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Going beyond persistent homology using persistent homology Johanna Immonen University of Helsinki
Augmenting these graph models with topological features via persistent homology (PH) has gained prominence, but identifying the class of attributed graphs that PH can recognize remains open. We introduce a novel concept of color-separating sets to provide a complete resolution to this important problem.
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Topological Spatial Graph Coarsening
Calissano, Anna, Lasalle, Etienne
Spatial graphs are particular graphs for which the nodes are localized in space (e.g., public transport network, molecules, branching biological structures). In this work, we consider the problem of spatial graph reduction, that aims to find a smaller spatial graph (i.e., with less nodes) with the same overall structure as the initial one. In this context, performing the graph reduction while preserving the main topological features of the initial graph is particularly relevant, due to the additional spatial information. Thus, we propose a topological spatial graph coarsening approach based on a new framework that finds a trade-off between the graph reduction and the preservation of the topological characteristics. The coarsening is realized by collapsing short edges. In order to capture the topological information required to calibrate the reduction level, we adapt the construction of classical topological descriptors made for point clouds (the so-called persistent diagrams) to spatial graphs. This construction relies on the introduction of a new filtration called triangle-aware graph filtration. Our coarsening approach is parameter-free and we prove that it is equivariant under rotations, translations and scaling of the initial spatial graph. We evaluate the performances of our method on synthetic and real spatial graphs, and show that it significantly reduces the graph sizes while preserving the relevant topological information.
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Phase diagram of early training dynamics in deep neural networks: effect of the learning rate, depth, and width
We systematically analyze optimization dynamics in deep neural networks (DNNs) trained with stochastic gradient descent (SGD) and study the effect of learning rate $\eta$, depth $d$, and width $w$ of the neural network. By analyzing the maximum eigenvalue $\lambda^H_t$ of the Hessian of the loss, which is a measure of sharpness of the loss landscape, we find that the dynamics can show four distinct regimes: (i) an early time transient regime, (ii) an intermediate saturation regime, (iii) a progressive sharpening regime, and (iv) a late time edge of stability regime.
Causal discovery from observational and interventional data across multiple environments
A fundamental problem in many sciences is the learning of causal structure underlying a system, typically through observation and experimentation. Commonly, one even collects data across multiple domains, such as gene sequencing from different labs, or neural recordings from different species. Although there exist methods for learning the equivalence class of causal diagrams from observational and experimental data, they are meant to operate in a single domain. In this paper, we develop a fundamental approach to structure learning in non-Markovian systems (i.e. when there exist latent confounders) leveraging observational and interventional data collected from multiple domains. Specifically, we start by showing that learning from observational data in multiple domains is equivalent to learning from interventional data with unknown targets in a single domain. But there are also subtleties when considering observational and experimental data. Using causal invariances derived from do-calculus, we define a property called S-Markov that connects interventional distributions from multiple-domains to graphical criteria on a selection diagram. Leveraging the S-Markov property, we introduce a new constraint-based causal discovery algorithm, S-FCI, that can learn from observational and interventional data from different domains. We prove that the algorithm is sound and subsumes existing constraint-based causal discovery algorithms.
CoSE: Compositional Stroke Embeddings
We present a generative model for stroke-based drawing tasks which is able to model complex free-form structures. While previous approaches rely on sequence-based models for drawings of basic objects or handwritten text, we propose a model that treats drawings as a collection of strokes that can be composed into complex structures such as diagrams (e.g., flow-charts). At the core of the approach lies a novel auto-encoder that projects variable-length strokes into a latent space of fixed dimension. This representation space allows a relational model, operating in latent space, to better capture the relationship between strokes and to predict subsequent strokes. We demonstrate qualitatively and quantitatively that our proposed approach is able to model the appearance of individual strokes, as well as the compositional structure of larger diagram drawings. Our approach is suitable for interactive use cases such as auto-completing diagrams. We make code and models publicly available at https://eth-ait.github.io/cose.
HOLE: Homological Observation of Latent Embeddings for Neural Network Interpretability
Athreya, Sudhanva Manjunath, Rosen, Paul
Deep learning models have achieved remarkable success across various domains, yet their learned representations and decision-making processes remain largely opaque and hard to interpret. This work introduces HOLE (Homological Observation of Latent Embeddings), a method for analyzing and interpreting deep neural networks through persistent homology. HOLE extracts topological features from neural activations and presents them using a suite of visualization techniques, including Sankey diagrams, heatmaps, dendrograms, and blob graphs. These tools facilitate the examination of representation structure and quality across layers. We evaluate HOLE on standard datasets using a range of discriminative models, focusing on representation quality, interpretability across layers, and robustness to input perturbations and model compression. The results indicate that topological analysis reveals patterns associated with class separation, feature disentanglement, and model robustness, providing a complementary perspective for understanding and improving deep learning systems.
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