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Jun 25

Transformers Discover Molecular Structure Without Graph Priors

Graph Neural Networks (GNNs) are the dominant architecture for molecular machine learning, particularly for molecular property prediction and machine learning interatomic potentials (MLIPs). GNNs perform message passing on predefined graphs often induced by a fixed radius cutoff or k-nearest neighbor scheme. While this design aligns with the locality present in many molecular tasks, a hard-coded graph can limit expressivity due to the fixed receptive field and slows down inference with sparse graph operations. In this work, we investigate whether pure, unmodified Transformers trained directly on Cartesian coordinatesx2013without predefined graphs or physical priorsx2013can approximate molecular energies and forces. As a starting point for our analysis, we demonstrate how to train a Transformer to competitive energy and force mean absolute errors under a matched training compute budget, relative to a state-of-the-art equivariant GNN on the OMol25 dataset. We discover that the Transformer learns physically consistent patternsx2013such as attention weights that decay inversely with interatomic distancex2013and flexibly adapts them across different molecular environments due to the absence of hard-coded biases. The use of a standard Transformer also unlocks predictable improvements with respect to scaling training resources, consistent with empirical scaling laws observed in other domains. Our results demonstrate that many favorable properties of GNNs can emerge adaptively in Transformers, challenging the necessity of hard-coded graph inductive biases and pointing toward standardized, scalable architectures for molecular modeling.

Berkeley UC Berkeley
·
Oct 2, 2025 2

Examining the Source of Defects from a Mechanical Perspective for 3D Anomaly Detection

In this paper, we explore a novel approach to 3D anomaly detection (AD) that goes beyond merely identifying anomalies based on structural characteristics. Our primary perspective is that most anomalies arise from unpredictable defective forces originating from both internal and external sources. To address these anomalies, we seek out opposing forces that can help correct them. Therefore, we introduce the Mechanics Complementary Model-based Framework for the 3D-AD task (MC4AD), which generates internal and external corrective forces for each point. We first propose a Diverse Anomaly-Generation (DA-Gen) module designed to simulate various types of anomalies. Next, we present the Corrective Force Prediction Network (CFP-Net), which uses complementary representations for point-level analysis to simulate the different contributions from internal and external corrective forces. To ensure the corrective forces are constrained effectively, we have developed a combined loss function that includes a new symmetric loss and an overall loss. Notably, we implement a Hierarchical Quality Control (HQC) strategy based on a three-way decision process and contribute a dataset titled Anomaly-IntraVariance, which incorporates intraclass variance to evaluate our model. As a result, the proposed MC4AD has been proven effective through theory and experimentation. The experimental results demonstrate that our approach yields nine state-of-the-art performances, achieving optimal results with minimal parameters and the fastest inference speed across five existing datasets, in addition to the proposed Anomaly-IntraVariance dataset. The source is available at https://github.com/hzzzzzhappy/MC4AD

  • 6 authors
·
May 9, 2025

Analyzing Data Quality and Decay in Mega-Constellations: A Physics-Informed Machine Learning Approach

In the era of mega-constellations, the need for accurate and publicly available information has become fundamental for satellite operators to guarantee the safety of spacecrafts and the Low Earth Orbit (LEO) space environment. This study critically evaluates the accuracy and reliability of publicly available ephemeris data for a LEO mega-constellation - Starlink. The goal of this work is twofold: (i) compare and analyze the quality of the data against high-precision numerical propagation. (ii) Leverage Physics-Informed Machine Learning to extract relevant satellite quantities, such as non-conservative forces, during the decay process. By analyzing two months of real orbital data for approximately 1500 Starlink satellites, we identify discrepancies between high precision numerical algorithms and the published ephemerides, recognizing the use of simplified dynamics at fixed thresholds, planned maneuvers, and limitations in uncertainty propagations. Furthermore, we compare data obtained from multiple sources to track and analyze deorbiting satellites over the same period. Empirically, we extract the acceleration profile of satellites during deorbiting and provide insights relating to the effects of non-conservative forces during reentry. For non-deorbiting satellites, the position Root Mean Square Error (RMSE) was approximately 300 m, while for deorbiting satellites it increased to about 600 m. Through this in-depth analysis, we highlight potential limitations in publicly available data for accurate and robust Space Situational Awareness (SSA), and importantly, we propose a data-driven model of satellite decay in mega-constellations.

  • 3 authors
·
Oct 13, 2025

Objects in Generated Videos Are Slower Than They Appear: Models Suffer Sub-Earth Gravity and Don't Know Galileo's Principle...for now

Video generators are increasingly evaluated as potential world models, which requires them to encode and understand physical laws. We investigate their representation of a fundamental law: gravity. Out-of-the-box video generators consistently generate objects falling at an effectively slower acceleration. However, these physical tests are often confounded by ambiguous metric scale. We first investigate if observed physical errors are artifacts of these ambiguities (e.g., incorrect frame rate assumptions). We find that even temporal rescaling cannot correct the high-variance gravity artifacts. To rigorously isolate the underlying physical representation from these confounds, we introduce a unit-free, two-object protocol that tests the timing ratio t_1^2/t_2^2 = h_1/h_2, a relationship independent of g, focal length, and scale. This relative test reveals violations of Galileo's equivalence principle. We then demonstrate that this physical gap can be partially mitigated with targeted specialization. A lightweight low-rank adaptor fine-tuned on only 100 single-ball clips raises g_{eff} from 1.81,m/s^2 to 6.43,m/s^2 (reaching 65% of terrestrial gravity). This specialist adaptor also generalizes zero-shot to two-ball drops and inclined planes, offering initial evidence that specific physical laws can be corrected with minimal data.

  • 4 authors
·
Dec 1, 2025

Silent Failures in Physical AI: A Literature Review of Runtime Action Authorization for Autonomous Systems

Physical AI systems increasingly map multimodal observations, language instructions, and learned world representations into physically consequential actions. Robotics foundation models, vision-language-action models, and world-model-based autonomous systems can condition decisions that move vehicles, robots, drones, and industrial machines. This transition exposes a safety problem that is not fully captured by conventional AI content moderation or by classical robot safety alone: a black-box model may issue a physically consequential action while appearing confident, plausible, and semantically aligned. The resulting failure can be silent, arising from sensor drift, occlusion, state-estimation error, distribution shift, hallucinated affordances, or invalid physical assumptions before downstream hardware controllers detect a violation. Across embodied foundation models, world models, robotics simulation, embodied safety benchmarks, safe control, runtime assurance, uncertainty estimation, verification, and guardrail evaluation, model capability and safety mechanisms have advanced along largely separate technical tracks. A recurring gap synthesized here is that no single stream surveyed in this review supplies a complete runtime authorization boundary between black-box Physical AI models and physical execution. The resulting analysis develops a bounded problem formulation, a definition of silent physical-action failure, a taxonomy of runtime guardrail functions, and evaluation requirements for comparing guardrails as Physical AI assurance mechanisms.

STATE16 STATE16
·
May 22 3

Abduct, Act, Predict: Scaffolding Causal Inference for Automated Failure Attribution in Multi-Agent Systems

Failure attribution in multi-agent systems -- pinpointing the exact step where a decisive error occurs -- is a critical yet unsolved challenge. Current methods treat this as a pattern recognition task over long conversation logs, leading to critically low step-level accuracy (below 17\%), which renders them impractical for debugging complex systems. Their core weakness is a fundamental inability to perform robust counterfactual reasoning: to determine if correcting a single action would have actually averted the task failure. To bridge this counterfactual inference gap, we introduce Abduct-Act-Predict (A2P) Scaffolding, a novel agent framework that transforms failure attribution from pattern recognition into a structured causal inference task. A2P explicitly guides a large language model through a formal three-step reasoning process within a single inference pass: (1) Abduction, to infer the hidden root causes behind an agent's actions; (2) Action, to define a minimal corrective intervention; and (3) Prediction, to simulate the subsequent trajectory and verify if the intervention resolves the failure. This structured approach leverages the holistic context of the entire conversation while imposing a rigorous causal logic on the model's analysis. Our extensive experiments on the Who\&When benchmark demonstrate its efficacy. On the Algorithm-Generated dataset, A2P achieves 47.46\% step-level accuracy, a 2.85times improvement over the 16.67\% of the baseline. On the more complex Hand-Crafted dataset, it achieves 29.31\% step accuracy, a 2.43times improvement over the baseline's 12.07\%. By reframing the problem through a causal lens, A2P Scaffolding provides a robust, verifiable, and significantly more accurate solution for automated failure attribution. Ours code are released at https://github.com/ResearAI/A2P.

  • 6 authors
·
Sep 12, 2025

The Devil in the Details: Emergent Misalignment, Format and Coherence in Open-Weights LLMs

Prior work has shown that fine-tuning models on a narrow domain with misaligned data can lead to broad misalignment - a phenomenon termed "emergent misalignment" (Betley et al. 2025). While all tested models were susceptible to emergent misalignment, some models showed more resistance than others. Specifically the Qwen-2.5 family proved to be relatively resistant, while GPT-4o exhibited the strongest misalignment. In this paper we evaluate if current-generation open-weights models exhibit similar resistance to the Qwen-2.5 family and measure misalignment robustness over a range of model architectures and scales. We replicate the effect across nine modern open-weights models (Gemma 3 and Qwen 3 families, 1B-32B parameters). Models fine-tuned on insecure code generation show a 0.68% misalignment rate (compared to 0.07% for base models), matching the lower end of prior open-model results but dramatically lower than GPT-4o's 20%. We identify a critical format-dependent vulnerability: requiring JSON output doubles misalignment rates compared to natural language prompts (0.96% vs 0.42%). This suggests that structural constraints may bypass safety training by reducing the model's 'degrees of freedom' to refuse. These findings confirm emergent misalignment as a reproducible phenomenon in modern open-weights models, with rates substantially lower than observed in proprietary systems.

  • 1 authors
·
Nov 25, 2025