Daily Papers

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.

k-means has historically been positioned primarily as an offline processing primitive, typically used for dataset organization or embedding preprocessing rather than as a first-class component in online systems. In this work, we revisit this classical algorithm under the lens of modern AI system design and enable k-means as an online primitive. We point out that existing GPU implementations of k-means remain fundamentally bottlenecked by low-level system constraints rather than theoretical algorithmic complexity. Specifically, the assignment stage suffers from a severe IO bottleneck due to the massive explicit materialization of the N times K distance matrix in High Bandwidth Memory (HBM). Simultaneously, the centroid update stage is heavily penalized by hardware-level atomic write contention caused by irregular, scatter-style token aggregations. To bridge this performance gap, we propose flash-kmeans, an IO-aware and contention-free k-means implementation for modern GPU workloads. Flash-kmeans introduces two core kernel-level innovations: (1) FlashAssign, which fuses distance computation with an online argmin to completely bypass intermediate memory materialization; (2) sort-inverse update, which explicitly constructs an inverse mapping to transform high-contention atomic scatters into high-bandwidth, segment-level localized reductions. Furthermore, we integrate algorithm-system co-designs, including chunked-stream overlap and cache-aware compile heuristics, to ensure practical deployability. Extensive evaluations on NVIDIA H200 GPUs demonstrate that flash-kmeans achieves up to 17.9times end-to-end speedup over best baselines, while outperforming industry-standard libraries like cuML and FAISS by 33times and over 200times, respectively.

Direct preference alignment methods are widely used to align large language models (LLMs) with human preferences because of their computational and memory efficiency. However, likelihood displacement motivates alternative ways to extract information from preference pairs with small likelihood margins. In this paper, we propose and analyze Comparison-based Preference Optimization (ComPO), a zeroth-order alignment method based on comparison oracles. ComPO extracts directional information from these pairs without directly optimizing a differentiable preference loss on them. We establish a convergence guarantee for its basic offline scheme under smoothness, gradient sparsity, and compatibility between the oracle and a latent objective. We further introduce online ComPO, which retains the offline comparison mechanism and uses unlabeled policy generations for reverse-KL control relative to a reference policy. Following the coverage perspective of preference fine-tuning, we establish a performance guarantee for a basic constrained scheme under local coverage and in-distribution pairwise reward accuracy. Experiments on Mistral, Llama, Gemma-2, Qwen3, and Gemma-3 models demonstrate improvements over existing direct alignment methods, including length-controlled win rates, with pair-level diagnostics providing evidence consistent with mitigating likelihood displacement.

Human hand-object interactions (HOIs) provide a rich source of demonstrations for dexterous manipulation, but learning directly from them presents challenges in bridging morphology gaps, ensuring dynamical feasibility, and sim-to-real deployment. We present Morphometric Imitation, a three-stage framework that transforms reconstructed HOIs into zero-shot sim-to-real visuomotor policies. First, morphometric optimization (MMO) kinematically retargets human motion across hand morphologies while preserving demonstrated contacts. Second, residual reinforcement learning (RL) refines the kinematic reference using object pose and contact information from the human motion to produce dynamically feasible robot demonstrations. Third, these demonstrations are distilled into visuomotor policies. Across three robot hands and ten HOIs, MMO improves contact F1 over the strongest of five baselines by at least 8 points for every hand, while also improving the success rate of downstream dynamic retargeting by as much as 35 points. Ablations on the residual RL show complementary benefits from using object pose and contact information. Finally, the visuomotor policies achieve 89.3% zero-shot success in 300 real-world trials on 30 objects. Project page: https://morphometricimitation.github.io{this https URL}

Training a model to generate visual content can encourage it to learn rich perceptual capabilities related to geometry, spatial relationships, and objectness; yet, its benefits for visual understanding remain unclear. We ask: when and how does visual generation supervision improve visual understanding? We study controlled pairs of image-to-image (I2I) generation and image-to-text (I2T) understanding tasks that express the same underlying problem in different output modalities. We find that under the correct recipe, I2I training improves downstream I2T performance, with larger gains as the amount of I2I training data increases. We next ask which generation tasks benefit which understanding capabilities. To study transfer beyond paired tasks, we introduce OmniTaskonomy, a unified taxonomy spanning 19 I2I generation tasks and 25 I2T understanding capabilities. The resulting transfer map reveals selective, task-dependent benefits. Some follow intuitive correspondences, e.g., depth prediction improving metric 3D reasoning, object pointing improving counting, and jigsaw reconstruction improving 2D ordering. Interestingly, we also uncover surprising connections: 2.5D segmentation improving category recognition and Z-depth prediction improving localization. To probe these patterns, we analyze gradient alignment between generation and understanding tasks and find that stronger alignment is associated with larger downstream transfer gains. Together, our results highlight visual generation as a rich source of supervision for visual understanding and provide a roadmap for unlocking its benefits through the right training curriculum and task selection. Project page: https://omni-taskonomy.github.io/.

Inspired by human vision, we introduce a framework using active gaze to enable fine-grained bimanual manipulation with only a single stereo camera. EyeRobot 2.0 physically attends to a 3D fixation point in the scene by swiveling two eye viewpoints to center their gaze on it. The resulting images are processed foveally by allocating more visual tokens to the image centers, focusing computation on task-relevant features. Such Active Visual Fixation (AVF) requires carefully coordinated gaze during task execution, which we accomplish hierarchically by first training a low-level gaze servoing policy conditioned on a goal object, then training a target selector which emits fixation goals based on task progress. Both modules are trained with RL on real-world data: the first is trained with a dense geometric reward and the second co-trains with the BC gripper policy which allows it to discover fixation sequences that can resemble a human's fixation sequence while performing the task. EyeRobot 2.0 further takes advantage of fixation by canonicalizing gripper information into a fixation-relative SE(3) frame, which compacts the size of the action distribution to learn. We collect teleoperation data for 7 real-world and 6 simulated tasks, and conduct over 1000 physical and 1800 simulated robot trials comparing EyeRobot 2.0 against passive stereo and ego + wrist camera policies trained on the same data. Removing wrist cameras is costly for standard policies: with only passive stereo, real-world success drops from 52% to 27%. EyeRobot 2.0 closes this gap with only stereo, outperforming passive stereo by 40% in real and 20% in sim. It matches ego + wrist policies when their wrist views are clear (69% vs. 64%), and more than doubles their success when grasped objects occlude the wrist cameras (48% vs. 22%)

This paper proposes a methodology for discovering meaningful properties in data by exploring the latent space of unsupervised deep generative models. We combine manipulation of individual latent variables to extreme values with methods inspired by causal inference into an approach we call causal disentanglement with extreme values (CDEV) and show that this method yields insights for model interpretability. With this, we can test for what properties of unknown data the model encodes as meaningful, using it to glean insight into the communication system of sperm whales (Physeter macrocephalus), one of the most intriguing and understudied animal communication systems. The network architecture used has been shown to learn meaningful representations of speech; here, it is used as a learning mechanism to decipher the properties of another vocal communication system in which case we have no ground truth. The proposed methodology suggests that sperm whales encode information using the number of clicks in a sequence, the regularity of their timing, and audio properties such as the spectral mean and the acoustic regularity of the sequences. Some of these findings are consistent with existing hypotheses, while others are proposed for the first time. We also argue that our models uncover rules that govern the structure of units in the communication system and apply them while generating innovative data not shown during training. This paper suggests that an interpretation of the outputs of deep neural networks with causal inference methodology can be a viable strategy for approaching data about which little is known and presents another case of how deep learning can limit the hypothesis space. Finally, the proposed approach can be extended to other architectures and datasets.

A central challenge in scaling flow models is maintaining stability in training and integration. In flow matching, this stability depends critically on how source samples are paired with data. Independent random pairing introduces substantial stochasticity, motivating minibatch optimal transport (OT) to construct online source-target couplings that reduce this randomness (Tong et al., 2024). However, as applications extend to larger and higher-dimensional datasets, small minibatches can limit these benefits, while scaling the coupling to substantially larger minibatches at every iteration is computationally prohibitive. Moreover, how OT coupling affects the full stochastic gradient and integration remains theoretically unresolved. In this work, we develop a scalable online entropic OT approximation that enables substantially larger source-target couplings while preserving the benefits of OT. We close the theoretical gap for both unregularized and entropic OT by proving strict reductions in full stochastic-gradient variance and integration error relative to independent pairing, and further characterize how these improvements strengthen as the online coupling minibatch grows. Experiments on single-cell gene interpolation-flow and image-flow training validate these predictions, showing that larger online couplings consistently improve training stability and final generation performance.

Extended reality (XR) devices such as the Meta Quest and Apple Vision Pro have seen a recent surge in attention, with motion tracking "telemetry" data lying at the core of nearly all XR and metaverse experiences. Researchers are just beginning to understand the implications of this data for security, privacy, usability, and more, but currently lack large-scale human motion datasets to study. The BOXRR-23 dataset contains 4,717,215 motion capture recordings, voluntarily submitted by 105,852 XR device users from over 50 countries. BOXRR-23 is over 200 times larger than the largest existing motion capture research dataset and uses a new, highly efficient purpose-built XR Open Recording (XROR) file format.

We introduce Berkeley Humanoid, a reliable and low-cost mid-scale humanoid research platform for learning-based control. Our lightweight, in-house-built robot is designed specifically for learning algorithms with low simulation complexity, anthropomorphic motion, and high reliability against falls. The robot's narrow sim-to-real gap enables agile and robust locomotion across various terrains in outdoor environments, achieved with a simple reinforcement learning controller using light domain randomization. Furthermore, we demonstrate the robot traversing for hundreds of meters, walking on a steep unpaved trail, and hopping with single and double legs as a testimony to its high performance in dynamical walking. Capable of omnidirectional locomotion and withstanding large perturbations with a compact setup, our system aims for scalable, sim-to-real deployment of learning-based humanoid systems. Please check http://berkeley-humanoid.com for more details.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

Coordinating workflows across heterogeneous control systems remains a central challenge in safety-critical environments such as scientific facilities, industrial plants, and energy infrastructures. Language-model-driven agents offer a natural interface for these tasks, but existing approaches often lack scalability, reliability, and human oversight. We introduce the Alpha Berkeley Framework, a production-ready architecture for scalable agentic systems that integrate conversational context with robust tool orchestration. The framework features dynamic capability classification to select only relevant tools per task, a plan-first orchestration model that generates execution plans with explicit dependencies and optional human approval, context-aware task extraction that combines dialogue history with external memory and domain resources, and production-ready execution environments with checkpointing, artifact management, and modular deployment. We demonstrate its versatility through two case studies: a tutorial-style wind farm monitoring example and a deployment at the Advanced Light Source particle accelerator. These results establish Alpha Berkeley as a reliable and transparent framework for agentic systems in high-stakes domains.

Despite significant interest and advancements in humanoid robotics, most existing commercially available hardware remains high-cost, closed-source, and non-transparent within the robotics community. This lack of accessibility and customization hinders the growth of the field and the broader development of humanoid technologies. To address these challenges and promote democratization in humanoid robotics, we demonstrate Berkeley Humanoid Lite, an open-source humanoid robot designed to be accessible, customizable, and beneficial for the entire community. The core of this design is a modular 3D-printed gearbox for the actuators and robot body. All components can be sourced from widely available e-commerce platforms and fabricated using standard desktop 3D printers, keeping the total hardware cost under $5,000 (based on U.S. market prices). The design emphasizes modularity and ease of fabrication. To address the inherent limitations of 3D-printed gearboxes, such as reduced strength and durability compared to metal alternatives, we adopted a cycloidal gear design, which provides an optimal form factor in this context. Extensive testing was conducted on the 3D-printed actuators to validate their durability and alleviate concerns about the reliability of plastic components. To demonstrate the capabilities of Berkeley Humanoid Lite, we conducted a series of experiments, including the development of a locomotion controller using reinforcement learning. These experiments successfully showcased zero-shot policy transfer from simulation to hardware, highlighting the platform's suitability for research validation. By fully open-sourcing the hardware design, embedded code, and training and deployment frameworks, we aim for Berkeley Humanoid Lite to serve as a pivotal step toward democratizing the development of humanoid robotics. All resources are available at https://lite.berkeley-humanoid.org.

A significant portion of roads, particularly in densely populated developing countries, lacks explicitly defined right-of-way rules. These understructured roads pose substantial challenges for autonomous vehicle motion planning, where efficient and safe navigation relies on understanding decentralized human coordination for collision avoidance. This coordination, often termed "social driving etiquette," remains underexplored due to limited open-source empirical data and suitable modeling frameworks. In this paper, we present a novel dataset and modeling framework designed to study motion planning in these understructured environments. The dataset includes 20 aerial videos of representative scenarios, an image dataset for training vehicle detection models, and a development kit for vehicle trajectory estimation. We demonstrate that a consensus-based modeling approach can effectively explain the emergence of priority orders observed in our dataset, and is therefore a viable framework for decentralized collision avoidance planning.