Steffen Schneider

Ori Press, Steffen Schneider, Matthias Kümmerer et al.

Test-Time Adaptation (TTA) allows to update pre-trained models to changing data distributions at deployment time. While early work tested these algorithms for individual fixed distribution shifts, recent work proposed and applied methods for continual adaptation over long timescales. To examine the reported progress in the field, we propose the Continually Changing Corruptions (CCC) benchmark to measure asymptotic performance of TTA techniques. We find that eventually all but one state-of-the-art methods collapse and perform worse than a non-adapting model, including models specifically proposed to be robust to performance collapse. In addition, we introduce a simple baseline, "RDumb", that periodically resets the model to its pretrained state. RDumb performs better or on par with the previously proposed state-of-the-art in all considered benchmarks. Our results show that previous TTA approaches are neither effective at regularizing adaptation to avoid collapse nor able to outperform a simplistic resetting strategy.

Steffen Schneider, Jin Hwa Lee, Mackenzie Weygandt Mathis

Mapping behavioral actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioral data increases, there is growing interest in modeling neural dynamics during adaptive behaviors to probe neural representations. In particular, neural latent embeddings can reveal underlying correlates of behavior, yet, we lack non-linear techniques that can explicitly and flexibly leverage joint behavior and neural data. Here, we fill this gap with a novel method, CEBRA, that jointly uses behavioral and neural data in a hypothesis- or discovery-driven manner to produce consistent, high-performance latent spaces. We validate its accuracy and demonstrate our tool's utility for both calcium and electrophysiology datasets, across sensory and motor tasks, and in simple or complex behaviors across species. It allows for single and multi-session datasets to be leveraged for hypothesis testing or can be used label-free. Lastly, we show that CEBRA can be used for the mapping of space, uncovering complex kinematic features, and rapid, high-accuracy decoding of natural movies from visual cortex.

Shaokai Ye, Anastasiia Filippova, Jessy Lauer et al.

Quantification of behavior is critical in applications ranging from neuroscience, veterinary medicine and animal conservation efforts. A common key step for behavioral analysis is first extracting relevant keypoints on animals, known as pose estimation. However, reliable inference of poses currently requires domain knowledge and manual labeling effort to build supervised models. We present a series of technical innovations that enable a new method, collectively called SuperAnimal, to develop unified foundation models that can be used on over 45 species, without additional human labels. Concretely, we introduce a method to unify the keypoint space across differently labeled datasets (via our generalized data converter) and for training these diverse datasets in a manner such that they don't catastrophically forget keypoints given the unbalanced inputs (via our keypoint gradient masking and memory replay approaches). These models show excellent performance across six pose benchmarks. Then, to ensure maximal usability for end-users, we demonstrate how to fine-tune the models on differently labeled data and provide tooling for unsupervised video adaptation to boost performance and decrease jitter across frames. If the models are fine-tuned, we show SuperAnimal models are 10-100$\times$ more data efficient than prior transfer-learning-based approaches. We illustrate the utility of our models in behavioral classification in mice and gait analysis in horses. Collectively, this presents a data-efficient solution for animal pose estimation.

Jinho Choi, Hyesu Lim, Steffen Schneider et al.

Dataset bias, where data points are skewed to certain concepts, is ubiquitous in machine learning datasets. Yet, systematically identifying these biases is challenging without costly, fine-grained attribute annotations. We present ConceptScope, a scalable and automated framework for analyzing visual datasets by discovering and quantifying human-interpretable concepts using Sparse Autoencoders trained on representations from vision foundation models. ConceptScope categorizes concepts into target, context, and bias types based on their semantic relevance and statistical correlation to class labels, enabling class-level dataset characterization, bias identification, and robustness evaluation through concept-based subgrouping. We validate that ConceptScope captures a wide range of visual concepts, including objects, textures, backgrounds, facial attributes, emotions, and actions, through comparisons with annotated datasets. Furthermore, we show that concept activations produce spatial attributions that align with semantically meaningful image regions. ConceptScope reliably detects known biases (e.g., background bias in Waterbirds) and uncovers previously unannotated ones (e.g, co-occurring objects in ImageNet), offering a practical tool for dataset auditing and model diagnostics.

Muhammed Furkan Dasdelen, Hyesu Lim, Michele Buck et al.

Sparse autoencoders (SAEs) emerged as a promising tool for mechanistic interpretability of transformer-based foundation models. Very recently, SAEs were also adopted for the visual domain, enabling the discovery of visual concepts and their patch-wise attribution to tokens in the transformer model. While a growing number of foundation models emerged for medical imaging, tools for explaining their inferences are still lacking. In this work, we show the applicability of SAEs for hematology. We propose CytoSAE, a sparse autoencoder which is trained on over 40,000 peripheral blood single-cell images. CytoSAE generalizes to diverse and out-of-domain datasets, including bone marrow cytology, where it identifies morphologically relevant concepts which we validated with medical experts. Furthermore, we demonstrate scenarios in which CytoSAE can generate patient-specific and disease-specific concepts, enabling the detection of pathognomonic cells and localized cellular abnormalities at the patch level. We quantified the effect of concepts on a patient-level AML subtype classification task and show that CytoSAE concepts reach performance comparable to the state-of-the-art, while offering explainability on the sub-cellular level. Source code and model weights are available at https://github.com/dynamical-inference/cytosae.

Hyesu Lim, Jinho Choi, Jaegul Choo et al.

Adapting foundation models for specific purposes has become a standard approach to build machine learning systems for downstream applications. Yet, it is an open question which mechanisms take place during adaptation. Here we develop a new Sparse Autoencoder (SAE) for the CLIP vision transformer, named PatchSAE, to extract interpretable concepts at granular levels (e.g., shape, color, or semantics of an object) and their patch-wise spatial attributions. We explore how these concepts influence the model output in downstream image classification tasks and investigate how recent state-of-the-art prompt-based adaptation techniques change the association of model inputs to these concepts. While activations of concepts slightly change between adapted and non-adapted models, we find that the majority of gains on common adaptation tasks can be explained with the existing concepts already present in the non-adapted foundation model. This work provides a concrete framework to train and use SAEs for Vision Transformers and provides insights into explaining adaptation mechanisms.

Steffen Schneider, Rodrigo González Laiz, Anastasiia Filippova et al.

Gradient-based attribution methods aim to explain decisions of deep learning models but so far lack identifiability guarantees. Here, we propose a method to generate attribution maps with identifiability guarantees by developing a regularized contrastive learning algorithm trained on time-series data plus a new attribution method called Inverted Neuron Gradient (collectively named xCEBRA). We show theoretically that xCEBRA has favorable properties for identifying the Jacobian matrix of the data generating process. Empirically, we demonstrate robust approximation of zero vs. non-zero entries in the ground-truth attribution map on synthetic datasets, and significant improvements across previous attribution methods based on feature ablation, Shapley values, and other gradient-based methods. Our work constitutes a first example of identifiable inference of time-series attribution maps and opens avenues to a better understanding of time-series data, such as for neural dynamics and decision-processes within neural networks.

Rodrigo González Laiz, Tobias Schmidt, Steffen Schneider

Self-supervised learning (SSL) approaches have brought tremendous success across many tasks and domains. It has been argued that these successes can be attributed to a link between SSL and identifiable representation learning: Temporal structure and auxiliary variables ensure that latent representations are related to the true underlying generative factors of the data. Here, we deepen this connection and show that SSL can perform system identification in latent space. We propose dynamics contrastive learning, a framework to uncover linear, switching linear and non-linear dynamics under a non-linear observation model, give theoretical guarantees and validate them empirically.

Tobias Schmidt, Steffen Schneider, Matthias Bethge

We propose Equivariance by Contrast (EbC) to learn equivariant embeddings from observation pairs $(\mathbf{y}, g \cdot \mathbf{y})$, where $g$ is drawn from a finite group acting on the data. Our method jointly learns a latent space and a group representation in which group actions correspond to invertible linear maps -- without relying on group-specific inductive biases. We validate our approach on the infinite dSprites dataset with structured transformations defined by the finite group $G:= (R_m \times \mathbb{Z}_n \times \mathbb{Z}_n)$, combining discrete rotations and periodic translations. The resulting embeddings exhibit high-fidelity equivariance, with group operations faithfully reproduced in latent space. On synthetic data, we further validate the approach on the non-abelian orthogonal group $O(n)$ and the general linear group $GL(n)$. We also provide a theoretical proof for identifiability. While broad evaluation across diverse group types on real-world data remains future work, our results constitute the first successful demonstration of general-purpose encoder-only equivariant learning from group action observations alone, including non-trivial non-abelian groups and a product group motivated by modeling affine equivariances in computer vision.

Matthias Tangemann, Steffen Schneider, Julius von Kügelgen et al.

Learning generative object models from unlabelled videos is a long standing problem and required for causal scene modeling. We decompose this problem into three easier subtasks, and provide candidate solutions for each of them. Inspired by the Common Fate Principle of Gestalt Psychology, we first extract (noisy) masks of moving objects via unsupervised motion segmentation. Second, generative models are trained on the masks of the background and the moving objects, respectively. Third, background and foreground models are combined in a conditional "dead leaves" scene model to sample novel scene configurations where occlusions and depth layering arise naturally. To evaluate the individual stages, we introduce the Fishbowl dataset positioned between complex real-world scenes and common object-centric benchmarks of simplistic objects. We show that our approach allows learning generative models that generalize beyond the occlusions present in the input videos, and represent scenes in a modular fashion that allows sampling plausible scenes outside the training distribution by permitting, for instance, object numbers or densities not observed in the training set.

Evgenia Rusak, Steffen Schneider, George Pachitariu et al.

We demonstrate that self-learning techniques like entropy minimization and pseudo-labeling are simple and effective at improving performance of a deployed computer vision model under systematic domain shifts. We conduct a wide range of large-scale experiments and show consistent improvements irrespective of the model architecture, the pre-training technique or the type of distribution shift. At the same time, self-learning is simple to use in practice because it does not require knowledge or access to the original training data or scheme, is robust to hyperparameter choices, is straight-forward to implement and requires only a few adaptation epochs. This makes self-learning techniques highly attractive for any practitioner who applies machine learning algorithms in the real world. We present state-of-the-art adaptation results on CIFAR10-C (8.5% error), ImageNet-C (22.0% mCE), ImageNet-R (17.4% error) and ImageNet-A (14.8% error), theoretically study the dynamics of self-supervised adaptation methods and propose a new classification dataset (ImageNet-D) which is challenging even with adaptation.

Roland S. Zimmermann, Yash Sharma, Steffen Schneider et al.

Contrastive learning has recently seen tremendous success in self-supervised learning. So far, however, it is largely unclear why the learned representations generalize so effectively to a large variety of downstream tasks. We here prove that feedforward models trained with objectives belonging to the commonly used InfoNCE family learn to implicitly invert the underlying generative model of the observed data. While the proofs make certain statistical assumptions about the generative model, we observe empirically that our findings hold even if these assumptions are severely violated. Our theory highlights a fundamental connection between contrastive learning, generative modeling, and nonlinear independent component analysis, thereby furthering our understanding of the learned representations as well as providing a theoretical foundation to derive more effective contrastive losses.

Alexander Mathis, Steffen Schneider, Jessy Lauer et al.

Extracting behavioral measurements non-invasively from video is stymied by the fact that it is a hard computational problem. Recent advances in deep learning have tremendously advanced predicting posture from videos directly, which quickly impacted neuroscience and biology more broadly. In this primer we review the budding field of motion capture with deep learning. In particular, we will discuss the principles of those novel algorithms, highlight their potential as well as pitfalls for experimentalists, and provide a glimpse into the future.

Steffen Schneider, Evgenia Rusak, Luisa Eck et al.

Today's state-of-the-art machine vision models are vulnerable to image corruptions like blurring or compression artefacts, limiting their performance in many real-world applications. We here argue that popular benchmarks to measure model robustness against common corruptions (like ImageNet-C) underestimate model robustness in many (but not all) application scenarios. The key insight is that in many scenarios, multiple unlabeled examples of the corruptions are available and can be used for unsupervised online adaptation. Replacing the activation statistics estimated by batch normalization on the training set with the statistics of the corrupted images consistently improves the robustness across 25 different popular computer vision models. Using the corrected statistics, ResNet-50 reaches 62.2% mCE on ImageNet-C compared to 76.7% without adaptation. With the more robust DeepAugment+AugMix model, we improve the state of the art achieved by a ResNet50 model up to date from 53.6% mCE to 45.4% mCE. Even adapting to a single sample improves robustness for the ResNet-50 and AugMix models, and 32 samples are sufficient to improve the current state of the art for a ResNet-50 architecture. We argue that results with adapted statistics should be included whenever reporting scores in corruption benchmarks and other out-of-distribution generalization settings.

Alexei Baevski, Steffen Schneider, Michael Auli

We propose vq-wav2vec to learn discrete representations of audio segments through a wav2vec-style self-supervised context prediction task. The algorithm uses either a gumbel softmax or online k-means clustering to quantize the dense representations. Discretization enables the direct application of algorithms from the NLP community which require discrete inputs. Experiments show that BERT pre-training achieves a new state of the art on TIMIT phoneme classification and WSJ speech recognition.

Alexander Mathis, Thomas Biasi, Steffen Schneider et al.

Neural networks are highly effective tools for pose estimation. However, as in other computer vision tasks, robustness to out-of-domain data remains a challenge, especially for small training sets that are common for real-world applications. Here, we probe the generalization ability with three architecture classes (MobileNetV2s, ResNets, and EfficientNets) for pose estimation. We developed a dataset of 30 horses that allowed for both "within-domain" and "out-of-domain" (unseen horse) benchmarking - this is a crucial test for robustness that current human pose estimation benchmarks do not directly address. We show that better ImageNet-performing architectures perform better on both within- and out-of-domain data if they are first pretrained on ImageNet. We additionally show that better ImageNet models generalize better across animal species. Furthermore, we introduce Horse-C, a new benchmark for common corruptions for pose estimation, and confirm that pretraining increases performance in this domain shift context as well. Overall, our results demonstrate that transfer learning is beneficial for out-of-domain robustness.

Steffen Schneider, Alexei Baevski, Ronan Collobert et al.

We explore unsupervised pre-training for speech recognition by learning representations of raw audio. wav2vec is trained on large amounts of unlabeled audio data and the resulting representations are then used to improve acoustic model training. We pre-train a simple multi-layer convolutional neural network optimized via a noise contrastive binary classification task. Our experiments on WSJ reduce WER of a strong character-based log-mel filterbank baseline by up to 36% when only a few hours of transcribed data is available. Our approach achieves 2.43% WER on the nov92 test set. This outperforms Deep Speech 2, the best reported character-based system in the literature while using two orders of magnitude less labeled training data.

Daniel Bug, Steffen Schneider, Anne Grote et al.

While human observers are able to cope with variations in color and appearance of histological stains, digital pathology algorithms commonly require a well-normalized setting to achieve peak performance, especially when a limited amount of labeled data is available. This work provides a fully automated, end-to-end learning-based setup for normalizing histological stains, which considers the texture context of the tissue. We introduce Feature Aware Normalization, which extends the framework of batch normalization in combination with gating elements from Long Short-Term Memory units for normalization among different spatial regions of interest. By incorporating a pretrained deep neural network as a feature extractor steering a pixelwise processing pipeline, we achieve excellent normalization results and ensure a consistent representation of color and texture. The evaluation comprises a comparison of color histogram deviations, structural similarity and measures the color volume obtained by the different methods.