arXiv subjects

Yisong Yue

Publications and source records attributed to Yisong Yue.

At least 37 records · Page 2Linked to original sources

arXiv2026

Unsupervised Representation Learning from Sparse Transformation Analysis

There is a vast literature on representation learning based on principles such as coding efficiency, statistical independence, causality, controllability, or symmetry. In this paper we propose to learn representations from sequence data by factorizing the transformations of the latent variables into sparse components. Input data are first encoded as distributions of latent activations and subsequently transformed using a probability flow model, before being decoded to predict a future input state. The flow model is decomposed into a number of rotational (divergence-free) vector fields and a number of potential flow (curl-free) fields. Our sparsity prior encourages only a small number of these fields to be active at any instant and infers the speed with which the probability flows along these fields. Training this model is completely unsupervised using a standard variational objective and results in a new form of disentangled representations where the input is not only represented by a combination of independent factors, but also by a combination of independent transformation primitives given by the learned flow fields. When viewing the transformations as symmetries one may interpret this as learning approximately equivariant representations. Empirically we demonstrate that this model achieves state of the art in terms of both data likelihood and unsupervised approximate equivariance errors on datasets composed of sequence transformations.

cs.LG↗

arXiv2026

Morphological-Symmetry-Equivariant Heterogeneous Graph Neural Network for Robotic Dynamics Learning

We present a morphological-symmetry-equivariant heterogeneous graph neural network, namely MS-HGNN, for robotic dynamics learning, that integrates robotic kinematic structures and morphological symmetries into a single graph network. These structural priors are embedded into the learning architecture as constraints, ensuring high generalizability, sample and model efficiency. The proposed MS-HGNN is a versatile and general architecture that is applicable to various multi-body dynamic systems and a wide range of dynamics learning problems. We formally prove the morphological-symmetry-equivariant property of our MS-HGNN and validate its effectiveness across multiple quadruped robot learning problems using both real-world and simulated data. Our code is made publicly available at https://github.com/lunarlab-gatech/MorphSym-HGNN/.

cs.RO↗

arXiv2026

Langevin Flows for Modeling Neural Latent Dynamics

Neural populations exhibit latent dynamical structures that drive time-evolving spiking activities, motivating the search for models that capture both intrinsic network dynamics and external unobserved influences. In this work, we introduce LangevinFlow, a sequential Variational Auto-Encoder where the time evolution of latent variables is governed by the underdamped Langevin equation. Our approach incorporates physical priors -- such as inertia, damping, a learned potential function, and stochastic forces -- to represent both autonomous and non-autonomous processes in neural systems. Crucially, the potential function is parameterized as a network of locally coupled oscillators, biasing the model toward oscillatory and flow-like behaviors observed in biological neural populations. Our model features a recurrent encoder, a one-layer Transformer decoder, and Langevin dynamics in the latent space. Empirically, our method outperforms state-of-the-art baselines on synthetic neural populations generated by a Lorenz attractor, closely matching ground-truth firing rates. On the Neural Latents Benchmark (NLB), the model achieves superior held-out neuron likelihoods (bits per spike) and forward prediction accuracy across four challenging datasets. It also matches or surpasses alternative methods in decoding behavioral metrics such as hand velocity. Overall, this work introduces a flexible, physics-inspired, high-performing framework for modeling complex neural population dynamics and their unobserved influences.

cs.LG↗

arXiv2026

Kuramoto Orientation Diffusion Models

Orientation-rich images, such as fingerprints and textures, often exhibit coherent angular directional patterns that are challenging to model using standard generative approaches based on isotropic Euclidean diffusion. Motivated by the role of phase synchronization in biological systems, we propose a score-based generative model built on periodic domains by leveraging stochastic Kuramoto dynamics in the diffusion process. In neural and physical systems, Kuramoto models capture synchronization phenomena across coupled oscillators -- a behavior that we re-purpose here as an inductive bias for structured image generation. In our framework, the forward process performs \textit{synchronization} among phase variables through globally or locally coupled oscillator interactions and attraction to a global reference phase, gradually collapsing the data into a low-entropy von Mises distribution. The reverse process then performs \textit{desynchronization}, generating diverse patterns by reversing the dynamics with a learned score function. This approach enables structured destruction during forward diffusion and a hierarchical generation process that progressively refines global coherence into fine-scale details. We implement wrapped Gaussian transition kernels and periodicity-aware networks to account for the circular geometry. Our method achieves competitive results on general image benchmarks and significantly improves generation quality on orientation-dense datasets like fingerprints and textures. Ultimately, this work demonstrates the promise of biologically inspired synchronization dynamics as structured priors in generative modeling.

cs.LG↗

arXiv2026

Actor-Curator: Co-adaptive Curriculum Learning via Policy-Improvement Bandits for RL Post-Training

Post-training large foundation models with reinforcement learning typically relies on massive and heterogeneous datasets, making effective curriculum learning both critical and challenging. In this work, we propose ACTOR-CURATOR, a scalable and fully automated curriculum learning framework for reinforcement learning post-training of large language models (LLMs). ACTOR-CURATOR learns a neural curator that dynamically selects training problems from large problem banks by directly optimizing for expected policy performance improvement. We formulate problem selection as a non-stationary stochastic bandit problem, derive a principled loss function based on online stochastic mirror descent, and establish regret guarantees under partial feedback. Empirically, ACTOR-CURATOR consistently outperforms uniform sampling and strong curriculum baselines across a wide range of challenging reasoning benchmarks, demonstrating improved training stability and efficiency. Notably, it achieves relative gains of 28.6% on AIME2024 and 30.5% on ARC-1D over the strongest baseline and up to 80% speedup. These results suggest that ACTOR-CURATOR is a powerful and practical approach for scalable LLM post-training.

cs.LG↗

arXiv2026

End-to-End Conformal Calibration for Optimization Under Uncertainty

Machine learning can significantly improve performance for decision-making under uncertainty across a wide range of domains. However, ensuring robustness guarantees requires well-calibrated uncertainty estimates, which can be difficult to achieve with neural networks. Moreover, in high-dimensional settings, there may be many valid uncertainty estimates, each with its own performance profile - i.e., not all uncertainty is equally valuable for downstream decision-making. To address this problem, this paper develops an end-to-end framework to learn uncertainty sets for conditional robust optimization in a way that is informed by the downstream decision-making loss, with robustness and calibration guarantees provided by conformal prediction. In addition, we propose to represent general convex uncertainty sets with partially input-convex neural networks, which are learned as part of our framework. Our approach consistently improves upon two-stage estimate-then-optimize baselines on concrete applications in energy storage arbitrage and portfolio optimization.

cs.LG↗

arXiv2026

Discrete Diffusion Trajectory Alignment via Stepwise Decomposition

Discrete diffusion models have demonstrated great promise in modeling various sequence data, ranging from human language to biological sequences. Inspired by the success of RL in language models, there is growing interest in further improving the models by alignment with a certain reward. In this work, we propose an offline preference optimization method to approach trajectory alignment for discrete diffusion models. Instead of applying the reward on the final output and backpropagating the gradient to the entire denoising process, we decompose the problem into a set of stepwise alignment objectives by matching the per-step posterior. This framework enables efficient diffusion optimization, is compatible with arbitrary reward functions, and importantly, yields an equivalent optimal solution under additive factorization of the trajectory reward. Experiments across multiple domains including DNA sequence design, protein inverse folding, and language modeling consistently demonstrate the superiority of our approach. Notably, it achieves an up to 12\% improvement over the most competitive RL-based baseline in terms of predicted activity on DNA sequence design, and further improves the GSM8K score from 78.6 to 81.2 on LLaDA-8B-Instruct for language modeling.

cs.LG↗

arXiv2026

NitroGen: An Open Foundation Model for Generalist Gaming Agents

We introduce NitroGen, a vision-action foundation model for generalist gaming agents that is trained on 40,000 hours of gameplay videos across more than 1,000 games. We incorporate three key ingredients: 1) an internet-scale video-action dataset constructed by automatically extracting player actions from publicly available gameplay videos, 2) a multi-game benchmark environment that can measure cross-game generalization, and 3) a unified vision-action model trained with large-scale behavior cloning. NitroGen exhibits strong competence across diverse domains, including combat encounters in 3D action games, high-precision control in 2D platformers, and exploration in procedurally generated worlds. It transfers effectively to unseen games, achieving up to 52% relative improvement in task success rates over models trained from scratch. We release the dataset, evaluation suite, and model weights to advance research on generalist embodied agents.

cs.CV↗

arXiv2025

CLF-RL: Control Lyapunov Function Guided Reinforcement Learning

Reinforcement learning (RL) has shown promise in generating robust locomotion policies for bipedal robots, but often suffers from tedious reward design and sensitivity to poorly shaped objectives. In this work, we propose a structured reward shaping framework that leverages model-based trajectory generation and control Lyapunov functions (CLFs) to guide policy learning. We explore two model-based planners for generating reference trajectories: a reduced-order linear inverted pendulum (LIP) model for velocity-conditioned motion planning, and a precomputed gait library based on hybrid zero dynamics (HZD) using full-order dynamics. These planners define desired end-effector and joint trajectories, which are used to construct CLF-based rewards that penalize tracking error and encourage rapid convergence. This formulation provides meaningful intermediate rewards, and is straightforward to implement once a reference is available. Both the reference trajectories and CLF shaping are used only during training, resulting in a lightweight policy at deployment. We validate our method both in simulation and through extensive real-world experiments on a Unitree G1 robot. CLF-RL demonstrates significantly improved robustness relative to the baseline RL policy and better performance than a classic tracking reward RL formulation.

cs.RO↗

arXiv2025

Embodied Learning of Reward for Musculoskeletal Control with Vision Language Models

Discovering effective reward functions remains a fundamental challenge in motor control of high-dimensional musculoskeletal systems. While humans can describe movement goals explicitly such as "walking forward with an upright posture," the underlying control strategies that realize these goals are largely implicit, making it difficult to directly design rewards from high-level goals and natural language descriptions. We introduce Motion from Vision-Language Representation (MoVLR), a framework that leverages vision-language models (VLMs) to bridge the gap between goal specification and movement control. Rather than relying on handcrafted rewards, MoVLR iteratively explores the reward space through iterative interaction between control optimization and VLM feedback, aligning control policies with physically coordinated behaviors. Our approach transforms language and vision-based assessments into structured guidance for embodied learning, enabling the discovery and refinement of reward functions for high-dimensional musculoskeletal locomotion and manipulation. These results suggest that VLMs can effectively ground abstract motion descriptions in the implicit principles governing physiological motor control.

cs.RO↗

arXiv2025

Feedforward 3D Editing via Text-Steerable Image-to-3D

Recent progress in image-to-3D has opened up immense possibilities for design, AR/VR, and robotics. However, to use AI-generated 3D assets in real applications, a critical requirement is the capability to edit them easily. We present a feedforward method, Steer3D, to add text steerability to image-to-3D models, which enables editing of generated 3D assets with language. Our approach is inspired by ControlNet, which we adapt to image-to-3D generation to enable text steering directly in a forward pass. We build a scalable data engine for automatic data generation, and develop a two-stage training recipe based on flow-matching training and Direct Preference Optimization (DPO). Compared to competing methods, Steer3D more faithfully follows the language instruction and maintains better consistency with the original 3D asset, while being 2.4x to 28.5x faster. Steer3D demonstrates that it is possible to add a new modality (text) to steer the generation of pretrained image-to-3D generative models with 100k data. Project website: https://glab-caltech.github.io/steer3d/

cs.CV↗

arXiv2025

EnCompass: Enhancing Agent Programming with Search Over Program Execution Paths

We introduce a new approach to agent programming, the development of LLM-based agents. Current approaches to agent programming often entangle two aspects of agent design: the core workflow logic and the inference-time strategy (e.g., tree search). We introduce "probabilistic angelic nondeterminism" ("PAN"), a programming model that disentangles these two concerns, allowing the programmer to describe the agent workflow and independently experiment with different inference-time strategies by simply changing a few inputs. We provide an implementation of PAN in Python as the EnCompass framework, which uses a Python decorator to compile agent workflow programs into a search space. We present three case studies that demonstrate how the framework lets the programmer quickly improve the reliability of an agent and easily switch between different inference-time strategies, all with little additional coding.

cs.AI↗

arXiv2025

KALIKO: Kalman-Implicit Koopman Operator Learning For Prediction of Nonlinear Dynamical Systems

Long-horizon dynamical prediction is fundamental in robotics and control, underpinning canonical methods like model predictive control. Yet, many systems and disturbance phenomena are difficult to model due to effects like nonlinearity, chaos, and high-dimensionality. Koopman theory addresses this by modeling the linear evolution of embeddings of the state under an infinite-dimensional linear operator that can be approximated with a suitable finite basis of embedding functions, effectively trading model nonlinearity for representational complexity. However, explicitly computing a good choice of basis is nontrivial, and poor choices may cause inaccurate forecasts or overfitting. To address this, we present Kalman-Implicit Koopman Operator (KALIKO) Learning, a method that leverages the Kalman filter to implicitly learn embeddings corresponding to latent dynamics without requiring an explicit encoder. KALIKO produces interpretable representations consistent with both theory and prior works, yielding high-quality reconstructions and inducing a globally linear latent dynamics. Evaluated on wave data generated by a high-dimensional PDE, KALIKO surpasses several baselines in open-loop prediction and in a demanding closed-loop simulated control task: stabilizing an underactuated manipulator's payload by predicting and compensating for strong wave disturbances.

cs.RO↗

arXiv2025

Simple Agents Outperform Experts in Biomedical Imaging Workflow Optimization

Adapting production-level computer vision tools to bespoke scientific datasets is a critical "last mile" bottleneck. Current solutions are impractical: fine-tuning requires large annotated datasets scientists often lack, while manual code adaptation costs scientists weeks to months of effort. We consider using AI agents to automate this manual coding, and focus on the open question of optimal agent design for this targeted task. We introduce a systematic evaluation framework for agentic code optimization and use it to study three production-level biomedical imaging pipelines. We demonstrate that a simple agent framework consistently generates adaptation code that outperforms human-expert solutions. Our analysis reveals that common, complex agent architectures are not universally beneficial, leading to a practical roadmap for agent design. We open source our framework and validate our approach by deploying agent-generated functions into a production pipeline, demonstrating a clear pathway for real-world impact.

cs.CV↗

arXiv2025

Learning Time-Scale Invariant Population-Level Neural Representations

General-purpose foundation models for neural time series can help accelerate neuroscientific discoveries and enable applications such as brain computer interfaces (BCIs). A key component in scaling these models is population-level representation learning, which leverages information across channels to capture spatial as well as temporal structure. Population-level approaches have recently shown that such representations can be both efficient to learn on top of pretrained temporal encoders and produce useful representations for decoding a variety of downstream tasks. However, these models remain sensitive to mismatches in preprocessing, particularly on time-scales, between pretraining and downstream settings. We systematically examine how time-scale mismatches affects generalization and find that existing representations lack invariance. To address this, we introduce Time-scale Augmented Pretraining (TSAP), which consistently improves robustness to different time-scales across decoding tasks and builds invariance in the representation space. These results highlight handling preprocessing diversity as a key step toward building generalizable neural foundation models.

cs.LG↗

arXiv2025

Split Gibbs Discrete Diffusion Posterior Sampling

We study the problem of posterior sampling in discrete-state spaces using discrete diffusion models. While posterior sampling methods for continuous diffusion models have achieved remarkable progress, analogous methods for discrete diffusion models remain challenging. In this work, we introduce a principled plug-and-play discrete diffusion posterior sampling algorithm based on split Gibbs sampling, which we call SGDD. Our algorithm enables reward-guided generation and solving inverse problems in discrete-state spaces. We demonstrate the convergence of SGDD to the target posterior distribution and verify this through controlled experiments on synthetic benchmarks. Our method enjoys state-of-the-art posterior sampling performance on a range of benchmarks for discrete data, including DNA sequence design, discrete image inverse problems, and music infilling, achieving more than 30% improved performance compared to existing baselines. Our code is available at https://github.com/chuwd19/Split-Gibbs-Discrete-Diffusion-Posterior-Sampling.

cs.LG↗

arXiv2025

CLEVER: A Curated Benchmark for Formally Verified Code Generation

We introduce ${\rm C{\small LEVER}}$, a high-quality, curated benchmark of 161 problems for end-to-end verified code generation in Lean. Each problem consists of (1) the task of generating a specification that matches a held-out ground-truth specification, and (2) the task of generating a Lean implementation that provably satisfies this specification. Unlike prior benchmarks, ${\rm C{\small LEVER}}$ avoids test-case supervision, LLM-generated annotations, and specifications that leak implementation logic or allow vacuous solutions. All outputs are verified post-hoc using Lean's type checker to ensure machine-checkable correctness. We use ${\rm C{\small LEVER}}$ to evaluate several few-shot and agentic approaches based on state-of-the-art language models. These methods all struggle to achieve full verification, establishing it as a challenging frontier benchmark for program synthesis and formal reasoning. Our benchmark can be found on GitHub(https://github.com/trishullab/clever) as well as HuggingFace(https://huggingface.co/datasets/amitayusht/clever). All our evaluation code is also available online(https://github.com/trishullab/clever-prover).

cs.LG↗

arXiv2025

Steering Generative Models with Experimental Data for Protein Fitness Optimization

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g., diffusion models and language models) with labeled data offer a promising approach. However, most previous studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured through low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages over alternatives such as reinforcement learning with protein language models. Overall, we provide practical insights into how to effectively steer modern generative models for next-generation protein fitness optimization.

q-bio.BM↗