arXiv subjects

Jan Niklas Böhm

Publications and source records attributed to Jan Niklas Böhm.

7 recordsLinked to original sources

arXiv2025

Node Embeddings via Neighbor Embeddings

Node embeddings are a paradigm in non-parametric graph representation learning, where graph nodes are embedded into a given vector space to enable downstream processing. State-of-the-art node-embedding algorithms, such as DeepWalk and node2vec, are based on random-walk notions of node similarity and on contrastive learning. In this work, we introduce the graph neighbor-embedding (graph NE) framework that directly pulls together embedding vectors of adjacent nodes without relying on any random walks. We show that graph NE strongly outperforms state-of-the-art node-embedding algorithms in terms of local structure preservation. Furthermore, we apply graph NE to the 2D node-embedding problem, obtaining graph t-SNE layouts that also outperform existing graph-layout algorithms.

cs.LG↗

arXiv2025

TRACE: Contrastive learning for multi-trial time-series data in neuroscience

Modern neural recording techniques such as two-photon imaging or Neuropixel probes allow to acquire vast time-series datasets with responses of hundreds or thousands of neurons. Contrastive learning is a powerful self-supervised framework for learning representations of complex datasets. Existing applications for neural time series rely on generic data augmentations and do not exploit the multi-trial data structure inherent in many neural datasets. Here we present TRACE, a new contrastive learning framework that averages across different subsets of trials to generate positive pairs. TRACE allows to directly learn a two-dimensional embedding, combining ideas from contrastive learning and neighbor embeddings. We show that TRACE outperforms other methods, resolving fine response differences in simulated data. Further, using in vivo recordings, we show that the representations learned by TRACE capture both biologically relevant continuous variation, cell-type-related cluster structure, and can assist data quality control.

q-bio.NC↗

arXiv2025

On the Importance of Embedding Norms in Self-Supervised Learning

Self-supervised learning (SSL) allows training data representations without a supervised signal and has become an important paradigm in machine learning. Most SSL methods employ the cosine similarity between embedding vectors and hence effectively embed data on a hypersphere. While this seemingly implies that embedding norms cannot play any role in SSL, a few recent works have suggested that embedding norms have properties related to network convergence and confidence. In this paper, we resolve this apparent contradiction and systematically establish the embedding norm's role in SSL training. Using theoretical analysis, simulations, and experiments, we show that embedding norms (i) govern SSL convergence rates and (ii) encode network confidence, with smaller norms corresponding to unexpected samples. Additionally, we show that manipulating embedding norms can have large effects on convergence speed. Our findings demonstrate that SSL embedding norms are integral to understanding and optimizing network behavior.

cs.LG↗

arXiv2024

Self-supervised Visualisation of Medical Image Datasets

Self-supervised learning methods based on data augmentations, such as SimCLR, BYOL, or DINO, allow obtaining semantically meaningful representations of image datasets and are widely used prior to supervised fine-tuning. A recent self-supervised learning method, $t$-SimCNE, uses contrastive learning to directly train a 2D representation suitable for visualisation. When applied to natural image datasets, $t$-SimCNE yields 2D visualisations with semantically meaningful clusters. In this work, we used $t$-SimCNE to visualise medical image datasets, including examples from dermatology, histology, and blood microscopy. We found that increasing the set of data augmentations to include arbitrary rotations improved the results in terms of class separability, compared to data augmentations used for natural images. Our 2D representations show medically relevant structures and can be used to aid data exploration and annotation, improving on common approaches for data visualisation.

cs.CV↗

arXiv2023

From $t$-SNE to UMAP with contrastive learning

Neighbor embedding methods $t$-SNE and UMAP are the de facto standard for visualizing high-dimensional datasets. Motivated from entirely different viewpoints, their loss functions appear to be unrelated. In practice, they yield strongly differing embeddings and can suggest conflicting interpretations of the same data. The fundamental reasons for this and, more generally, the exact relationship between $t$-SNE and UMAP have remained unclear. In this work, we uncover their conceptual connection via a new insight into contrastive learning methods. Noise-contrastive estimation can be used to optimize $t$-SNE, while UMAP relies on negative sampling, another contrastive method. We find the precise relationship between these two contrastive methods and provide a mathematical characterization of the distortion introduced by negative sampling. Visually, this distortion results in UMAP generating more compact embeddings with tighter clusters compared to $t$-SNE. We exploit this new conceptual connection to propose and implement a generalization of negative sampling, allowing us to interpolate between (and even extrapolate beyond) $t$-SNE and UMAP and their respective embeddings. Moving along this spectrum of embeddings leads to a trade-off between discrete / local and continuous / global structures, mitigating the risk of over-interpreting ostensible features of any single embedding. We provide a PyTorch implementation.

cs.LG↗

arXiv2023

Unsupervised visualization of image datasets using contrastive learning

Visualization methods based on the nearest neighbor graph, such as t-SNE or UMAP, are widely used for visualizing high-dimensional data. Yet, these approaches only produce meaningful results if the nearest neighbors themselves are meaningful. For images represented in pixel space this is not the case, as distances in pixel space are often not capturing our sense of similarity and therefore neighbors are not semantically close. This problem can be circumvented by self-supervised approaches based on contrastive learning, such as SimCLR, relying on data augmentation to generate implicit neighbors, but these methods do not produce two-dimensional embeddings suitable for visualization. Here, we present a new method, called t-SimCNE, for unsupervised visualization of image data. T-SimCNE combines ideas from contrastive learning and neighbor embeddings, and trains a parametric mapping from the high-dimensional pixel space into two dimensions. We show that the resulting 2D embeddings achieve classification accuracy comparable to the state-of-the-art high-dimensional SimCLR representations, thus faithfully capturing semantic relationships. Using t-SimCNE, we obtain informative visualizations of the CIFAR-10 and CIFAR-100 datasets, showing rich cluster structure and highlighting artifacts and outliers.

cs.LG↗

arXiv2022

Attraction-Repulsion Spectrum in Neighbor Embeddings

Neighbor embeddings are a family of methods for visualizing complex high-dimensional datasets using $k$NN graphs. To find the low-dimensional embedding, these algorithms combine an attractive force between neighboring pairs of points with a repulsive force between all points. One of the most popular examples of such algorithms is t-SNE. Here we empirically show that changing the balance between the attractive and the repulsive forces in t-SNE using the exaggeration parameter yields a spectrum of embeddings, which is characterized by a simple trade-off: stronger attraction can better represent continuous manifold structures, while stronger repulsion can better represent discrete cluster structures and yields higher $k$NN recall. We find that UMAP embeddings correspond to t-SNE with increased attraction; mathematical analysis shows that this is because the negative sampling optimisation strategy employed by UMAP strongly lowers the effective repulsion. Likewise, ForceAtlas2, commonly used for visualizing developmental single-cell transcriptomic data, yields embeddings corresponding to t-SNE with the attraction increased even more. At the extreme of this spectrum lie Laplacian Eigenmaps. Our results demonstrate that many prominent neighbor embedding algorithms can be placed onto the attraction-repulsion spectrum, and highlight the inherent trade-offs between them.

cs.LG↗