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Mathias Niepert

Publications and source records attributed to Mathias Niepert.

At least 19 recordsLinked to original sources

Equivariance Breaks the Learning Rate

Equivariant networks are commonly trained with Adam, yet recent work reports that matrix-structured optimizers such as Muon can perform better on these architectures without explaining why. We identify one source of this difference inside equivariant linear layers. Each irrep block learns a channel-mixing matrix $W_l$ shared across its $2l+1$ components, giving the expanded map $W_l \otimes I_{2l+1}$. For a single application of the layer, the gradient of $W_l$ sums $2l+1$ outer product contributions and has rank at most $2l+1$. Adam rescales stored weights individually without using the irrep boundaries, so one learning rate can produce different spectral step sizes across blocks within a layer. We address this mismatch by normalizing each block update separately, without introducing a new hyperparameter. This changes only the scale of the update, leaving Adam's moment estimates and its direction within each block unchanged. We evaluate the mechanism in a controlled $\mathrm{SO}(3)$-equivariant model with a matched dense control and in an e3nn interatomic potential model trained on rMD17 and MD22. The toy setup isolates a mismatch that grows with width while the dense control shows no corresponding growth. In the interatomic potential model, block normalization and tuning Adam's momentum coefficients independently improve performance, but neither alone matches Muon. Combined, they make Adam competitive with Muon on all datasets, indicating that blockwise step control and momentum accumulation account for much of Muon's advantage.

cs.LG

Distillation of Foundation Models for Time-dependent PDEs

Foundation models for time-dependent partial differential equations (PDEs) are trained on large and diverse collections of physical systems and can generalize effectively to new downstream tasks. After fine-tuning on only a few trajectories from a target domain, they can achieve strong accuracy in low-data regimes. However, these models are typically large and computationally intensive, limiting their usefulness as fast surrogates for numerical solvers. We propose Teacher Rollout Extension (TREX), a knowledge distillation framework that transfers the predictive capability of a pretrained foundation model into a compact and efficient student. Starting from a fine-tuned teacher, TREX augments limited downstream data by generating long synthetic trajectories through teacher rollouts, optionally with periodic noise injection. This procedure samples from the teacher-induced rollout distribution without requiring explicit knowledge of the initial-condition distribution, while exposing the student to long-horizon states and local recovery behavior around states encountered during autoregressive prediction. The student can further incorporate task-specific inductive biases, such as equivariance, that the teacher does not necessarily enforce. We evaluate TREX on multiple PDE benchmarks. The resulting students can match or surpass the teacher's accuracy while reducing the number of parameters by several orders of magnitude and achieving more than an order-of-magnitude speedup in inference.

cs.LG

The RAIL Principles for Neurosymbolic AI: Reasoning, Assurances, Interfacing and Learning

Neurosymbolic AI systems that integrate machine learning and symbolic reasoning are rapidly gaining attention. They complement the data-intensive statistical approaches of neural networks and language models with symbolic reasoning algorithms to function in high-stakes domains or in low-data regimes that characterize many real-world applications. We argue that the neurosymbolic combination of machine learning and formal reasoning is not a niche approach within AI, but rather includes many already successful techniques that are of crucial importance to the development of reliable, efficient and, ultimately, trustworthy systems. This perspective prompts a re-examination of the design of current AI systems. We show that many leading AI systems, including some that are not traditionally considered as neurosymbolic, can be analysed from the perspective of four principles of neurosymbolic AI design: Reasoning, Assurances, Interfacing and Learning (RAIL). Applying the RAIL framework offers a unified view of seemingly disparate AI systems, ranging from physics-aware machine learning to neuro-guided search (such as Google DeepMind's Alpha-* suite), causal learning and tool-augmented Large Language Models. Importantly, the RAIL principles will enable engineers to make better-informed and more principled decisions about the design and deployment of production-level AI systems. In this article, we introduce the RAIL principles, examine how they can be applied across major areas of AI, and illustrate how they may guide practitioners to integrate neurosymbolic methods into next-generation AI technologies.

cs.AI

ARIA: Adaptive Region-Based Importance Allocation for Conditional Diffusion Distillation

Distilling conditional diffusion models aims to transfer the behavior of a large teacher to a smaller student while preserving alignment across conditioning inputs. Unlike recognition tasks, knowledge distillation in conditional diffusion often struggles to transfer knowledge beyond the training distribution, since the predicted noise strongly depends on the conditioning signal. As a result, effective distillation requires exploring a large conditioning space. In practical settings, this creates a major bottleneck. Paired image-condition data may be limited, and generating synthetic images for every available condition is often computationally infeasible, while the pool of conditions, such as text prompts, can be extremely large. Recent work addresses this issue by switching conditions during training, exposing the student to a broader conditioning space without changing the distillation objective. Yet this raises a complementary question: once a large conditioning corpus is available, how should the training effort be allocated? In this work, we introduce ARIA, a framework that adaptively allocates training effort across coarse regions of the conditioning space. By maintaining online estimates of teacher-student discrepancy at the region level, ARIA focuses updates where misalignment persists while preserving the original distillation objective. Empirically, ARIA improves over RC across most architectures and settings, with the clearest gains observed in unseen and underrepresented regimes. We also provide a theoretical analysis showing that the proposed tracking mechanism follows the evolving discrepancy during training under bounded variance and drift assumptions.

cs.LG

Self-Improving VLA Policies: Selected Diffusion Noise for Spurious-Robust Action Smoothing

Diffusion-based Vision-Language-Action (VLA) policies enable strong generalization in robotic manipulation, but remain sensitive to spurious visual correlations and noisy action generation, leading to brittle behavior under perturbations. We introduce Selected Diffusion Noise (SDN), a simple, training-free test-time method that improves both robustness and success rate by leveraging the diffusion noise space as a controllable degree of freedom. SDN dynamically samples noise vectors that are maximally separated from a reference set to mitigate reliance on spurious cues, while selecting candidates that yield more coherent action trajectories. This dual objective encourages stable behavior even under object-masked observations and reduces action jitter without modifying model parameters. We evaluate SDN on two simulation benchmarks (Google Robot, Widow-X) and two real-world robotic datasets across multiple VLA policies, including pi_0, Groot-N1.5, and Groot-N1.6. SDN consistently improves success rates by +8% in simulation and +10% in real-world settings, while producing smoother and more stable actions. Our results highlight that diffusion noise selection can serve as an effective and general mechanism for enhancing VLA policies at test time.

cs.RO

Protein Fold Classification at Scale: Benchmarking and Pretraining

Classifying protein topology is essential for deciphering biological function, but progress is held back by the lack of large-scale benchmarks that avoid duplicates and by models that do not scale well. We introduce TEDBench, a large-scale, non-redundant benchmark for protein fold classification constructed from the Encyclopedia of Domains (TED) and Foldseek-clustered AlphaFold structures. We show that on TEDBench, current protein representation learning methods either require very large models or fail to deliver strong performance. To address this challenge, we propose Masked Invariant Autoencoders (MiAE), a self-supervised framework for protein structure representation learning. MiAE uses an extremely high masking ratio of up to 90% with an $\mathrm{SE(3)}$-invariant encoder and a lightweight decoder that reconstructs backbone coordinates from the latent representation and mask tokens. MiAE scales well and outperforms supervised counterparts and state-of-the-art baselines on TEDBench, establishing a strong recipe for protein fold classification. To test transfer beyond AlphaFold structures, we further benchmark on a curated dataset from experimental structures of CATH v4.4. TEDBench is available at https://github.com/BorgwardtLab/TEDBench.

cs.LG

SparseSAM: Structured Sparsification of Activations in Segment Anything Models

The Segment Anything Model (SAM) achieves strong open-vocabulary segmentation, but its ViT-based image encoders dominate inference latency and memory. Existing activation compression methods, such as token merging, reduce the token length to process, yet introduce non-trivial runtime overhead and encounter catastrophic quality drop under high compression. Other methods applying Sparse Attention focus on attention alone, leaving the MLP fully dense and capping achievable speedup. We propose SparseSAM, a (i) training-free structured sparsification framework that jointly accelerates attention and MLP layers while preserving token identity. SparseSAM introduces (ii) Stripe-Sort Attention, which uses a deterministic Z-order permutation to transform dense attention into static hardware-friendly sparse patterns, eliminating dynamic masking overhead. SparseSAM further introduces a (iii) Residual-Consistency MLP that routes only informative tokens through the MLP while propagating remaining tokens through the residual pathway. Across four segmentation benchmarks, SparseSAM loses only 0.004 mIoU at a 0.4 density and 0.021 mIoU at 0.3, a 2.10x reduction in accuracy loss versus token merging advances, while achieving 2x faster inference and 2.8x memory reduction.

cs.CV

SymDrift: One-Shot Generative Modeling under Symmetries

Generative modeling of physical systems, such as molecules, requires learning distributions that are invariant under global symmetries, such as rotations in three-dimensional space. Equivariant diffusion and flow matching models can incorporate such invariances effectively, even when trained on a non-invariant empirical distribution, but they typically rely on costly multi-step sampling. Recently, drifting models have emerged as an efficient alternative, enabling single-step generation and achieving state-of-the-art performance in generative modeling tasks. However, we show that drifting models face a symmetry-specific challenge, since an equivariant generator does not generally produce the same drifting field as the one obtained from the symmetrized target distribution. Addressing this issue would require expensive symmetrization of the empirical distribution. To avoid this cost, we propose SymDrift, a framework that makes the drifting field itself symmetry-aware. We introduce two complementary strategies: (i) a symmetrized drift in coordinate space based on optimal alignment, and (ii) a $G$-invariant embedding that removes symmetry ambiguity by construction. Empirically, SymDrift outperforms existing one-shot methods on standard benchmarks for conformer and transition state generation, while remaining competitive with significantly more expensive multi-step approaches. By enabling one-shot inference, SymDrift reduces computational overhead by up to 40$\times$ compared to existing baselines, making it promising for high-throughput applications such as virtual drug screening and large-scale reaction network exploration.

cs.LG

StructSAM: Structure- and Spectrum-Preserving Token Merging for Segment Anything Models

Recent token merging techniques for Vision Transformers (ViTs) provide substantial speedups by reducing the number of tokens processed by self-attention, often without retraining. However, their direct application to the Segment Anything Model (SAM) family is nontrivial: SAM's image encoder mixes windowed and global attention, and its mask decoder relies on dense, prompt-conditioned features for precise boundary prediction. We systematically evaluate representative token-merging methods on SAM and Medical SAM in a strict off-the-shelf setting, and find that existing destination-selection heuristics can erode boundaries and leak prompt information as merge rates increase. We propose \textbf{StructSAM}, a resolution-preserving merge-unmerge framework tailored to SAM. StructSAM computes a lightweight token-energy score from first-order feature gradients, uses grid-based flatness screening to protect boundary and prompt regions, and merges tokens within flat areas toward low-energy destinations with explicit token recovery. We further provide a spectral graph coarsening view showing that score-guided merging yields bounded Laplacian spectral distortion compared to random or window-restricted baselines. Across eight natural and medical benchmarks, StructSAM reduces encoder FLOPs by 25-30\% (up to 40\%+ with prompt-aware merging) with minor drops in mIoU/Dice, consistently outperforming ToMe, PiToMe, ToMeSD, VidToMe, and ALGM at the same compute.

cs.CV

Logical Guidance for the Exact Composition of Diffusion Models

We propose LOGDIFF (Logical Guidance for the Exact Composition of Diffusion Models), a guidance framework for diffusion models that enables principled constrained generation with complex logical expressions at inference time. We study when exact score-based guidance for complex logical formulas can be obtained from guidance signals associated with atomic properties. First, we derive an exact Boolean calculus that provides a sufficient condition for exact logical guidance. Specifically, if a formula admits a circuit representation in which conjunctions combine conditionally independent subformulas and disjunctions combine subformulas that are either conditionally independent or mutually exclusive, exact logical guidance is achievable. In this case, the guidance signal can be computed exactly from atomic scores and posterior probabilities using an efficient recursive algorithm. Moreover, we show that, for commonly encountered classes of distributions, any desired Boolean formula is compilable into such a circuit representation. Second, by combining atomic guidance scores with posterior probability estimates, we introduce a hybrid guidance approach that bridges classifier guidance and classifier-free guidance, applicable to both compositional logical guidance and standard conditional generation. We demonstrate the effectiveness of our framework on multiple image and protein structure generation tasks.

cs.LG

SMART: Scalable Mesh-free Aerodynamic Simulations from Raw Geometries using a Transformer-based Surrogate Model

Machine learning-based surrogate models have emerged as more efficient alternatives to numerical solvers for physical simulations over complex geometries, such as car bodies. Many existing models incorporate the simulation mesh as an additional input, thereby reducing prediction errors. However, generating a simulation mesh for new geometries is computationally costly. In contrast, mesh-free methods, which do not rely on the simulation mesh, typically incur higher errors. Motivated by these considerations, we introduce SMART, a neural surrogate model that predicts physical quantities at arbitrary query locations using only a point-cloud representation of the geometry, without requiring access to the simulation mesh. The geometry and simulation parameters are encoded into a shared latent space that captures both structural and parametric characteristics of the physical field. A physics decoder then attends to the encoder's intermediate latent representations to map spatial queries to physical quantities. Through this cross-layer interaction, the model jointly updates latent geometric features and the evolving physical field. Extensive experiments show that SMART is competitive with and often outperforms existing methods that rely on the simulation mesh as input, demonstrating its capabilities for industry-level simulations.

cs.LG

GraIP: A Benchmarking Framework For Neural Graph Inverse Problems

A wide range of graph learning tasks, such as structure discovery, temporal graph analysis, and combinatorial optimization, focus on inferring graph structures from data, rather than making predictions on given graphs. However, the respective methods to solve such problems are often developed in an isolated, task-specific manner and thus lack a unifying theoretical foundation. Here, we provide a stepping stone towards the formation of such a foundation and further development by introducing the Neural Graph Inverse Problem (GraIP) conceptual framework, which formalizes and reframes a broad class of graph learning tasks as inverse problems. Unlike discriminative approaches that directly predict target variables from given graph inputs, the GraIP paradigm addresses inverse problems, i.e., it relies on observational data and aims to recover the underlying graph structure by reversing the forward process, such as message passing or network dynamics, that produced the observed outputs. We demonstrate the versatility of GraIP across various graph learning tasks, including rewiring, causal discovery, and neural relational inference. We also propose benchmark datasets and metrics for each GraIP domain considered, and characterize and empirically evaluate existing baseline methods used to solve them. Overall, our unifying perspective bridges seemingly disparate applications and provides a principled approach to structural learning in constrained and combinatorial settings while encouraging cross-pollination of existing methods across graph inverse problems.

cs.LG

Beyond the Training Domain: Robust Generative Transition State Models for Unseen Chemistry

Transition states (TSs) govern the rates and outcomes of chemical reactions, making their accurate prediction a central challenge in computational chemistry. Although recent machine-learning models achieve near chemical accuracy in the prediction of TS structures and the associated reaction barriers for small organic reactions, their ability to generalize beyond the training domain remains largely unexplored. Here, we introduce targeted benchmarks to probe chemical and structural novelty in generative TS prediction. Building on Transition1x, a large-scale dataset of reactions involving small organic molecules, we construct curated extensions incorporating controlled elemental substitutions and diverse transition-metal complexes (TMC). These benchmarks reveal fundamental limitations of generative models in the generalization to previously unseen elements. As a result, they produce unphysical geometries and large energetic errors, even for reactions structurally similar to well-predicted organic systems. To address this challenge, we introduce a self-supervised pretraining strategy based on equilibrium conformers that exposes generative TS models to novel chemical environments prior to targeted fine-tuning. Across the newly proposed benchmarks, self-supervised pretraining substantially improves TS prediction for previously unseen systems, lowering the median RMSD of TS geometries on T1x-TMC reactions from 0.39 to 0.19 $\mathring{A}$ and reducing fine-tuning data requirements by up to 75%, enabling reliable performance even in low-data regimes. Overall, the integration of generative TS models with self-supervised pseudo-reaction pretraining provides an efficient, scalable, and chemically robust framework for elucidating TSs well beyond the small organic molecule domain, establishing a foundation for investigating complex and catalytically relevant reaction landscapes.

physics.chem-ph

GraphBench: Next-generation graph learning benchmarking

Machine learning on graphs has made substantial progress across domains such as molecular property prediction and chip design. Yet benchmarking practices remain fragmented, often relying on narrow, task-specific datasets and inconsistent evaluation protocols, hindering reproducibility and broader progress. With the recent popularity of graph foundation models, these weaknesses have become apparent, as existing benchmarks are insufficient for thorough evaluation. To address these challenges, we introduce GraphBench, a comprehensive benchmark suite spanning diverse real-world domains and task settings, including node-level, edge-level, graph-level, and generative tasks. GraphBench provides standardized evaluation protocols, including consistent dataset splits and metrics for assessing out-of-distribution generalization across selected tasks, as well as a unified hyperparameter-tuning framework. We further evaluate GraphBench with recent message-passing neural networks and graph transformer models, establishing principled baselines for future research. See www.graphbench.io for further details.

cs.LG

How Many Tokens Do 3D Point Cloud Transformer Architectures Really Need?

Recent advances in 3D point cloud transformers have led to state-of-the-art results in tasks such as semantic segmentation and reconstruction. However, these models typically rely on dense token representations, incurring high computational and memory costs during training and inference. In this work, we present the finding that tokens are remarkably redundant, leading to substantial inefficiency. We introduce gitmerge3D, a globally informed graph token merging method that can reduce the token count by up to 90-95% while maintaining competitive performance. This finding challenges the prevailing assumption that more tokens inherently yield better performance and highlights that many current models are over-tokenized and under-optimized for scalability. We validate our method across multiple 3D vision tasks and show consistent improvements in computational efficiency. This work is the first to assess redundancy in large-scale 3D transformer models, providing insights into the development of more efficient 3D foundation architectures. Our code and checkpoints are publicly available at https://gitmerge3d.github.io

cs.CV

S-Chain: Structured Visual Chain-of-Thought For Medicine

Faithful reasoning in medical vision-language models (VLMs) requires not only accurate predictions but also transparent alignment between textual rationales and visual evidence. While Chain-of-Thought (CoT) prompting has shown promise in medical visual question answering (VQA), no large-scale expert-level dataset has captured stepwise reasoning with precise visual grounding. We introduce S-Chain, the first large-scale dataset of 12,000 expert-annotated medical images with bounding boxes and structured visual CoT (SV-CoT), explicitly linking visual regions to reasoning steps. The dataset further supports 16 languages, totaling over 700k VQA pairs for broad multilingual applicability. Using S-Chain, we benchmark state-of-the-art medical VLMs (ExGra-Med, LLaVA-Med) and general-purpose VLMs (Qwen2.5-VL, InternVL2.5), showing that SV-CoT supervision significantly improves interpretability, grounding fidelity, and robustness. Beyond benchmarking, we study its synergy with retrieval-augmented generation, revealing how domain knowledge and visual grounding interact during autoregressive reasoning. Finally, we propose a new mechanism that strengthens the alignment between visual evidence and reasoning, improving both reliability and efficiency. S-Chain establishes a new benchmark for grounded medical reasoning and paves the way toward more trustworthy and explainable medical VLMs.

cs.LG

Learning the Neighborhood: Contrast-Free Multimodal Self-Supervised Molecular Graph Pretraining

High-quality molecular representations are essential for property prediction and molecular design, yet large labeled datasets remain scarce. While self-supervised pretraining on molecular graphs has shown promise, many existing approaches either depend on hand-crafted augmentations or complex generative objectives, and often rely solely on 2D topology, leaving valuable 3D structural information underutilized. To address this gap, we introduce C-FREE (Contrast-Free Representation learning on Ego-nets), a simple framework that integrates 2D graphs with ensembles of 3D conformers. C-FREE learns molecular representations by predicting subgraph embeddings from their complementary neighborhoods in the latent space, using fixed-radius ego-nets as modeling units across different conformers. This design allows us to integrate both geometric and topological information within a hybrid Graph Neural Network (GNN)-Transformer backbone, without negatives, positional encodings, or expensive pre-processing. Pretraining on the GEOM dataset, which provides rich 3D conformational diversity, C-FREE achieves state-of-the-art results on MoleculeNet, surpassing contrastive, generative, and other multimodal self-supervised methods. Fine-tuning across datasets with diverse sizes and molecule types further demonstrates that pretraining transfers effectively to new chemical domains, highlighting the importance of 3D-informed molecular representations.

cs.LG

Performance of universal machine-learned potentials with explicit long-range interactions in biomolecular simulations

Universal machine-learned potentials promise transferable accuracy across compositional and vibrational degrees of freedom, yet their application to biomolecular simulations remains underexplored. This work systematically evaluates equivariant message-passing architectures trained on the SPICE-v2 dataset with and without explicit long-range dispersion and electrostatics. We assess the impact of model size, training data composition, and electrostatic treatment across in- and out-of-distribution benchmark datasets, as well as molecular simulations of bulk liquid water, aqueous NaCl solutions, and biomolecules, including alanine tripeptide, the mini-protein Trp-cage, and Crambin. While larger models improve accuracy on benchmark datasets, this trend does not consistently extend to properties obtained from simulations. Predicted properties also depend on the composition of the training dataset. Long-range electrostatics show no systematic impact across systems. However, for Trp-cage, their inclusion yields increased conformational variability. Our results suggest that imbalanced datasets and immature evaluation practices currently challenge the applicability of universal machine-learned potentials to biomolecular simulations.

physics.chem-ph