitigate these issues by enforcing orthogonality between the learned features. By implementing a new training procedure that penalizes high pairwise cosine similarity between SAE features, OrtSAE promotes the development of disentangled features while scaling linearly with the SAE size, avoiding significant computational overhead. We train OrtSAE across different models and layers and compare it with other methods. We find that OrtSAE discovers 9% more distinct features, reduces feature absorption (by 65%) and composition (by 15%), improves performance on spurious correlation removal (+6%), and achieves on-par performance for other downstream tasks compared to traditional SAEs.

One of the roadblocks to a better understanding of neural networks' internals is polysemanticity, where neurons appear to activate in multiple, semantically distinct contexts. Polysemanticity prevents us from identifying concise, human-understandable explanations for what neural networks are doing internally. One hypothesised cause of polysemanticity is superposition, where neural networks represent more features than they have neurons by assigning features to an overcomplete set of directions in activation space, rather than to individual neurons. Here, we attempt to identify those directions, using sparse autoencoders to reconstruct the internal activations of a language model. These autoencoders learn sets of sparsely activating features that are more interpretable and monosemantic than directions identified by alternative approaches, where interpretability is measured by automated methods. Ablating these features enables precise model editing, for example, by removing capabilities such as pronoun prediction, while disrupting model behaviour less than prior techniques. This work indicates that it is possible to resolve superposition in language models using a scalable, unsupervised method. Our method may serve as a foundation for future mechanistic interpretability work, which we hope will enable greater model transparency and steerability.

Sparse autoencoders (SAEs) have emerged as a promising method for interpreting neural network representations by decomposing activations into sparse combinations of dictionary atoms. However, SAEs assume that features combine additively through linear reconstruction, an assumption that cannot capture compositional structure: linear models cannot distinguish whether "Starbucks" arises from the composition of "star" and "coffee" features or merely their co-occurrence. This forces SAEs to allocate monolithic features for compound concepts rather than decomposing them into interpretable constituents. We introduce PolySAE, which extends the SAE decoder with higher-order terms to model feature interactions while preserving the linear encoder essential for interpretability. Through low-rank tensor factorization on a shared projection subspace, PolySAE captures pairwise and triple feature interactions with small parameter overhead (3% on GPT2). Across four language models and three SAE variants, PolySAE achieves an average improvement of approximately 8% in probing F1 while maintaining comparable reconstruction error, and produces 2-10times larger Wasserstein distances between class-conditional feature distributions. Critically, learned interaction weights exhibit negligible correlation with co-occurrence frequency (r = 0.06 vs. r = 0.82 for SAE feature covariance), suggesting that polynomial terms capture compositional structure, such as morphological binding and phrasal composition, largely independent of surface statistics.

Sparse autoencoders (SAEs) have emerged as a powerful tool for interpreting neural networks by extracting the concepts represented in their activations. However, choosing the size of the SAE dictionary (i.e. number of learned concepts) creates a tension: as dictionary size increases to capture more relevant concepts, sparsity incentivizes features to be split or absorbed into more specific features, leaving high-level features missing or warped. We introduce Matryoshka SAEs, a novel variant that addresses these issues by simultaneously training multiple nested dictionaries of increasing size, forcing the smaller dictionaries to independently reconstruct the inputs without using the larger dictionaries. This organizes features hierarchically - the smaller dictionaries learn general concepts, while the larger dictionaries learn more specific concepts, without incentive to absorb the high-level features. We train Matryoshka SAEs on Gemma-2-2B and TinyStories and find superior performance on sparse probing and targeted concept erasure tasks, more disentangled concept representations, and reduced feature absorption. While there is a minor tradeoff with reconstruction performance, we believe Matryoshka SAEs are a superior alternative for practical tasks, as they enable training arbitrarily large SAEs while retaining interpretable features at different levels of abstraction.

Sparse autoencoders (SAEs) are a promising approach to extracting features from neural networks, enabling model interpretability as well as causal interventions on model internals. SAEs generate sparse feature representations using a sparsifying activation function that implicitly defines a set of token-feature matches. We frame the token-feature matching as a resource allocation problem constrained by a total sparsity upper bound. For example, TopK SAEs solve this allocation problem with the additional constraint that each token matches with at most k features. In TopK SAEs, the k active features per token constraint is the same across tokens, despite some tokens being more difficult to reconstruct than others. To address this limitation, we propose two novel SAE variants, Feature Choice SAEs and Mutual Choice SAEs, which each allow for a variable number of active features per token. Feature Choice SAEs solve the sparsity allocation problem under the additional constraint that each feature matches with at most m tokens. Mutual Choice SAEs solve the unrestricted allocation problem where the total sparsity budget can be allocated freely between tokens and features. Additionally, we introduce a new auxiliary loss function, aux_zipf_loss, which generalises the aux_k_loss to mitigate dead and underutilised features. Our methods result in SAEs with fewer dead features and improved reconstruction loss at equivalent sparsity levels as a result of the inherent adaptive computation. More accurate and scalable feature extraction methods provide a path towards better understanding and more precise control of foundation models.

Rapid growth of high-dimensional datasets in fields such as single-cell RNA sequencing and spatial genomics has led to unprecedented opportunities for scientific discovery, but it also presents unique computational and statistical challenges. Traditional methods struggle with geometry-aware data generation, interpolation along meaningful trajectories, and transporting populations via feasible paths. To address these issues, we introduce Geometry-Aware Generative Autoencoder (GAGA), a novel framework that combines extensible manifold learning with generative modeling. GAGA constructs a neural network embedding space that respects the intrinsic geometries discovered by manifold learning and learns a novel warped Riemannian metric on the data space. This warped metric is derived from both the points on the data manifold and negative samples off the manifold, allowing it to characterize a meaningful geometry across the entire latent space. Using this metric, GAGA can uniformly sample points on the manifold, generate points along geodesics, and interpolate between populations across the learned manifold using geodesic-guided flows. GAGA shows competitive performance in simulated and real-world datasets, including a 30% improvement over the state-of-the-art methods in single-cell population-level trajectory inference.

Sparse Autoencoders (SAEs) can efficiently identify candidate monosemantic features from pretrained neural networks for galaxy morphology. We demonstrate this on Euclid Q1 images using both supervised (Zoobot) and new self-supervised (MAE) models. Our publicly released MAE achieves superhuman image reconstruction performance. While a Principal Component Analysis (PCA) on the supervised model primarily identifies features already aligned with the Galaxy Zoo decision tree, SAEs can identify interpretable features outside of this framework. SAE features also show stronger alignment than PCA with Galaxy Zoo labels. Although challenges in interpretability remain, SAEs provide a powerful engine for discovering astrophysical phenomena beyond the confines of human-defined classification.

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 methods into SAE architectures can improve feature organization and interpretability. We introduce the Variational Sparse Autoencoder (vSAE), which replaces deterministic ReLU gating with stochastic sampling from learned Gaussian posteriors and incorporates KL divergence regularization toward a standard normal prior. Our hypothesis is that this probabilistic sampling creates dispersive pressure, causing features to organize more coherently in the latent space while avoiding overlap. We evaluate a TopK vSAE against a standard TopK SAE on Pythia-70M transformer residual stream activations using comprehensive benchmarks including SAE Bench, individual feature interpretability analysis, and global latent space visualization through t-SNE. The vSAE underperforms standard SAE across core evaluation metrics, though excels at feature independence and ablation metrics. The KL divergence term creates excessive regularization pressure that substantially reduces the fraction of living features, leading to observed performance degradation. While vSAE features demonstrate improved robustness, they exhibit many more dead features than baseline. Our findings suggest that naive application of variational methods to SAEs does not improve feature organization or interpretability.

We frame the problem of unifying representations in neural models as one of sparse model recovery and introduce a framework that extends sparse autoencoders (SAEs) to lifted spaces and infinite-dimensional function spaces, enabling mechanistic interpretability of large neural operators (NO). While the Platonic Representation Hypothesis suggests that neural networks converge to similar representations across architectures, the representational properties of neural operators remain underexplored despite their growing importance in scientific computing. We compare the inference and training dynamics of SAEs, lifted-SAE, and SAE neural operators. We highlight how lifting and operator modules introduce beneficial inductive biases, enabling faster recovery, improved recovery of smooth concepts, and robust inference across varying resolutions, a property unique to neural operators.

In recent years, the wood product industry has been facing a skilled labor shortage. The result is more frequent sudden failures, resulting in additional costs for these companies already operating in a very competitive market. Moreover, sawmills are challenging environments for machinery and sensors. Given that experienced machine operators may be able to diagnose defects or malfunctions, one possible way of assisting novice operators is through acoustic monitoring. As a step towards the automation of wood-processing equipment and decision support systems for machine operators, in this paper, we explore using a deep convolutional autoencoder for acoustic anomaly detection of wood planers on a new real-life dataset. Specifically, our convolutional autoencoder with skip connections (Skip-CAE) and our Skip-CAE transformer outperform the DCASE autoencoder baseline, one-class SVM, isolation forest and a published convolutional autoencoder architecture, respectively obtaining an area under the ROC curve of 0.846 and 0.875 on a dataset of real-factory planer sounds. Moreover, we show that adding skip connections and attention mechanism under the form of a transformer encoder-decoder helps to further improve the anomaly detection capabilities.

Sparse autoencoders (SAEs) are an unsupervised method for learning a sparse decomposition of a neural network's latent representations into seemingly interpretable features. Despite recent excitement about their potential, research applications outside of industry are limited by the high cost of training a comprehensive suite of SAEs. In this work, we introduce Gemma Scope, an open suite of JumpReLU SAEs trained on all layers and sub-layers of Gemma 2 2B and 9B and select layers of Gemma 2 27B base models. We primarily train SAEs on the Gemma 2 pre-trained models, but additionally release SAEs trained on instruction-tuned Gemma 2 9B for comparison. We evaluate the quality of each SAE on standard metrics and release these results. We hope that by releasing these SAE weights, we can help make more ambitious safety and interpretability research easier for the community. Weights and a tutorial can be found at https://huggingface.co/google/gemma-scope and an interactive demo can be found at https://www.neuronpedia.org/gemma-scope

AI led chess systems to a superhuman level, yet these systems heavily rely on black-box algorithms. This is unsustainable in ensuring transparency to the end-user, particularly when these systems are responsible for sensitive decision-making. Recent interpretability work has shown that the inner representations of Deep Neural Networks (DNNs) were fathomable and contained human-understandable concepts. Yet, these methods are seldom contextualised and are often based on a single hidden state, which makes them unable to interpret multi-step reasoning, e.g. planning. In this respect, we propose contrastive sparse autoencoders (CSAE), a novel framework for studying pairs of game trajectories. Using CSAE, we are able to extract and interpret concepts that are meaningful to the chess-agent plans. We primarily focused on a qualitative analysis of the CSAE features before proposing an automated feature taxonomy. Furthermore, to evaluate the quality of our trained CSAE, we devise sanity checks to wave spurious correlations in our results.

Sparse autoencoders (SAEs) have shown promise in extracting interpretable features from complex neural networks. We present one of the first applications of SAEs to dense text embeddings from large language models, demonstrating their effectiveness in disentangling semantic concepts. By training SAEs on embeddings of over 420,000 scientific paper abstracts from computer science and astronomy, we show that the resulting sparse representations maintain semantic fidelity while offering interpretability. We analyse these learned features, exploring their behaviour across different model capacities and introducing a novel method for identifying ``feature families'' that represent related concepts at varying levels of abstraction. To demonstrate the practical utility of our approach, we show how these interpretable features can be used to precisely steer semantic search, allowing for fine-grained control over query semantics. This work bridges the gap between the semantic richness of dense embeddings and the interpretability of sparse representations. We open source our embeddings, trained sparse autoencoders, and interpreted features, as well as a web app for exploring them.

Graph anomaly detection (GAD) has become an increasingly important task across various domains. With the rapid development of graph neural networks (GNNs), GAD methods have achieved significant performance improvements. However, fairness considerations in GAD remain largely underexplored. Indeed, GNN-based GAD models can inherit and amplify biases present in training data, potentially leading to unfair outcomes. While existing efforts have focused on developing fair GNNs, most approaches target node classification tasks, where models often rely on simple layer architectures rather than autoencoder-based structures, which are the most widely used architecturs for anomaly detection. To address fairness in autoencoder-based GAD models, we propose DisEntangled Counterfactual Adversarial Fair (DECAF)-GAD, a framework that alleviates bias while preserving GAD performance. Specifically, we introduce a structural causal model (SCM) to disentangle sensitive attributes from learned representations. Based on this causal framework, we formulate a specialized autoencoder architecture along with a fairness-guided loss function. Through extensive experiments on both synthetic and real-world datasets, we demonstrate that DECAF-GAD not only achieves competitive anomaly detection performance but also significantly enhances fairness metrics compared to baseline GAD methods. Our code is available at https://github.com/Tlhey/decaf_code.

Sparse autoencoders (SAEs) bricken2023monosemanticity,gao2024scalingevaluatingsparseautoencoders rely on dictionary learning to extract interpretable features from neural networks at scale in an unsupervised manner, with applications to representation engineering and information retrieval. SAEs are, however, computationally expensive lieberum2024gemmascopeopensparse, especially when multiple SAEs of different sizes are needed. We show that dictionary importance in vanilla SAEs follows a power law. We compare progressive coding based on subset pruning of SAEs -- to jointly training nested SAEs, or so-called {\em Matryoshka} SAEs bussmann2024learning,nabeshima2024Matryoshka -- on a language modeling task. We show Matryoshka SAEs exhibit lower reconstruction loss and recaptured language modeling loss, as well as higher representational similarity. Pruned vanilla SAEs are more interpretable, however. We discuss the origins and implications of this trade-off.

Heart diseases remain the leading cause of mortality worldwide, implying approximately 18 million deaths according to the WHO. In particular, heart failures (HF) press the healthcare industry to develop systems for their early, rapid, and effective prediction. This work presents an automatic system based on a novel framework which combines Modal Decomposition and Masked Autoencoders (MAE) to extend the application from heart disease classification to the more challenging and specific task of heart failure time prediction, not previously addressed to the best of authors' knowledge. This system comprises two stages. The first one transforms the data from a database of echocardiography video sequences into a large collection of annotated images compatible with the training phase of machine learning-based frameworks and deep learning-based ones. This stage includes the use of the Higher Order Dynamic Mode Decomposition (HODMD) algorithm for both data augmentation and feature extraction. The second stage builds and trains a Vision Transformer (ViT). MAEs based on a combined scheme of self-supervised (SSL) and supervised learning, so far barely explored in the literature about heart failure prediction, are adopted to effectively train the ViT from scratch, even with scarce databases. The designed neural network analyses in real-time images from echocardiography sequences to estimate the time of happening a heart failure. This approach demonstrates to improve prediction accuracy from scarce databases and to be superior to several established ViT and Convolutional Neural Network (CNN) architectures. The source code will be incorporated into the next version release of the ModelFLOWs-app software (https://github.com/modelflows/ModelFLOWs-app).

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 features, SAEs are particularly valuable for analyzing large-scale vision-language models (e.g., CLIP and SigLIP), which are fundamental building blocks in modern systems yet remain challenging to interpret and control. However, current SAE methods are limited by optimizing both reconstruction quality and sparsity simultaneously, as they rely on either activation suppression or rigid sparsity constraints. To this end, we introduce Matryoshka SAE (MSAE), a new architecture that learns hierarchical representations at multiple granularities simultaneously, enabling a direct optimization of both metrics without compromise. MSAE establishes a new state-of-the-art Pareto frontier between reconstruction quality and sparsity for CLIP, achieving 0.99 cosine similarity and less than 0.1 fraction of variance unexplained while maintaining ~80% sparsity. Finally, we demonstrate the utility of MSAE as a tool for interpreting and controlling CLIP by extracting over 120 semantic concepts from its representation to perform concept-based similarity search and bias analysis in downstream tasks like CelebA.

Regularization of inverse problems is of paramount importance in computational imaging. The ability of neural networks to learn efficient image representations has been recently exploited to design powerful data-driven regularizers. While state-of-the-art plug-and-play (PnP) methods rely on an implicit regularization provided by neural denoisers, alternative Bayesian approaches consider Maximum A Posteriori (MAP) estimation in the latent space of a generative model, thus with an explicit regularization. However, state-of-the-art deep generative models require a huge amount of training data compared to denoisers. Besides, their complexity hampers the optimization involved in latent MAP derivation. In this work, we first propose to use compressive autoencoders instead. These networks, which can be seen as variational autoencoders with a flexible latent prior, are smaller and easier to train than state-of-the-art generative models. As a second contribution, we introduce the Variational Bayes Latent Estimation (VBLE) algorithm, which performs latent estimation within the framework of variational inference. Thanks to a simple yet efficient parameterization of the variational posterior, VBLE allows for fast and easy (approximate) posterior sampling. Experimental results on image datasets BSD and FFHQ demonstrate that VBLE reaches similar performance as state-of-the-art PnP methods, while being able to quantify uncertainties significantly faster than other existing posterior sampling techniques. The code associated to this paper is available in https://github.com/MaudBqrd/VBLE.

Music classification and genre detection are topics in music information retrieval (MIR) that many articles have been published regarding their utilities in the modern world. However, this contribution is insufficient in non-western music, such as Iranian modal music. In this work, we have implemented several deep neural networks to recognize Iranian modal music in seven highly correlated categories. The best model, BiLGNet, which achieved 92 percent overall accuracy, uses an architecture inspired by autoencoders, including bidirectional LSTM and GRU layers. We trained the models using the Nava dataset, which includes 1786 records and up to 55 hours of music played solo by Kamanche, Tar, Setar, Reed, and Santoor (Dulcimer). We considered Multiple features such as MFCC, Chroma CENS, and Mel spectrogram as input. The results indicate that MFCC carries more valuable information for detecting Iranian modal music (Dastgah) than other sound representations. Moreover, the architecture inspired by autoencoders is robust in distinguishing highly correlated data like Dastgahs. It also shows that because of the precise order in Iranian Dastgah Music, Bidirectional Recurrent networks are more efficient than any other networks that have been implemented in this study.

This paper introduces a novel hierarchical autoencoder that maps 3D models into a highly compressed latent space. The hierarchical autoencoder is specifically designed to tackle the challenges arising from large-scale datasets and generative modeling using diffusion. Different from previous approaches that only work on a regular image or volume grid, our hierarchical autoencoder operates on unordered sets of vectors. Each level of the autoencoder controls different geometric levels of detail. We show that the model can be used to represent a wide range of 3D models while faithfully representing high-resolution geometry details. The training of the new architecture takes 0.70x time and 0.58x memory compared to the baseline. We also explore how the new representation can be used for generative modeling. Specifically, we propose a cascaded diffusion framework where each stage is conditioned on the previous stage. Our design extends existing cascaded designs for image and volume grids to vector sets.

Stability guarantees are crucial when ensuring a fully autonomous robot does not take undesirable or potentially harmful actions. Unfortunately, global stability guarantees are hard to provide in dynamical systems learned from data, especially when the learned dynamics are governed by neural networks. We propose a novel methodology to learn neural contractive dynamical systems, where our neural architecture ensures contraction, and hence, global stability. To efficiently scale the method to high-dimensional dynamical systems, we develop a variant of the variational autoencoder that learns dynamics in a low-dimensional latent representation space while retaining contractive stability after decoding. We further extend our approach to learning contractive systems on the Lie group of rotations to account for full-pose end-effector dynamic motions. The result is the first highly flexible learning architecture that provides contractive stability guarantees with capability to perform obstacle avoidance. Empirically, we demonstrate that our approach encodes the desired dynamics more accurately than the current state-of-the-art, which provides less strong stability guarantees.

Vision Transformer (ViT) has become one of the most popular neural architectures due to its great scalability, computational efficiency, and compelling performance in many vision tasks. However, ViT has shown inferior performance to Convolutional Neural Network (CNN) on medical tasks due to its data-hungry nature and the lack of annotated medical data. In this paper, we pre-train ViTs on 266,340 chest X-rays using Masked Autoencoders (MAE) which reconstruct missing pixels from a small part of each image. For comparison, CNNs are also pre-trained on the same 266,340 X-rays using advanced self-supervised methods (e.g., MoCo v2). The results show that our pre-trained ViT performs comparably (sometimes better) to the state-of-the-art CNN (DenseNet-121) for multi-label thorax disease classification. This performance is attributed to the strong recipes extracted from our empirical studies for pre-training and fine-tuning ViT. The pre-training recipe signifies that medical reconstruction requires a much smaller proportion of an image (10% vs. 25%) and a more moderate random resized crop range (0.5~1.0 vs. 0.2~1.0) compared with natural imaging. Furthermore, we remark that in-domain transfer learning is preferred whenever possible. The fine-tuning recipe discloses that layer-wise LR decay, RandAug magnitude, and DropPath rate are significant factors to consider. We hope that this study can direct future research on the application of Transformers to a larger variety of medical imaging tasks.

We introduce a novel masked graph autoencoder (MGAE) framework to perform effective learning on graph structure data. Taking insights from self-supervised learning, we randomly mask a large proportion of edges and try to reconstruct these missing edges during training. MGAE has two core designs. First, we find that masking a high ratio of the input graph structure, e.g., 70%, yields a nontrivial and meaningful self-supervisory task that benefits downstream applications. Second, we employ a graph neural network (GNN) as an encoder to perform message propagation on the partially-masked graph. To reconstruct the large number of masked edges, a tailored cross-correlation decoder is proposed. It could capture the cross-correlation between the head and tail nodes of anchor edge in multi-granularity. Coupling these two designs enables MGAE to be trained efficiently and effectively. Extensive experiments on multiple open datasets (Planetoid and OGB benchmarks) demonstrate that MGAE generally performs better than state-of-the-art unsupervised learning competitors on link prediction and node classification.

Variational AutoEncoders (VAEs) are powerful generative models that merge elements from statistics and information theory with the flexibility offered by deep neural networks to efficiently solve the generation problem for high dimensional data. The key insight of VAEs is to learn the latent distribution of data in such a way that new meaningful samples can be generated from it. This approach led to tremendous research and variations in the architectural design of VAEs, nourishing the recent field of research known as unsupervised representation learning. In this article, we provide a comparative evaluation of some of the most successful, recent variations of VAEs. We particularly focus the analysis on the energetic efficiency of the different models, in the spirit of the so called Green AI, aiming both to reduce the carbon footprint and the financial cost of generative techniques. For each architecture we provide its mathematical formulation, the ideas underlying its design, a detailed model description, a running implementation and quantitative results.

Sparse autoencoders provide a promising unsupervised approach for extracting interpretable features from a language model by reconstructing activations from a sparse bottleneck layer. Since language models learn many concepts, autoencoders need to be very large to recover all relevant features. However, studying the properties of autoencoder scaling is difficult due to the need to balance reconstruction and sparsity objectives and the presence of dead latents. We propose using k-sparse autoencoders [Makhzani and Frey, 2013] to directly control sparsity, simplifying tuning and improving the reconstruction-sparsity frontier. Additionally, we find modifications that result in few dead latents, even at the largest scales we tried. Using these techniques, we find clean scaling laws with respect to autoencoder size and sparsity. We also introduce several new metrics for evaluating feature quality based on the recovery of hypothesized features, the explainability of activation patterns, and the sparsity of downstream effects. These metrics all generally improve with autoencoder size. To demonstrate the scalability of our approach, we train a 16 million latent autoencoder on GPT-4 activations for 40 billion tokens. We release training code and autoencoders for open-source models, as well as a visualizer.

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning. Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.

Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how self-supervised deep learning approaches scale when training larger models on larger microscopy datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised baselines. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 93-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised baseline at inferring known biological relationships curated from public databases. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.

Structured variational autoencoders (SVAEs) combine probabilistic graphical model priors on latent variables, deep neural networks to link latent variables to observed data, and structure-exploiting algorithms for approximate posterior inference. These models are particularly appealing for sequential data, where the prior can capture temporal dependencies. However, despite their conceptual elegance, SVAEs have proven difficult to implement, and more general approaches have been favored in practice. Here, we revisit SVAEs using modern machine learning tools and demonstrate their advantages over more general alternatives in terms of both accuracy and efficiency. First, we develop a modern implementation for hardware acceleration, parallelization, and automatic differentiation of the message passing algorithms at the core of the SVAE. Second, we show that by exploiting structure in the prior, the SVAE learns more accurate models and posterior distributions, which translate into improved performance on prediction tasks. Third, we show how the SVAE can naturally handle missing data, and we leverage this ability to develop a novel, self-supervised training approach. Altogether, these results show that the time is ripe to revisit structured variational autoencoders.

We develop data-driven methods incorporating geometric and topological information to learn parsimonious representations of nonlinear dynamics from observations. The approaches learn nonlinear state-space models of the dynamics for general manifold latent spaces using training strategies related to Variational Autoencoders (VAEs). Our methods are referred to as Geometric Dynamic (GD) Variational Autoencoders (GD-VAEs). We learn encoders and decoders for the system states and evolution based on deep neural network architectures that include general Multilayer Perceptrons (MLPs), Convolutional Neural Networks (CNNs), and other architectures. Motivated by problems arising in parameterized PDEs and physics, we investigate the performance of our methods on tasks for learning reduced dimensional representations of the nonlinear Burgers Equations, Constrained Mechanical Systems, and spatial fields of Reaction-Diffusion Systems. GD-VAEs provide methods that can be used to obtain representations in manifold latent spaces for diverse learning tasks involving dynamics.

Although mission-critical applications require the use of deep neural networks (DNNs), their continuous execution at mobile devices results in a significant increase in energy consumption. While edge offloading can decrease energy consumption, erratic patterns in channel quality, network and edge server load can lead to severe disruption of the system's key operations. An alternative approach, called split computing, generates compressed representations within the model (called "bottlenecks"), to reduce bandwidth usage and energy consumption. Prior work has proposed approaches that introduce additional layers, to the detriment of energy consumption and latency. For this reason, we propose a new framework called BottleFit, which, in addition to targeted DNN architecture modifications, includes a novel training strategy to achieve high accuracy even with strong compression rates. We apply BottleFit on cutting-edge DNN models in image classification, and show that BottleFit achieves 77.1% data compression with up to 0.6% accuracy loss on ImageNet dataset, while state of the art such as SPINN loses up to 6% in accuracy. We experimentally measure the power consumption and latency of an image classification application running on an NVIDIA Jetson Nano board (GPU-based) and a Raspberry PI board (GPU-less). We show that BottleFit decreases power consumption and latency respectively by up to 49% and 89% with respect to (w.r.t.) local computing and by 37% and 55% w.r.t. edge offloading. We also compare BottleFit with state-of-the-art autoencoders-based approaches, and show that (i) BottleFit reduces power consumption and execution time respectively by up to 54% and 44% on the Jetson and 40% and 62% on Raspberry PI; (ii) the size of the head model executed on the mobile device is 83 times smaller. We publish the code repository for reproducibility of the results in this study.

We extend variational autoencoders (VAEs) to collaborative filtering for implicit feedback. This non-linear probabilistic model enables us to go beyond the limited modeling capacity of linear factor models which still largely dominate collaborative filtering research.We introduce a generative model with multinomial likelihood and use Bayesian inference for parameter estimation. Despite widespread use in language modeling and economics, the multinomial likelihood receives less attention in the recommender systems literature. We introduce a different regularization parameter for the learning objective, which proves to be crucial for achieving competitive performance. Remarkably, there is an efficient way to tune the parameter using annealing. The resulting model and learning algorithm has information-theoretic connections to maximum entropy discrimination and the information bottleneck principle. Empirically, we show that the proposed approach significantly outperforms several state-of-the-art baselines, including two recently-proposed neural network approaches, on several real-world datasets. We also provide extended experiments comparing the multinomial likelihood with other commonly used likelihood functions in the latent factor collaborative filtering literature and show favorable results. Finally, we identify the pros and cons of employing a principled Bayesian inference approach and characterize settings where it provides the most significant improvements.

Variational Autoencoders (VAEs) have been a pioneering force in the realm of deep generative models. Amongst its legions of progenies, Wasserstein Autoencoders (WAEs) stand out in particular due to the dual offering of heightened generative quality and a strong theoretical backbone. WAEs consist of an encoding and a decoding network forming a bottleneck with the prime objective of generating new samples resembling the ones it was catered to. In the process, they aim to achieve a target latent representation of the encoded data. Our work is an attempt to offer a theoretical understanding of the machinery behind WAEs. From a statistical viewpoint, we pose the problem as concurrent density estimation tasks based on neural network-induced transformations. This allows us to establish deterministic upper bounds on the realized errors WAEs commit. We also analyze the propagation of these stochastic errors in the presence of adversaries. As a result, both the large sample properties of the reconstructed distribution and the resilience of WAE models are explored.

This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does not require computationally expensive higher-order representations in intermediate layers while it still achieves competitive or better performance. In addition, whereas existing methods are limited to equivariance on 3 dimensional spaces, our model is easily scaled to higher-dimensional spaces. We demonstrate the effectiveness of our method on dynamical systems modelling, representation learning in graph autoencoders and predicting molecular properties.

In this paper, we adapt triplet neural networks (TNNs) to a regression task, music emotion prediction. Since TNNs were initially introduced for classification, and not for regression, we propose a mechanism that allows them to provide meaningful low dimensional representations for regression tasks. We then use these new representations as the input for regression algorithms such as support vector machines and gradient boosting machines. To demonstrate the TNNs' effectiveness at creating meaningful representations, we compare them to different dimensionality reduction methods on music emotion prediction, i.e., predicting valence and arousal values from musical audio signals. Our results on the DEAM dataset show that by using TNNs we achieve 90% feature dimensionality reduction with a 9% improvement in valence prediction and 4% improvement in arousal prediction with respect to our baseline models (without TNN). Our TNN method outperforms other dimensionality reduction methods such as principal component analysis (PCA) and autoencoders (AE). This shows that, in addition to providing a compact latent space representation of audio features, the proposed approach has a higher performance than the baseline models.

Diffusion probabilistic models (DPMs) have become the state-of-the-art in high-quality image generation. However, DPMs have an arbitrary noisy latent space with no interpretable or controllable semantics. Although there has been significant research effort to improve image sample quality, there is little work on representation-controlled generation using diffusion models. Specifically, causal modeling and controllable counterfactual generation using DPMs is an underexplored area. In this work, we propose CausalDiffAE, a diffusion-based causal representation learning framework to enable counterfactual generation according to a specified causal model. Our key idea is to use an encoder to extract high-level semantically meaningful causal variables from high-dimensional data and model stochastic variation using reverse diffusion. We propose a causal encoding mechanism that maps high-dimensional data to causally related latent factors and parameterize the causal mechanisms among latent factors using neural networks. To enforce the disentanglement of causal variables, we formulate a variational objective and leverage auxiliary label information in a prior to regularize the latent space. We propose a DDIM-based counterfactual generation procedure subject to do-interventions. Finally, to address the limited label supervision scenario, we also study the application of CausalDiffAE when a part of the training data is unlabeled, which also enables granular control over the strength of interventions in generating counterfactuals during inference. We empirically show that CausalDiffAE learns a disentangled latent space and is capable of generating high-quality counterfactual images.

Deep generative models applied to audio have improved by a large margin the state-of-the-art in many speech and music related tasks. However, as raw waveform modelling remains an inherently difficult task, audio generative models are either computationally intensive, rely on low sampling rates, are complicated to control or restrict the nature of possible signals. Among those models, Variational AutoEncoders (VAE) give control over the generation by exposing latent variables, although they usually suffer from low synthesis quality. In this paper, we introduce a Realtime Audio Variational autoEncoder (RAVE) allowing both fast and high-quality audio waveform synthesis. We introduce a novel two-stage training procedure, namely representation learning and adversarial fine-tuning. We show that using a post-training analysis of the latent space allows a direct control between the reconstruction fidelity and the representation compactness. By leveraging a multi-band decomposition of the raw waveform, we show that our model is the first able to generate 48kHz audio signals, while simultaneously running 20 times faster than real-time on a standard laptop CPU. We evaluate synthesis quality using both quantitative and qualitative subjective experiments and show the superiority of our approach compared to existing models. Finally, we present applications of our model for timbre transfer and signal compression. All of our source code and audio examples are publicly available.

Integrating physics models within machine learning models holds considerable promise toward learning robust models with improved interpretability and abilities to extrapolate. In this work, we focus on the integration of incomplete physics models into deep generative models. In particular, we introduce an architecture of variational autoencoders (VAEs) in which a part of the latent space is grounded by physics. A key technical challenge is to strike a balance between the incomplete physics and trainable components such as neural networks for ensuring that the physics part is used in a meaningful manner. To this end, we propose a regularized learning method that controls the effect of the trainable components and preserves the semantics of the physics-based latent variables as intended. We not only demonstrate generative performance improvements over a set of synthetic and real-world datasets, but we also show that we learn robust models that can consistently extrapolate beyond the training distribution in a meaningful manner. Moreover, we show that we can control the generative process in an interpretable manner.

Recently, Neural Topic Models (NTM), inspired by variational autoencoders, have attracted a lot of research interest; however, these methods have limited applications in the real world due to the challenge of incorporating human knowledge. This work presents a semi-supervised neural topic modeling method, vONTSS, which uses von Mises-Fisher (vMF) based variational autoencoders and optimal transport. When a few keywords per topic are provided, vONTSS in the semi-supervised setting generates potential topics and optimizes topic-keyword quality and topic classification. Experiments show that vONTSS outperforms existing semi-supervised topic modeling methods in classification accuracy and diversity. vONTSS also supports unsupervised topic modeling. Quantitative and qualitative experiments show that vONTSS in the unsupervised setting outperforms recent NTMs on multiple aspects: vONTSS discovers highly clustered and coherent topics on benchmark datasets. It is also much faster than the state-of-the-art weakly supervised text classification method while achieving similar classification performance. We further prove the equivalence of optimal transport loss and cross-entropy loss at the global minimum.

Sequential VAEs have been successfully considered for many high-dimensional time series modelling problems, with many variant models relying on discrete-time mechanisms such as recurrent neural networks (RNNs). On the other hand, continuous-time methods have recently gained attraction, especially in the context of irregularly-sampled time series, where they can better handle the data than discrete-time methods. One such class are Gaussian process variational autoencoders (GPVAEs), where the VAE prior is set as a Gaussian process (GP). However, a major limitation of GPVAEs is that it inherits the cubic computational cost as GPs, making it unattractive to practioners. In this work, we leverage the equivalent discrete state space representation of Markovian GPs to enable linear time GPVAE training via Kalman filtering and smoothing. We show on a variety of high-dimensional temporal and spatiotemporal tasks that our method performs favourably compared to existing approaches whilst being computationally highly scalable.

Anomaly detection in supercomputers is a very difficult problem due to the big scale of the systems and the high number of components. The current state of the art for automated anomaly detection employs Machine Learning methods or statistical regression models in a supervised fashion, meaning that the detection tool is trained to distinguish among a fixed set of behaviour classes (healthy and unhealthy states). We propose a novel approach for anomaly detection in High Performance Computing systems based on a Machine (Deep) Learning technique, namely a type of neural network called autoencoder. The key idea is to train a set of autoencoders to learn the normal (healthy) behaviour of the supercomputer nodes and, after training, use them to identify abnormal conditions. This is different from previous approaches which where based on learning the abnormal condition, for which there are much smaller datasets (since it is very hard to identify them to begin with). We test our approach on a real supercomputer equipped with a fine-grained, scalable monitoring infrastructure that can provide large amount of data to characterize the system behaviour. The results are extremely promising: after the training phase to learn the normal system behaviour, our method is capable of detecting anomalies that have never been seen before with a very good accuracy (values ranging between 88% and 96%).

Unsupervised learning with functional data is an emerging paradigm of machine learning research with applications to computer vision, climate modeling and physical systems. A natural way of modeling functional data is by learning operators between infinite dimensional spaces, leading to discretization invariant representations that scale independently of the sample grid resolution. Here we present Variational Autoencoding Neural Operators (VANO), a general strategy for making a large class of operator learning architectures act as variational autoencoders. For this purpose, we provide a novel rigorous mathematical formulation of the variational objective in function spaces for training. VANO first maps an input function to a distribution over a latent space using a parametric encoder and then decodes a sample from the latent distribution to reconstruct the input, as in classic variational autoencoders. We test VANO with different model set-ups and architecture choices for a variety of benchmarks. We start from a simple Gaussian random field where we can analytically track what the model learns and progressively transition to more challenging benchmarks including modeling phase separation in Cahn-Hilliard systems and real world satellite data for measuring Earth surface deformation.

Lossy image compression aims to represent images in as few bits as possible while maintaining fidelity to the original. Theoretical results indicate that optimizing distortion metrics such as PSNR or MS-SSIM necessarily leads to a discrepancy in the statistics of original images from those of reconstructions, in particular at low bitrates, often manifested by the blurring of the compressed images. Previous work has leveraged adversarial discriminators to improve statistical fidelity. Yet these binary discriminators adopted from generative modeling tasks may not be ideal for image compression. In this paper, we introduce a non-binary discriminator that is conditioned on quantized local image representations obtained via VQ-VAE autoencoders. Our evaluations on the CLIC2020, DIV2K and Kodak datasets show that our discriminator is more effective for jointly optimizing distortion (e.g., PSNR) and statistical fidelity (e.g., FID) than the state-of-the-art HiFiC model. On the CLIC2020 test set, we obtain the same FID as HiFiC with 30-40% fewer bits.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

The computer vision domain has greatly benefited from an abundance of data across many modalities to improve on various visual tasks. Recently, there has been a lot of focus on self-supervised pre-training methods through Masked Autoencoders (MAE) he2022masked,bachmann2022multimae, usually used as a first step before optimizing for a downstream task, such as classification or regression. This is very useful as it doesn't require any manually labeled data. In this work, we introduce Probabilistic Hyper-Graphs using Masked Autoencoders (PHG-MAE): a novel model that unifies the classical work on neural graphs leordeanu2021semi with the modern approach of masked autoencoders under a common theoretical framework. Through random masking of entire modalities, not just patches, the model samples from the distribution of hyper-edges on each forward pass. Additionally, the model adapts the standard MAE algorithm by combining pre-training and fine-tuning into a single training loop. Moreover, our approach enables the creation of inference-time ensembles which, through aggregation, boost the final prediction performance and consistency. Lastly, we show that we can apply knowledge distillation on top of the ensembles with little loss in performance, even with models that have fewer than 1M parameters. While our work mostly focuses on outdoor UAV scenes that contain multiple world interpretations and modalities, the same steps can be followed in other similar domains, such as autonomous driving or indoor robotics. In order to streamline the process of integrating external pre-trained experts for computer vision multi-modal multi-task learning (MTL) scenarios, we developed a data-pipeline software. Using this tool, we have created and released a fully-automated extension of the Dronescapes dataset. All the technical details, code and reproduction steps are publicly released.

We study the challenge of achieving theoretically grounded feature recovery using Sparse Autoencoders (SAEs) for the interpretation of Large Language Models. Existing SAE training algorithms often lack rigorous mathematical guarantees and suffer from practical limitations such as hyperparameter sensitivity and instability. To address these issues, we first propose a novel statistical framework for the feature recovery problem, which includes a new notion of feature identifiability by modeling polysemantic features as sparse mixtures of underlying monosemantic concepts. Building on this framework, we introduce a new SAE training algorithm based on ``bias adaptation'', a technique that adaptively adjusts neural network bias parameters to ensure appropriate activation sparsity. We theoretically prove that this algorithm correctly recovers all monosemantic features when input data is sampled from our proposed statistical model. Furthermore, we develop an improved empirical variant, Group Bias Adaptation (GBA), and demonstrate its superior performance against benchmark methods when applied to LLMs with up to 1.5 billion parameters. This work represents a foundational step in demystifying SAE training by providing the first SAE algorithm with theoretical recovery guarantees, thereby advancing the development of more transparent and trustworthy AI systems through enhanced mechanistic interpretability.

Major complications arise from the recent increase in the amount of high-dimensional data, including high computational costs and memory requirements. Feature selection, which identifies the most relevant and informative attributes of a dataset, has been introduced as a solution to this problem. Most of the existing feature selection methods are computationally inefficient; inefficient algorithms lead to high energy consumption, which is not desirable for devices with limited computational and energy resources. In this paper, a novel and flexible method for unsupervised feature selection is proposed. This method, named QuickSelection, introduces the strength of the neuron in sparse neural networks as a criterion to measure the feature importance. This criterion, blended with sparsely connected denoising autoencoders trained with the sparse evolutionary training procedure, derives the importance of all input features simultaneously. We implement QuickSelection in a purely sparse manner as opposed to the typical approach of using a binary mask over connections to simulate sparsity. It results in a considerable speed increase and memory reduction. When tested on several benchmark datasets, including five low-dimensional and three high-dimensional datasets, the proposed method is able to achieve the best trade-off of classification and clustering accuracy, running time, and maximum memory usage, among widely used approaches for feature selection. Besides, our proposed method requires the least amount of energy among the state-of-the-art autoencoder-based feature selection methods.

Effective treatment for rectal cancer relies on accurate lymph node metastasis (LNM) staging. However, radiological criteria based on lymph node (LN) size, shape and texture morphology have limited diagnostic accuracy. In this work, we investigate applying a Variational Autoencoder (VAE) as a feature encoder model to replace the large pre-trained Convolutional Neural Network (CNN) used in existing approaches. The motivation for using a VAE is that the generative model aims to reconstruct the images, so it directly encodes visual features and meaningful patterns across the data. This leads to a disentangled and structured latent space which can be more interpretable than a CNN. Models are deployed on an in-house MRI dataset with 168 patients who did not undergo neo-adjuvant treatment. The post-operative pathological N stage was used as the ground truth to evaluate model predictions. Our proposed model 'VAE-MLP' achieved state-of-the-art performance on the MRI dataset, with cross-validated metrics of AUC 0.86 +/- 0.05, Sensitivity 0.79 +/- 0.06, and Specificity 0.85 +/- 0.05. Code is available at: https://github.com/benkeel/Lymph_Node_Classification_MIUA.

Large Language Models (LLMs) have achieved remarkable success in natural language processing. Recent advances have led to the developing of a new class of reasoning LLMs; for example, open-source DeepSeek-R1 has achieved state-of-the-art performance by integrating deep thinking and complex reasoning. Despite these impressive capabilities, the internal reasoning mechanisms of such models remain unexplored. In this work, we employ Sparse Autoencoders (SAEs), a method to learn a sparse decomposition of latent representations of a neural network into interpretable features, to identify features that drive reasoning in the DeepSeek-R1 series of models. First, we propose an approach to extract candidate ''reasoning features'' from SAE representations. We validate these features through empirical analysis and interpretability methods, demonstrating their direct correlation with the model's reasoning abilities. Crucially, we demonstrate that steering these features systematically enhances reasoning performance, offering the first mechanistic account of reasoning in LLMs. Code available at https://github.com/AIRI-Institute/SAE-Reasoning

The autoencoder is an unsupervised learning paradigm that aims to create a compact latent representation of data by minimizing the reconstruction loss. However, it tends to overlook the fact that most data (images) are embedded in a lower-dimensional space, which is crucial for effective data representation. To address this limitation, we propose a novel approach called Low-Rank Autoencoder (LoRAE). In LoRAE, we incorporated a low-rank regularizer to adaptively reconstruct a low-dimensional latent space while preserving the basic objective of an autoencoder. This helps embed the data in a lower-dimensional space while preserving important information. It is a simple autoencoder extension that learns low-rank latent space. Theoretically, we establish a tighter error bound for our model. Empirically, our model's superiority shines through various tasks such as image generation and downstream classification. Both theoretical and practical outcomes highlight the importance of acquiring low-dimensional embeddings.

At the most basic level, pixels are the source of the visual information through which we perceive the world. Pixels contain information at all levels, ranging from low-level attributes to high-level concepts. Autoencoders represent a classical and long-standing paradigm for learning representations from pixels or other raw inputs. In this work, we demonstrate that autoencoder-based self-supervised learning remains competitive today and can produce strong representations for downstream tasks, while remaining simple, stable, and efficient. Our model, codenamed "Pixio", is an enhanced masked autoencoder (MAE) with more challenging pre-training tasks and more capable architectures. The model is trained on 2B web-crawled images with a self-curation strategy with minimal human curation. Pixio performs competitively across a wide range of downstream tasks in the wild, including monocular depth estimation (e.g., Depth Anything), feed-forward 3D reconstruction (i.e., MapAnything), semantic segmentation, and robot learning, outperforming or matching DINOv3 trained at similar scales. Our results suggest that pixel-space self-supervised learning can serve as a promising alternative and a complement to latent-space approaches.

For learned image representations, basic autoencoders often produce blurry results. Reconstruction quality can be improved by incorporating additional penalties such as adversarial (GAN) and perceptual losses. Arguably, these approaches lack a principled interpretation. Concurrently, in generative settings diffusion has demonstrated a remarkable ability to create crisp, high quality results and has solid theoretical underpinnings (from variational inference to direct study as the Fisher Divergence). Our work combines autoencoder representation learning with diffusion and is, to our knowledge, the first to demonstrate the efficacy of jointly learning a continuous encoder and decoder under a diffusion-based loss. We demonstrate that this approach yields better reconstruction quality as compared to GAN-based autoencoders while being easier to tune. We also show that the resulting representation is easier to model with a latent diffusion model as compared to the representation obtained from a state-of-the-art GAN-based loss. Since our decoder is stochastic, it can generate details not encoded in the otherwise deterministic latent representation; we therefore name our approach "Sample what you can't compress", or SWYCC for short.

We present a novel masked image modeling (MIM) approach, context autoencoder (CAE), for self-supervised representation pretraining. We pretrain an encoder by making predictions in the encoded representation space. The pretraining tasks include two tasks: masked representation prediction - predict the representations for the masked patches, and masked patch reconstruction - reconstruct the masked patches. The network is an encoder-regressor-decoder architecture: the encoder takes the visible patches as input; the regressor predicts the representations of the masked patches, which are expected to be aligned with the representations computed from the encoder, using the representations of visible patches and the positions of visible and masked patches; the decoder reconstructs the masked patches from the predicted encoded representations. The CAE design encourages the separation of learning the encoder (representation) from completing the pertaining tasks: masked representation prediction and masked patch reconstruction tasks, and making predictions in the encoded representation space empirically shows the benefit to representation learning. We demonstrate the effectiveness of our CAE through superior transfer performance in downstream tasks: semantic segmentation, object detection and instance segmentation, and classification. The code will be available at https://github.com/Atten4Vis/CAE.

Learning latent representations from long text sequences is an important first step in many natural language processing applications. Recurrent Neural Networks (RNNs) have become a cornerstone for this challenging task. However, the quality of sentences during RNN-based decoding (reconstruction) decreases with the length of the text. We propose a sequence-to-sequence, purely convolutional and deconvolutional autoencoding framework that is free of the above issue, while also being computationally efficient. The proposed method is simple, easy to implement and can be leveraged as a building block for many applications. We show empirically that compared to RNNs, our framework is better at reconstructing and correcting long paragraphs. Quantitative evaluation on semi-supervised text classification and summarization tasks demonstrate the potential for better utilization of long unlabeled text data.

Dense retrieval (DR) has shown promising results in information retrieval. In essence, DR requires high-quality text representations to support effective search in the representation space. Recent studies have shown that pre-trained autoencoder-based language models with a weak decoder can provide high-quality text representations, boosting the effectiveness and few-shot ability of DR models. However, even a weak autoregressive decoder has the bypass effect on the encoder. More importantly, the discriminative ability of learned representations may be limited since each token is treated equally important in decoding the input texts. To address the above problems, in this paper, we propose a contrastive pre-training approach to learn a discriminative autoencoder with a lightweight multi-layer perception (MLP) decoder. The basic idea is to generate word distributions of input text in a non-autoregressive fashion and pull the word distributions of two masked versions of one text close while pushing away from others. We theoretically show that our contrastive strategy can suppress the common words and highlight the representative words in decoding, leading to discriminative representations. Empirical results show that our method can significantly outperform the state-of-the-art autoencoder-based language models and other pre-trained models for dense retrieval.

We consider learning representations (features) in the setting in which we have access to multiple unlabeled views of the data for learning while only one view is available for downstream tasks. Previous work on this problem has proposed several techniques based on deep neural networks, typically involving either autoencoder-like networks with a reconstruction objective or paired feedforward networks with a batch-style correlation-based objective. We analyze several techniques based on prior work, as well as new variants, and compare them empirically on image, speech, and text tasks. We find an advantage for correlation-based representation learning, while the best results on most tasks are obtained with our new variant, deep canonically correlated autoencoders (DCCAE). We also explore a stochastic optimization procedure for minibatch correlation-based objectives and discuss the time/performance trade-offs for kernel-based and neural network-based implementations.

Recent research has shown the advantages of using autoencoders based on deep neural networks for collaborative filtering. In particular, the recently proposed Mult-VAE model, which used the multinomial likelihood variational autoencoders, has shown excellent results for top-N recommendations. In this work, we propose the Recommender VAE (RecVAE) model that originates from our research on regularization techniques for variational autoencoders. RecVAE introduces several novel ideas to improve Mult-VAE, including a novel composite prior distribution for the latent codes, a new approach to setting the β hyperparameter for the β-VAE framework, and a new approach to training based on alternating updates. In experimental evaluation, we show that RecVAE significantly outperforms previously proposed autoencoder-based models, including Mult-VAE and RaCT, across classical collaborative filtering datasets, and present a detailed ablation study to assess our new developments. Code and models are available at https://github.com/ilya-shenbin/RecVAE.

There is an increasingly apparent need for validating the classifications made by deep learning systems in safety-critical applications like autonomous vehicle systems. A number of recent papers have proposed methods for detecting anomalous image data that appear different from known inlier data samples, including reconstruction-based autoencoders. Autoencoders optimize the compression of input data to a latent space of a dimensionality smaller than the original input and attempt to accurately reconstruct the input using that compressed representation. Since the latent vector is optimized to capture the salient features from the inlier class only, it is commonly assumed that images of objects from outside of the training class cannot effectively be compressed and reconstructed. Some thus consider reconstruction error as a kind of novelty measure. Here we suggest that reconstruction-based approaches fail to capture particular anomalies that lie far from known inlier samples in latent space but near the latent dimension manifold defined by the parameters of the model. We propose incorporating the Mahalanobis distance in latent space to better capture these out-of-distribution samples and our results show that this method often improves performance over the baseline approach.

Autoencoders and their variants are among the most widely used models in representation learning and generative modeling. However, autoencoder-based models usually assume that the learned representations are i.i.d. and fail to capture the correlations between the data samples. To address this issue, we propose a novel Sparse Gaussian Process Bayesian Autoencoder (SGPBAE) model in which we impose fully Bayesian sparse Gaussian Process priors on the latent space of a Bayesian Autoencoder. We perform posterior estimation for this model via stochastic gradient Hamiltonian Monte Carlo. We evaluate our approach qualitatively and quantitatively on a wide range of representation learning and generative modeling tasks and show that our approach consistently outperforms multiple alternatives relying on Variational Autoencoders.

We tackle the problem disentangling the latent space of an autoencoder in order to separate labelled attribute information from other characteristic information. This then allows us to change selected attributes while preserving other information. Our method, matrix subspace projection, is much simpler than previous approaches to latent space factorisation, for example not requiring multiple discriminators or a careful weighting among their loss functions. Furthermore our new model can be applied to autoencoders as a plugin, and works across diverse domains such as images or text. We demonstrate the utility of our method for attribute manipulation in autoencoders trained across varied domains, using both human evaluation and automated methods. The quality of generation of our new model (e.g. reconstruction, conditional generation) is highly competitive to a number of strong baselines.

We describe an end-to-end trainable model for image compression based on variational autoencoders. The model incorporates a hyperprior to effectively capture spatial dependencies in the latent representation. This hyperprior relates to side information, a concept universal to virtually all modern image codecs, but largely unexplored in image compression using artificial neural networks (ANNs). Unlike existing autoencoder compression methods, our model trains a complex prior jointly with the underlying autoencoder. We demonstrate that this model leads to state-of-the-art image compression when measuring visual quality using the popular MS-SSIM index, and yields rate-distortion performance surpassing published ANN-based methods when evaluated using a more traditional metric based on squared error (PSNR). Furthermore, we provide a qualitative comparison of models trained for different distortion metrics.

The variational autoencoder (VAE; Kingma, Welling (2014)) is a recently proposed generative model pairing a top-down generative network with a bottom-up recognition network which approximates posterior inference. It typically makes strong assumptions about posterior inference, for instance that the posterior distribution is approximately factorial, and that its parameters can be approximated with nonlinear regression from the observations. As we show empirically, the VAE objective can lead to overly simplified representations which fail to use the network's entire modeling capacity. We present the importance weighted autoencoder (IWAE), a generative model with the same architecture as the VAE, but which uses a strictly tighter log-likelihood lower bound derived from importance weighting. In the IWAE, the recognition network uses multiple samples to approximate the posterior, giving it increased flexibility to model complex posteriors which do not fit the VAE modeling assumptions. We show empirically that IWAEs learn richer latent space representations than VAEs, leading to improved test log-likelihood on density estimation benchmarks.

Masked autoencoders have become popular training paradigms for self-supervised visual representation learning. These models randomly mask a portion of the input and reconstruct the masked portion according to the target representations. In this paper, we first show that a careful choice of the target representation is unnecessary for learning good representations, since different targets tend to derive similarly behaved models. Driven by this observation, we propose a multi-stage masked distillation pipeline and use a randomly initialized model as the teacher, enabling us to effectively train high-capacity models without any efforts to carefully design target representations. Interestingly, we further explore using teachers of larger capacity, obtaining distilled students with remarkable transferring ability. On different tasks of classification, transfer learning, object detection, and semantic segmentation, the proposed method to perform masked knowledge distillation with bootstrapped teachers (dBOT) outperforms previous self-supervised methods by nontrivial margins. We hope our findings, as well as the proposed method, could motivate people to rethink the roles of target representations in pre-training masked autoencoders.The code and pre-trained models are publicly available at https://github.com/liuxingbin/dbot.

Image-generating machine learning models are typically trained with loss functions based on distance in the image space. This often leads to over-smoothed results. We propose a class of loss functions, which we call deep perceptual similarity metrics (DeePSiM), that mitigate this problem. Instead of computing distances in the image space, we compute distances between image features extracted by deep neural networks. This metric better reflects perceptually similarity of images and thus leads to better results. We show three applications: autoencoder training, a modification of a variational autoencoder, and inversion of deep convolutional networks. In all cases, the generated images look sharp and resemble natural images.

Neural sequence-to-sequence models are currently the dominant approach in several natural language processing tasks, but require large parallel corpora. We present a sequence-to-sequence-to-sequence autoencoder (SEQ^3), consisting of two chained encoder-decoder pairs, with words used as a sequence of discrete latent variables. We apply the proposed model to unsupervised abstractive sentence compression, where the first and last sequences are the input and reconstructed sentences, respectively, while the middle sequence is the compressed sentence. Constraining the length of the latent word sequences forces the model to distill important information from the input. A pretrained language model, acting as a prior over the latent sequences, encourages the compressed sentences to be human-readable. Continuous relaxations enable us to sample from categorical distributions, allowing gradient-based optimization, unlike alternatives that rely on reinforcement learning. The proposed model does not require parallel text-summary pairs, achieving promising results in unsupervised sentence compression on benchmark datasets.

We present a self-supervised U-Net-based masked autoencoder and noise removal model designed to reconstruct original images. Once adequately trained, this model extracts high-level features, which are then combined with features from the EfficientNet B7 model. These integrated features are subsequently fed into dense layers for classification. Among the approaches of masked input and Gaussian noise removal, we selected the best U-Net reconstruction model. Additionally, we explored various configurations, including EfficientNet with attention, attention fusion of the autoencoder, and classification utilizing U-Net encoder features. The best performance was achieved with EfficientNet B7 combined with U-Net encoder features. We employed the Adam optimizer with a learning rate of 0.0001, achieving a top accuracy of 0.94 on the validation set.

Latent variable generative models have emerged as powerful tools for generative tasks including image and video synthesis. These models are enabled by pretrained autoencoders that map high resolution data into a compressed lower dimensional latent space, where the generative models can subsequently be developed while requiring fewer computational resources. Despite their effectiveness, the direct application of latent variable models to higher dimensional domains such as videos continues to pose challenges for efficient training and inference. In this paper, we propose an autoencoder that projects volumetric data onto a four-plane factorized latent space that grows sublinearly with the input size, making it ideal for higher dimensional data like videos. The design of our factorized model supports straightforward adoption in a number of conditional generation tasks with latent diffusion models (LDMs), such as class-conditional generation, frame prediction, and video interpolation. Our results show that the proposed four-plane latent space retains a rich representation needed for high-fidelity reconstructions despite the heavy compression, while simultaneously enabling LDMs to operate with significant improvements in speed and memory.

Recent studies have shown that autoencoder-based models can achieve superior performance on anomaly detection tasks due to their excellent ability to fit complex data in an unsupervised manner. In this work, we propose a novel autoencoder-based model, named StackVAE-G that can significantly bring the efficiency and interpretability to multivariate time series anomaly detection. Specifically, we utilize the similarities across the time series channels by the stacking block-wise reconstruction with a weight-sharing scheme to reduce the size of learned models and also relieve the overfitting to unknown noises in the training data. We also leverage a graph learning module to learn a sparse adjacency matrix to explicitly capture the stable interrelation structure among multiple time series channels for the interpretable pattern reconstruction of interrelated channels. Combining these two modules, we introduce the stacking block-wise VAE (variational autoencoder) with GNN (graph neural network) model for multivariate time series anomaly detection. We conduct extensive experiments on three commonly used public datasets, showing that our model achieves comparable (even better) performance with the state-of-the-art modelsand meanwhile requires much less computation and memory cost. Furthermore, we demonstrate that the adjacency matrix learned by our model accurately captures the interrelation among multiple channels, and can provide valuable information for failure diagnosis applications.

Understanding neural networks is challenging in part because of the dense, continuous nature of their hidden states. We explore whether we can train neural networks to have hidden states that are sparse, discrete, and more interpretable by quantizing their continuous features into what we call codebook features. Codebook features are produced by finetuning neural networks with vector quantization bottlenecks at each layer, producing a network whose hidden features are the sum of a small number of discrete vector codes chosen from a larger codebook. Surprisingly, we find that neural networks can operate under this extreme bottleneck with only modest degradation in performance. This sparse, discrete bottleneck also provides an intuitive way of controlling neural network behavior: first, find codes that activate when the desired behavior is present, then activate those same codes during generation to elicit that behavior. We validate our approach by training codebook Transformers on several different datasets. First, we explore a finite state machine dataset with far more hidden states than neurons. In this setting, our approach overcomes the superposition problem by assigning states to distinct codes, and we find that we can make the neural network behave as if it is in a different state by activating the code for that state. Second, we train Transformer language models with up to 410M parameters on two natural language datasets. We identify codes in these models representing diverse, disentangled concepts (ranging from negative emotions to months of the year) and find that we can guide the model to generate different topics by activating the appropriate codes during inference. Overall, codebook features appear to be a promising unit of analysis and control for neural networks and interpretability. Our codebase and models are open-sourced at https://github.com/taufeeque9/codebook-features.

We introduce the Autoregressive Block-Based Iterative Encoder (AbbIE), a novel recursive generalization of the encoder-only Transformer architecture, which achieves better perplexity than a standard Transformer and allows for the dynamic scaling of compute resources at test time. This simple, recursive approach is a complement to scaling large language model (LLM) performance through parameter and token counts. AbbIE performs its iterations in latent space, but unlike latent reasoning models, does not require a specialized dataset or training protocol. We show that AbbIE upward generalizes (ability to generalize to arbitrary iteration lengths) at test time by only using 2 iterations during train time, far outperforming alternative iterative methods. AbbIE's ability to scale its computational expenditure based on the complexity of the task gives it an up to 12\% improvement in zero-shot in-context learning tasks versus other iterative and standard methods and up to 5\% improvement in language perplexity. The results from this study open a new avenue to Transformer performance scaling. We perform all of our evaluations on model sizes up to 350M parameters.

In this article, we focus on decomposing latent representations in generative adversarial networks or learned feature representations in deep autoencoders into semantically controllable factors in a semisupervised manner, without modifying the original trained models. Particularly, we propose factors' decomposer-entangler network (FDEN) that learns to decompose a latent representation into mutually independent factors. Given a latent representation, the proposed framework draws a set of interpretable factors, each aligned to independent factors of variations by minimizing their total correlation in an information-theoretic means. As a plug-in method, we have applied our proposed FDEN to the existing networks of adversarially learned inference and pioneer network and performed computer vision tasks of image-to-image translation in semantic ways, e.g., changing styles, while keeping the identity of a subject, and object classification in a few-shot learning scheme. We have also validated the effectiveness of the proposed method with various ablation studies in the qualitative, quantitative, and statistical examination.

Neural fields, also known as implicit neural representations (INRs), have shown a remarkable capability of representing, generating, and manipulating various data types, allowing for continuous data reconstruction at a low memory footprint. Though promising, INRs applied to video compression still need to improve their rate-distortion performance by a large margin, and require a huge number of parameters and long training iterations to capture high-frequency details, limiting their wider applicability. Resolving this problem remains a quite challenging task, which would make INRs more accessible in compression tasks. We take a step towards resolving these shortcomings by introducing neural representations for videos NeRV++, an enhanced implicit neural video representation, as more straightforward yet effective enhancement over the original NeRV decoder architecture, featuring separable conv2d residual blocks (SCRBs) that sandwiches the upsampling block (UB), and a bilinear interpolation skip layer for improved feature representation. NeRV++ allows videos to be directly represented as a function approximated by a neural network, and significantly enhance the representation capacity beyond current INR-based video codecs. We evaluate our method on UVG, MCL JVC, and Bunny datasets, achieving competitive results for video compression with INRs. This achievement narrows the gap to autoencoder-based video coding, marking a significant stride in INR-based video compression research.

Recent studies have introduced a new class of generative models for synthesizing implicit neural representations (INRs) that capture arbitrary continuous signals in various domains. These models opened the door for domain-agnostic generative models, but they often fail to achieve high-quality generation. We observed that the existing methods generate the weights of neural networks to parameterize INRs and evaluate the network with fixed positional embeddings (PEs). Arguably, this architecture limits the expressive power of generative models and results in low-quality INR generation. To address this limitation, we propose Domain-agnostic Latent Diffusion Model for INRs (DDMI) that generates adaptive positional embeddings instead of neural networks' weights. Specifically, we develop a Discrete-to-continuous space Variational AutoEncoder (D2C-VAE), which seamlessly connects discrete data and the continuous signal functions in the shared latent space. Additionally, we introduce a novel conditioning mechanism for evaluating INRs with the hierarchically decomposed PEs to further enhance expressive power. Extensive experiments across four modalities, e.g., 2D images, 3D shapes, Neural Radiance Fields, and videos, with seven benchmark datasets, demonstrate the versatility of DDMI and its superior performance compared to the existing INR generative models.

Much recent effort has been invested in non-autoregressive neural machine translation, which appears to be an efficient alternative to state-of-the-art autoregressive machine translation on modern GPUs. In contrast to the latter, where generation is sequential, the former allows generation to be parallelized across target token positions. Some of the latest non-autoregressive models have achieved impressive translation quality-speed tradeoffs compared to autoregressive baselines. In this work, we reexamine this tradeoff and argue that autoregressive baselines can be substantially sped up without loss in accuracy. Specifically, we study autoregressive models with encoders and decoders of varied depths. Our extensive experiments show that given a sufficiently deep encoder, a single-layer autoregressive decoder can substantially outperform strong non-autoregressive models with comparable inference speed. We show that the speed disadvantage for autoregressive baselines compared to non-autoregressive methods has been overestimated in three aspects: suboptimal layer allocation, insufficient speed measurement, and lack of knowledge distillation. Our results establish a new protocol for future research toward fast, accurate machine translation. Our code is available at https://github.com/jungokasai/deep-shallow.

This paper presents a novel, fast and privacy preserving implementation of deep autoencoders. DAEF (Deep Autoencoder for Federated learning), unlike traditional neural networks, trains a deep autoencoder network in a non-iterative way, which drastically reduces its training time. Its training can be carried out in a distributed way (several partitions of the dataset in parallel) and incrementally (aggregation of partial models), and due to its mathematical formulation, the data that is exchanged does not endanger the privacy of the users. This makes DAEF a valid method for edge computing and federated learning scenarios. The method has been evaluated and compared to traditional (iterative) deep autoencoders using seven real anomaly detection datasets, and their performance have been shown to be similar despite DAEF's faster training.

We present a framework for the unsupervised learning of neurosymbolic encoders, which are encoders obtained by composing neural networks with symbolic programs from a domain-specific language. Our framework naturally incorporates symbolic expert knowledge into the learning process, which leads to more interpretable and factorized latent representations compared to fully neural encoders. We integrate modern program synthesis techniques with the variational autoencoding (VAE) framework, in order to learn a neurosymbolic encoder in conjunction with a standard decoder. The programmatic descriptions from our encoders can benefit many analysis workflows, such as in behavior modeling where interpreting agent actions and movements is important. We evaluate our method on learning latent representations for real-world trajectory data from animal biology and sports analytics. We show that our approach offers significantly better separation of meaningful categories than standard VAEs and leads to practical gains on downstream analysis tasks, such as for behavior classification.

Instruction tuning improves the ability of large language models (LLMs) to follow diverse human instructions, but achieving strong performance on specific target tasks remains challenging. A critical bottleneck is selecting the most relevant data to maximize task-specific performance. Existing data selection approaches include unstable influence-based methods and more stable distribution alignment methods, the latter of which critically rely on the underlying sample representation. In practice, most distribution alignment methods, from shallow features (e.g., BM25) to neural embeddings (e.g., BGE, LLM2Vec), may fail to capture how the model internally processes samples. To bridge this gap, we adopt a model-centric strategy in which each sample is represented by its neuronal activation pattern in the model, directly reflecting internal computation. However, directly using raw neuron activations leads to spurious similarity between unrelated samples due to neuron polysemanticity, where a single neuron may respond to multiple, unrelated concepts. To address this, we employ sparse autoencoders to disentangle polysemantic activations into sparse, monosemantic representations, and introduce a dedicated similarity metric for this space to better identify task-relevant data. Comprehensive experiments across multiple instruction datasets, models, tasks, and selection ratios show that our approach consistently outperforms existing data selection baselines in both stability and task-specific performance.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

Identifying low-dimensional latent structures within high-dimensional data has long been a central topic in the machine learning community, driven by the need for data compression, storage, transmission, and deeper data understanding. Traditional methods, such as principal component analysis (PCA) and autoencoders (AE), operate in an unsupervised manner, ignoring label information even when it is available. In this work, we introduce a unified method capable of learning latent spaces in both unsupervised and supervised settings. We formulate the problem as a nonlinear multiple-response regression within an index model context. By applying the generalized Stein's lemma, the latent space can be estimated without knowing the nonlinear link functions. Our method can be viewed as a nonlinear generalization of PCA. Moreover, unlike AE and other neural network methods that operate as "black boxes", our approach not only offers better interpretability but also reduces computational complexity while providing strong theoretical guarantees. Comprehensive numerical experiments and real data analyses demonstrate the superior performance of our method.

Sparse Autoencoders (SAEs) have demonstrated significant promise in interpreting the hidden states of language models by decomposing them into interpretable latent directions. However, training SAEs at scale remains challenging, especially when large dictionary sizes are used. While decoders can leverage sparse-aware kernels for efficiency, encoders still require computationally intensive linear operations with large output dimensions. To address this, we propose KronSAE, a novel architecture that factorizes the latent representation via Kronecker product decomposition, drastically reducing memory and computational overhead. Furthermore, we introduce mAND, a differentiable activation function approximating the binary AND operation, which improves interpretability and performance in our factorized framework.

Sparse Autoencoders (SAEs) are a promising approach for extracting neural network representations by learning a sparse and overcomplete decomposition of the network's internal activations. However, SAEs are traditionally trained considering only activation values and not the effect those activations have on downstream computations. This limits the information available to learn features, and biases the autoencoder towards neglecting features which are represented with small activation values but strongly influence model outputs. To address this, we introduce Gradient SAEs (g-SAEs), which modify the k-sparse autoencoder architecture by augmenting the TopK activation function to rely on the gradients of the input activation when selecting the k elements. For a given sparsity level, g-SAEs produce reconstructions that are more faithful to original network performance when propagated through the network. Additionally, we find evidence that g-SAEs learn latents that are on average more effective at steering models in arbitrary contexts. By considering the downstream effects of activations, our approach leverages the dual nature of neural network features as both representations, retrospectively, and actions, prospectively. While previous methods have approached the problem of feature discovery primarily focused on the former aspect, g-SAEs represent a step towards accounting for the latter as well.

Sparse Autoencoders (SAEs) have proven to be powerful tools for interpreting neural networks by decomposing hidden representations into disentangled, interpretable features via sparsity constraints. However, conventional SAEs are constrained by the fixed sparsity level chosen during training; meeting different sparsity requirements therefore demands separate models and increases the computational footprint during both training and evaluation. We introduce a novel training objective, HierarchicalTopK, which trains a single SAE to optimise reconstructions across multiple sparsity levels simultaneously. Experiments with Gemma-2 2B demonstrate that our approach achieves Pareto-optimal trade-offs between sparsity and explained variance, outperforming traditional SAEs trained at individual sparsity levels. Further analysis shows that HierarchicalTopK preserves high interpretability scores even at higher sparsity. The proposed objective thus closes an important gap between flexibility and interpretability in SAE design.

This paper describes a method for learning low-dimensional approximations of nonlinear dynamical systems, based on neural-network approximations of the underlying Koopman operator. Extended Dynamic Mode Decomposition (EDMD) provides a useful data-driven approximation of the Koopman operator for analyzing dynamical systems. This paper addresses a fundamental problem associated with EDMD: a trade-off between representational capacity of the dictionary and over-fitting due to insufficient data. A new neural network architecture combining an autoencoder with linear recurrent dynamics in the encoded state is used to learn a low-dimensional and highly informative Koopman-invariant subspace of observables. A method is also presented for balanced model reduction of over-specified EDMD systems in feature space. Nonlinear reconstruction using partially linear multi-kernel regression aims to improve reconstruction accuracy from the low-dimensional state when the data has complex but intrinsically low-dimensional structure. The techniques demonstrate the ability to identify Koopman eigenfunctions of the unforced Duffing equation, create accurate low-dimensional models of an unstable cylinder wake flow, and make short-time predictions of the chaotic Kuramoto-Sivashinsky equation.

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 the observed inconsistency of learned SAE features across different training runs, undermining the reliability and efficiency of MI research. This position paper argues that mechanistic interpretability should prioritize feature consistency in SAEs -- the reliable convergence to equivalent feature sets across independent runs. We propose using the Pairwise Dictionary Mean Correlation Coefficient (PW-MCC) as a practical metric to operationalize consistency and demonstrate that high levels are achievable (0.80 for TopK SAEs on LLM activations) with appropriate architectural choices. Our contributions include detailing the benefits of prioritizing consistency; providing theoretical grounding and synthetic validation using a model organism, which verifies PW-MCC as a reliable proxy for ground-truth recovery; and extending these findings to real-world LLM data, where high feature consistency strongly correlates with the semantic similarity of learned feature explanations. We call for a community-wide shift towards systematically measuring feature consistency to foster robust cumulative progress in MI.

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 been restricted to models within the same modality. We propose a novel indicator allowing quantitative comparison of models across SAE features, and use it to conduct a comparative study of visual, textual and multimodal encoders. We also propose to quantify the Comparative Sharedness of individual features between different classes of models. With these two new tools, we conduct several studies on 21 encoders of the three types, with two significantly different sizes, and considering generalist and domain specific datasets. The results allow to revisit previous studies at the light of encoders trained in a multimodal context and to quantify to which extent all these models share some representations or features. They also suggest that visual features that are specific to VLMs among vision encoders are shared with text encoders, highlighting the impact of text pretraining. The code is available at https://github.com/CEA-LIST/SAEshareConcepts

Despite unconditional feature inversion being the foundation of many image synthesis applications, training an inverter demands a high computational budget, large decoding capacity and imposing conditions such as autoregressive priors. To address these limitations, we propose the use of adversarially robust representations as a perceptual primitive for feature inversion. We train an adversarially robust encoder to extract disentangled and perceptually-aligned image representations, making them easily invertible. By training a simple generator with the mirror architecture of the encoder, we achieve superior reconstruction quality and generalization over standard models. Based on this, we propose an adversarially robust autoencoder and demonstrate its improved performance on style transfer, image denoising and anomaly detection tasks. Compared to recent ImageNet feature inversion methods, our model attains improved performance with significantly less complexity.