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Nina Miolane

Publications and source records attributed to Nina Miolane.

At least 19 recordsLinked to original sources
arXiv2026

TopoSHAP: Shapley for Explainable and Efficient Topological Deep Learning

Topological deep learning (TDL) extends learning on graphs, such as molecules or social networks, to higher-order structures, such as rings in a molecule or groups in a social network. Explaining which of these structures drive a model's predictions, and which architectural components matter most for its performance, remains challenging. We introduce TopoSHAP, an efficient and general explanation framework that addresses both questions across topological domains and model architectures. TopoSHAP-cell assigns Shapley values to topological data cells and extracts compact explanations. These explanations match or outperform graph-based counterparts on GraphXAI benchmark data while running up to 112$\times$ faster. They also reveal advantageous topological feature design, leading to measured improvements in explanation recovery and predictive accuracy. On the architecture side, TopoSHAP-neighbor explains how neighborhoods contribute to model performance, and turns these evaluations into a backward-elimination search that identifies smaller, competitive architectures early in training. This is up to $11.3\times$ cheaper than traditional TDL training sweeps.

cs.LG↗
arXiv2026

MotionBench-XAI: Benchmarking What Shapes Shapley Explanations in Spatiotemporal Machine Learning

Predicting outcomes from spatiotemporal data, such as assessing Parkinson's severity from human motion, often requires explainability in addition to accuracy. Practitioners need to know what drove the prediction, whether it be spatial (a body joint), temporal (a specific window), or both. Shapley values are attributions computed by treating input features as players in a cooperative game and measuring how the model output changes as coalitions of players are removed. Computing them involves choosing what counts as players, how absent players are imputed, and how the game is evaluated. How these choices affect explanation quality is poorly understood for spatiotemporal data, and real data carries no ground-truth attributions to check against. We present MotionBench-XAI, a benchmark built on i) five synthetic spatiotemporal datasets with exact ground-truth Shapley values, ii) three real datasets across clinical gait, electrocardiogram, and audio, iii) ten attribution methods across three player sets, and iv) three trained architectures. We show that grouping features into players, across time, space, or both, matters more than the choice of imputer. Generative imputers improve explanations only when their conditional models are accurate. On real data, the standard proxy metrics select contradictory best methods. We distill these findings into practical insights and provide an open-source pipeline.

cs.LG↗
arXiv2026

A Phenomenology of Neural Geometry in Vision-Language-Action Models

Robotic manipulation is inherently geometric, but what shape does the world take inside the policy that performs it? Prior work on vision-language-action (VLA) policies establishes that task-relevant variables are linearly readable from activations, yet readability certifies only that a variable is present and says nothing about the shape its values trace, which may be curved and multi-dimensional. Using controlled sweeps, natural rollouts, linear probes, and activation interventions, we build a taxonomy of seven task-relevant concepts in VLA models. We find that realized geometry is predominantly multi-dimensional and is shaped by the constraints under which the policy acts. Physical joint limits, for example, leave wrist orientation an open arc rather than a circle, and distance to the target, a single scalar, is realized in two orthogonal subspaces, a coarse ruler for the approach and a fine ruler for the grasp. The same geometries reappear in two further VLA models on real-world robot data, indicating that they are neither model-specific nor artifacts of simulation. We demonstrate how the findings are actionable by steering along the geometry a concept realizes. Overall, this work lays out an initial phenomenology of realized geometry in VLA policies and demonstrates that a concept's shape carries as much importance as its readability.

cs.RO↗
arXiv2026

Emergent topological structure in spontaneous brain-organoid activity

Neural activity is widely held to organize on low-dimensional structure embedded in a high-dimensional state space. Persistent homology reads such structure directly from the pattern of pairwise correlations, without assuming in advance which variables are relevant. We apply persistent homology to microelectrode-array (MEA) recordings of spontaneous activity from human (Lancaster) and mouse (Pasca) cortical organoids, spanning 25-197 sorted units, and ask whether topological data analysis resolves structure at the node counts that neural recordings actually deliver. Building weighted networks in correlation space and characterizing them by Vietoris-Rips filtration, we find that the first homology (H1, loops) rises significantly above a rate- and population-preserving null in 14 of 18 datasets, all of which remain significant after correction for testing 18 datasets. Random removal of neural units leaves the loops largely intact. Removing the units that form the loops disrupts them more than removing equally connected units does. Topological richness grows with network size, and second homology (H2) exceeds the null only in the larger networks. These results show that persistent homology resolves structured topology in neural recordings at the scale experiments actually deliver.

q-bio.NC↗
arXiv2026

Projecting Latent RL Actions: Towards Generalizable and Scalable Graph Combinatorial Optimization

Graph combinatorial optimization (GCO) has attracted growing interest, as many NP-hard problems naturally admit graph formulations, yet their combinatorial explosion renders exact methods computationally intractable. Recent advances in Reinforcement Learning (RL) combined with Graph Neural Networks (GNNs) have significantly improved learning-based GCO solvers. However, existing approaches face limitations in both generalization across diverse graph instances and computational scalability as action spaces grow. To address both challenges, we introduce \textit{projection agents}, a GCO methodology built on the Wolpertinger framework and adapted to a shared GNN-based latent space for observations and actions. These agents are trained to solve GCO problems by predicting a desired latent action in a single forward pass, which is subsequently decoded into a valid discrete action in the graph using the latent space. Across diverse benchmarks, our approach achieves up to 6.41$\times$ faster inference and up to 75\% better generalization than existing solutions using a simple nearest-neighbor decoding, while opening the door to strong RL performance in super-linear decision spaces with multiple interdependent variables. Finally, we release \texttt{LaGCO-RL}, a Python library that automates latent action-space construction and supports existing RL-GCO solutions, promoting reproducibility and adaptation to new GCO benchmarks.

cs.AI↗
arXiv2026

Batch Before You Lift: Scalable Topological Deep Learning on Large Graphs

Topological Deep Learning extends graph-based learning to higher-order domains, such as hypergraphs, cellular, and simplicial complexes. These domains are typically constructed from patterns in an input graph through a process of graph lifting. Full-domain training constructs and stores the complete lifted representation before model execution. On large and dense datasets like Reddit (233k nodes and 57.3M edges), this global materialization becomes a severe computational bottleneck, often rendering training infeasible. To address this limitation, we introduce Cluster-TNN, a domain-agnostic framework that avoids this bottleneck by lifting locally instead. After partitioning the input graph during preprocessing, at runtime Cluster-TNN dynamically samples groups of node clusters, reconstructs their induced subgraphs to form mini-batches, and applies the chosen lifting within each mini-batch. Retaining all edges among sampled nodes preserves the connectivity needed to construct higher-order structures across clusters, producing topological mini-batches that existing Topological Neural Networks can process directly. Across 21 matched comparisons with full-graph execution, Cluster-TNN reduces peak GPU memory in every configuration, by 83.2% on average while maintaining competitive predictive performance. Notably, such a reduction enables, to our knowledge, the first training of multiple different higher-order Topological Neural Networks on large datasets such as Reddit and OGBN Products. These results establish Cluster-TNN as a general strategy for scaling Topological Deep Learning beyond the limitations of global domain construction.

cs.LG↗
arXiv2026

Group-Invariant Statistics Determine Embedding Geometry: Harmonic Analysis of Representations from Bach to the Night Sky

The representations that language models learn for concepts such as months, weekdays, and places display consistent geometric structure: circles and saddle-shaped "Pringle" manifolds. Recent work traced these structures to $\textit{translation symmetry}$ in word co-occurrence statistics, deriving the observed Fourier geometry when co-occurrence depends only on distance on an abelian lattice of concepts. We demonstrate that more general notions of symmetry lead to equally structured predictions. Considering symmetries defined by arbitrary finite groups, compact groups, and homogeneous spaces, we prove that whenever the co-occurrence statistics of a word family are invariant under a group $G$, the learned word embeddings consist of matrix elements of the irreducible representations (irreps) of $G$. Circles and Pringles arise when $G$ is cyclic, in which case the irreps are Fourier modes. We verify the irrep structure in three experimental settings. (i) The cyclic group $\mathbb{Z}_{12}$: for the months of the year we recover the known circular geometry. (ii) A dihedral group acting on the major and minor triads: we unify two classical observations -- that transposition and chord inversion form a group ($T/I$) acting on chords (music theory), which $\textit{implies}$ that the well-known "circle of fifths" emerges in learned chord embeddings (machine learning). (iii) We explain and reproduce a recently discovered spherical representation of celestial objects in large language models (LLMs) as a spherical-harmonic embedding derived from our theory. Our results demonstrate that the geometry of learned representations is often a consequence of the statistical symmetry of underlying data.

cs.LG↗
arXiv2026

Look Before You Lift: Visual and Quantitative Diagnostics for Topological Deep Learning

Topological deep learning (TDL) methods rely on lifting raw data into higher-order discrete domains such as simplicial complexes, cell complexes, and hypergraphs. In practice, this lifting step is often treated as a black box: practitioners select a lifting and then tune architectures, with limited visibility into whether the induced higher-order connectivity is meaningful for the downstream task. To address this missing diagnostic layer, we propose a visualization technique called TopoExplorer that leverages the strictly augmented Hasse graph form of topological datasets for exploratory data analysis. For the first time, practitioners can easily visualize the incidence- and adjacency-based neighborhoods that define the lifted dataset, as well as read off key graph metrics that describe its structural and feature landscape. Via an extensive set of experiments across many datasets and liftings, we show that several of these metrics correlate with downstream model performance, suggesting they can help inform TDL preprocessing design. Our perspective reframes the TDL workflow from lift-train to lift-look-design-train, enabling more principled, interpretable, and efficient model development. TopoExplorer is hosted at https://topoexplorer.pagekite.me, and its source code is available at github.com/geometric-intelligence/topoexplorer.

cs.LG↗
arXiv2026

Selective Disk Bispectrum: A Complete and Rotation Invariant Image Descriptor

Rotation invariance is a fundamental requirement across many computer vision tasks. Historically, this inductive bias has been encoded through hand-crafted rotation-invariant representations. These are compact, interpretable, and fast to compute, but they come at the cost of descriptive power. More recently, architectures achieve inductive bias through learned representations. These are highly descriptive and achieve strong empirical performance, at the cost of efficiency and interpretability. In this work, we propose an alternative at the intersection of both paradigms. We introduce the selective disk bispectrum (SDB), a complex-valued rotation-invariant vector that preserves all information about the image except its orientation. Our key theoretical contributions are the selective disk bispectrum, its inversion, its (reduced) spatial and computational complexities (compared to the full disk bispectrum), and its expectation and variance under noise. Furthermore, we propose a numerical SDB approximation and provide theoretical guarantees for its accuracy and rotation invariance. Empirically, we validate SDB's invariance and robustness to noise classification tasks. We test our reconstruction algorithm on multi-reference alignment of rotated images.

eess.IV↗
arXiv2026

HOPSE: Scalable Higher-Order Positional and Structural Encoder for Combinatorial Representations

While Graph Neural Networks (GNNs) have proven highly effective at modeling relational data, pairwise connections cannot fully capture multi-way relationships naturally present in complex real-world systems. In response to this, Topological Deep Learning (TDL) leverages more general combinatorial representations--such as simplicial or cellular complexes--to accommodate higher-order interactions. Existing TDL methods often extend GNNs through Higher-Order Message Passing (HOMP), but face critical scalability challenges due to the steep complexity overhead of propagating messages through combinatorial structures. To overcome this limitation, we propose HOPSE (Higher-Order Positional and Structural Encoder), a framework free of message passing layers that uses Hasse graph decompositions to derive efficient and expressive encodings over arbitrary higher-order domains. Notably, HOPSE scales linearly with the size of combinatorial representations while preserving the expressive power and permutation equivariance of the HOMP approaches. Experiments on molecular and topological benchmarks show that it matches or surpasses state-of-the-art performance while consistently achieving speedups over HOMP-based models, opening a new path for scalable TDL. The code is available at https://github.com/geometric-intelligence/topobench.git.

cs.LG↗
arXiv2026

Sequential Group Composition: A Window into the Mechanics of Deep Learning

How do neural networks trained over sequences acquire the ability to perform structured operations, such as arithmetic, geometric, and algorithmic computation? To gain insight into this question, we introduce the sequential group composition task. In this task, networks receive a sequence of elements from a finite group encoded in a real vector space and must predict their cumulative product. This task can be order-sensitive and cannot be solved by a linear model. Our analysis isolates the roles of the group structure, encoding statistics, and sequence length in shaping learning. We prove that two-layer networks from vanishing initialization learn this task one irreducible representation of the group at a time in an order determined by the Fourier statistics of the encoding. To perfectly learn the task, these networks require a hidden width exponential in the sequence length $k$. In contrast, we construct deeper architectures that exploit associativity to dramatically improve this scaling: recurrent neural networks can compose elements sequentially in $k$ steps, while multilayer networks can compose adjacent pairs in parallel in $\log k$ layers. Overall, the sequential group composition task offers a tractable window into the mechanics of deep learning.

cs.LG↗
arXiv2026

OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning. Yet most benchmarks focus on the regime $n \gg p$, where the number of graphs $n$ greatly exceeds the number of nodes per graph $p$. This overlooks biological domains such as omics, which operate in the opposite $n \ll p$ regime, characterized by large graphs of genes, transcripts, or proteins across few patient samples. This raises the question: \textit{how do GNNs perform in this low-sample, high-node omics setting?} We introduce \texttt{OgBench} (Omics-Graph Bench), the first benchmarking platform for graph-level prediction in the $n \ll p$ regime characteristic of omics data. We provide a standardized, end-to-end modular infrastructure from raw omics data to families of featured graphs with varied structural properties. We benchmark classical GNNs, as well as GNNs designed for large graphs and omics applications, alongside MLPs and machine learning baselines to establish reference performances. Our results show that widely used GNNs often do not outperform simple MLPs and classical baselines. These findings challenge the prevailing assumption that graph structure inherently adds value in this domain, fostering a critical reassessment of current learning paradigms. Ultimately, by exposing these limitations, OgBench provides the open-source ecosystem necessary for the community to develop and validate novel architectures explicitly tailored for biological graphs. The code is available at https://github.com/geometric-intelligence/ogbench.

cs.LG↗
arXiv2026

bispectrum: Selective $G$-Bispectra Made Practical

Many machine learning tasks are invariant under the action of a group $G$ of transformations: signal classification can be invariant under translations, image classification under 2D rotations, and spherical-image classification under 3D rotations. The $G$-bispectrum is a principled complete invariant of a signal (retaining all all signal's information up to the group action) with proven benefits in machine learning and as a pooling layer in deep networks. However, its deployment has been hampered by high computational cost and a patchwork of group-specific implementations. We present bispectrum, an open-source, fully unit-tested PyTorch library that implements selective $G$-bispectra for seven different group actions, as differentiable modules that can be directly incorporated into machine learning pipelines and deep learning architectures. For finite groups $G$, selectivity reduces the computational cost from $O(|G|^2)$ to $O(|G|)$. For planar rotations, we leverage the disk bispectrum. For spherical 3D rotations, we introduce an augmented selective bispectrum at band-limit $L$ which reduces the cost from $O(L^3)$ to $Θ(L^2)$ coefficients. We profile the entire library (for which we implemented various compute optimizations), showing that it delivers near-exact $G$-invariance with its selective $G$-bispectra computed in sub-millisecond time on GPU (up to commonly used bandlimits). We evaluate the benefits of incorporating $G$-bispectra as pooling layers into deep learning architectures on three classical benchmark datasets --comparing against norm pooling, gated pooling, Fourier-ELU pooling, max pooling, and (non-equivariant) data-augmented convolutional baselines. Results show that $G$-bispectra consistently outperform alternatives in the low-data, moderate-capacity regime.

cs.LG↗
arXiv2026

When Machine Learning Gets Personal: Evaluating Prediction and Explanation

In high-stakes domains like healthcare, users often expect that sharing personal information with machine learning systems will yield tangible benefits, such as more accurate diagnoses and clearer explanations of contributing factors. However, the validity of this assumption remains largely unexplored. We propose a unified framework to quantify how personalizing a model influences both prediction and explanation. We show that its impacts on prediction and explanation can diverge: a model may become more or less explainable even when prediction is unchanged. For practical settings, we study a standard hypothesis test for detecting personalization effects on demographic groups. We derive a finite-sample lower bound on its probability of error as a function of group sizes, number of personal attributes, and desired benefit from personalization. This provides actionable insights, such as which dataset characteristics are necessary to test an effect, or the maximum effect that can be tested given a dataset. We apply our framework to real-world tabular datasets using feature-attribution methods, uncovering scenarios where effects are fundamentally untestable due to the dataset statistics. Our results highlight the need for joint evaluation of prediction and explanation in personalized models and the importance of designing models and datasets with sufficient information for such evaluation.

cs.LG↗
arXiv2026

GraphUniverse: Synthetic Graph Generation for Evaluating Inductive Generalization

A fundamental challenge in graph learning is understanding how models generalize to new, unseen graphs. While synthetic benchmarks offer controlled settings for analysis, existing approaches are confined to single-graph, transductive settings where models train and test on the same graph structure. Addressing this gap, we introduce GraphUniverse, a framework for generating entire families of graphs to enable the first systematic evaluation of inductive generalization at scale. Our core innovation is the generation of graphs with persistent semantic communities, ensuring conceptual consistency while allowing fine-grained control over structural properties like homophily and degree distributions. This enables crucial but underexplored robustness tests, such as performance under controlled distribution shifts. Benchmarking a wide range of architectures -- from GNNs to graph transformers and topological architectures -- reveals that strong transductive performance is a poor predictor of inductive generalization. Furthermore, we find that robustness to distribution shift is highly sensitive not only to model architecture choice but also to the initial graph regime (e.g., high vs. low homophily). Beyond benchmarking, GraphUniverse's flexibility and scalability can facilitate the development of robust and truly generalizable architectures. The framework is open-source at https://github.com/LouisVanLangendonck/GraphUniverse.

cs.LG↗
arXiv2026

Unsupervised cell segmentation by fast Gaussian Processes

Cell boundary information is crucial for analyzing cell behaviors from time-lapse microscopy videos. Existing supervised cell segmentation tools, such as ImageJ, require tuning various parameters and rely on restrictive assumptions about the shape of the objects. While recent supervised segmentation tools based on convolutional neural networks enhance accuracy, they depend on high-quality labeled images, making them unsuitable for segmenting new types of objects not in the database. We developed a novel unsupervised cell segmentation algorithm based on fast Gaussian processes for noisy microscopy images without the need for parameter tuning or restrictive assumptions about the shape of the object. We derived robust thresholding criteria adaptive for heterogeneous images containing distinct brightness at different parts to separate objects from the background, and employed watershed segmentation to distinguish touching cell objects. Both simulated studies and real-data analysis of large microscopy images demonstrate the scalability and accuracy of our approach compared with the alternatives.

stat.AP↗
arXiv2025

Alternating Gradient Flows: A Theory of Feature Learning in Two-layer Neural Networks

What features neural networks learn, and how, remains an open question. In this paper, we introduce Alternating Gradient Flows (AGF), an algorithmic framework that describes the dynamics of feature learning in two-layer networks trained from small initialization. Prior works have shown that gradient flow in this regime exhibits a staircase-like loss curve, alternating between plateaus where neurons slowly align to useful directions and sharp drops where neurons rapidly grow in norm. AGF approximates this behavior as an alternating two-step process: maximizing a utility function over dormant neurons and minimizing a cost function over active ones. AGF begins with all neurons dormant. At each iteration, a dormant neuron activates, triggering the acquisition of a feature and a drop in the loss. AGF quantifies the order, timing, and magnitude of these drops, matching experiments across several commonly studied architectures. We show that AGF unifies and extends existing saddle-to-saddle analyses in fully connected linear networks and attention-only linear transformers, where the learned features are singular modes and principal components, respectively. In diagonal linear networks, we prove AGF converges to gradient flow in the limit of vanishing initialization. Applying AGF to quadratic networks trained to perform modular addition, we give the first complete characterization of the training dynamics, revealing that networks learn Fourier features in decreasing order of coefficient magnitude. Altogether, AGF offers a promising step towards understanding feature learning in neural networks.

cs.LG↗
arXiv2025

TopoTune : A Framework for Generalized Combinatorial Complex Neural Networks

Graph Neural Networks (GNNs) effectively learn from relational data by leveraging graph symmetries. However, many real-world systems -- such as biological or social networks -- feature multi-way interactions that GNNs fail to capture. Topological Deep Learning (TDL) addresses this by modeling and leveraging higher-order structures, with Combinatorial Complex Neural Networks (CCNNs) offering a general and expressive approach that has been shown to outperform GNNs. However, TDL lacks the principled and standardized frameworks that underpin GNN development, restricting its accessibility and applicability. To address this issue, we introduce Generalized CCNNs (GCCNs), a simple yet powerful family of TDL models that can be used to systematically transform any (graph) neural network into its TDL counterpart. We prove that GCCNs generalize and subsume CCNNs, while extensive experiments on a diverse class of GCCNs show that these architectures consistently match or outperform CCNNs, often with less model complexity. In an effort to accelerate and democratize TDL, we introduce TopoTune, a lightweight software for defining, building, and training GCCNs with unprecedented flexibility and ease.

cs.LG↗