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Yisong Yue

Publications and source records attributed to Yisong Yue.

At least 19 recordsLinked to original sources
arXiv2026

iMINDBench: iEEG Multi-Institution Neural Decoding Benchmark

Intracranial electroencephalography (iEEG) is widely used to record electrical activity directly from electrodes inside the human brain, making it an attractive modality for neural decoding. However, progress in iEEG decoding, especially toward general-purpose foundation models, remains difficult to measure reliably: datasets are task- or institution-specific, limiting evidence of generalization across tasks and recording environments, and preprocessing choices can strongly influence performance, making model improvements difficult to distinguish from preprocessing gains. Thus, we introduce iMINDBench, an iEEG Multi-Institution Neural Decoding Benchmark that evaluates models on a shared suite of fifteen decoding tasks across three naturalistic movie-watching datasets. The benchmark additionally defines standardized preprocessing tracks and fixed evaluation splits to support consistent model comparisons. Using iMINDBench, we find that the evaluated pretrained systems generally outperform baselines within their respective preprocessing tracks, while strong spectral baselines remain competitive across institutional datasets. In our scaling study, adding up to 25 times more supervised data from other subjects or institutions yields only small or task-dependent gains over within-session training. Together, these findings highlight the need for iEEG models that improve on strong preprocessing baselines and make more effective use of data across subjects and institutions. Project website: https://imindbench.github.io/

cs.LG↗
arXiv2026

Beyond Pairwise Preferences: Listwise Reward-Aware Alignment for Diffusion Models

Preference optimization has emerged as an efficient alternative to online reinforcement learning from human feedback (RLHF) for aligning text-to-image diffusion models. However, existing methods largely reduce supervision to binary pairwise comparisons. This pairwise reduction is limiting when training data naturally contains multiple candidate images for the same prompt, and when continuous reward scores can provide richer information than a single winner-loser label. To address these limitations, we propose Diffusion LAIR, a reward-aware listwise preference optimization method for diffusion models. For each prompt, LAIR converts reward scores across a group of candidate images into centered advantage weights, then optimizes an advantage-weighted regression objective on the implicit reward, defined as the denoising-loss improvement of the current model over a fixed reference model, with a quadratic penalty that regularizes the magnitude of the implicit reward. The resulting objective uses all candidates simultaneously rather than selecting pairs, and remains conservative by explicitly controlling the magnitude of the implicit reward. The LAIR objective admits a bounded closed-form optimum in implicit-reward space, clarifying how the regularization strength controls the magnitude of the preference update. Experiments show that Diffusion LAIR outperforms strong preference optimization baselines on SD1.5 and SDXL across text-to-image generation, compositional generation, and image editing benchmarks.

cs.LG↗
arXiv2026

Wind-Informed Rapid Flight-Planning in Complex Urban Topologies via Machine Learning and Experimental Validation

Advanced air mobility operations hold the potential to enhance and expand regional transportation of both people and goods in populated areas. However, hazardous flight conditions arising from interactions between wind and the built environment remain a significant challenge for aerial vehicles in urban settings. This work proposes a novel framework towards safe flight planning of aerial vehicles in windy urban environments. A learning-based surrogate model is trained to rapidly predict flow fields from readily available information such as building geometry and incident wind. This surrogate prediction is used to calculate a volumetric flight challenge scalar field based on critical flow parameters and proximity to structures. A safe, flow-informed flight trajectory is then identified through a cost-minimizing pathfinder. The complete system is demonstrated experimentally through flight tests of a micro aerial vehicle through a model urban geometry placed in a large fan-array wind tunnel. Comparing this approach to trajectories generated without knowledge of the wind field, we find the flow-informed approach reduces undesired vehicle displacement and improves flight stability. This work is among the first practical demonstrations of safe, wind-aware methodologies for advanced air mobility in urban environments.

physics.flu-dyn↗
arXiv2026

Knowledge-Centric Self-Improvement

Self-improving AI systems typically treat the agent as the object that improves, by optimizing prompts, workflows, harnesses, or even the agent's own code. This agent-centric view can make improvements expensive to maintain and difficult to transfer, because gains become tied to a particular agent design, task distribution, or adaptation run. We study a complementary paradigm: knowledge-centric self-improvement, in which agents remain generic and disposable while the persistent object is a curated knowledge base that agents can leverage for future tasks. We conduct controlled case studies to operationalize this idea via a simple protocol. Agents attempt one task, then contribute evidence-grounded insights to a shared knowledge base via task-level and cross-task forums, followed by knowledge distillation. Because self-improvement is contained in the knowledge rather than the agent, improvement can be more inspectable, transferable, and portable. Across abstract reasoning, coding, and terminal benchmarks, this protocol improves solve rates while reducing dollar cost relative to agent-centric baselines. The resulting distilled knowledge also transfers to held-out tasks and across LLM families, indicating that the improvement is not merely an LLM- or run-specific behavior. These results support a new view of self-improving agentic systems: progress can be driven primarily by the curated persistent knowledge. Code is available at https://github.com/recursive-knowledge/KSI.

cs.AI↗
arXiv2026

FormulaCode: Evaluating Agentic Optimization on Large Codebases

Large language model (LLM) coding agents increasingly operate at the repository level, motivating benchmarks that evaluate their ability to optimize entire codebases under realistic constraints. Existing code benchmarks largely rely on synthetic tasks, binary correctness signals, or single-objective evaluation, limiting their ability to assess holistic optimization behavior. We introduce FormulaCode, a benchmark for evaluating agentic optimization on large, real-world codebases with fine-grained, multi-objective performance metrics. FormulaCode comprises 957 performance bottlenecks mined from scientific Python repositories on GitHub, each paired with expert-authored patches and, on average, 264.6 community-maintained performance workloads per task, enabling the holistic ability of LLM agents to optimize codebases under realistic correctness and performance constraints. Our evaluations reveal that repository-scale, multi-objective optimization remains a major challenge for frontier LLM agents. Project website at: https://formula-code.github.io

cs.SE↗
arXiv2026

On the Design Space of Discrete Diffusion Online Adaptation for Molecular Optimization

Molecular optimization often starts from a pretrained generative model that captures a broad prior over valid molecular structures. At test time, however, the goal is not to sample from this prior, but to use a limited oracle budget to shift generation toward task-specific high-reward molecules. We study this adaptation problem for discrete diffusion models. Each online round couples several choices. The loop must decide which candidates to evaluate, how rewards become model updates, which feedback to reuse, and how far to move beyond the pretrained prior. These choices have mostly been studied in isolation, leaving open whether they complement one another, become redundant, or interfere inside a full online adaptation loop. We conduct controlled studies across six small-molecule binding-affinity tasks and three protein-fitness tasks. We find that acquisition, reward shaping, and model debiasing provide complementary routes to higher reward, especially for small molecules. Replay further stabilizes learning, while validity penalties keep small-molecule exploration on the valid molecular manifold. Together, these findings point to a practical recipe for feedback-efficient molecular optimization: online fine-tuning with acquisition, reward shaping, debiasing, replay, and validity control. This recipe outperforms offline fine-tuning and inference-time search baselines under matched oracle-call budgets and GPU-hour accounting. The gains are largest when high-reward candidates require larger shifts from the pretrained prior.

cs.LG↗
arXiv2026

Vera: A Layered Diffusion Model for Content-Preserving Video Editing

Video diffusion models have enabled remarkable progress in video generation and editing. However, content preservation remains a core challenge: existing methods regenerate every pixel and often alter elements that should remain unchanged, such as characters or background scenes. We introduce Vera, a layered diffusion framework for content-preserving video editing. Instead of regenerating the entire video, Vera generates an edit layer along with an alpha matte for compositing with the source video, separating creative editing from content preservation by design. To encourage coherent composition with the source video, we extend the text-to-video DiT into a Mixture-of-Transformers (MoT) architecture, with separate DiTs for each layer that interact through joint self-attention. To support the training of Vera, we further construct a high-quality layered dataset with accurate alpha mattes, diverse scenes and dynamics, and visual effects. Across our quantitative benchmark and human preference study, Vera outperforms leading open-source video editing models in content preservation while remaining competitive in edit quality, using 486K frames of layered training data.

cs.CV↗
arXiv2026

Flow Annealing Posterior Sampling for Function-Space Regression and Inverse Problems

Principled regression for stochastic processes is a long-standing challenge with deep connections to scientific inverse problems. We introduce Flow Annealing Posterior Sampling (FAPS), to our knowledge the first function-space posterior sampling framework that unifies stochastic-process regression and PDE inverse problems. Built on pretrained function-space flow-matching priors, FAPS enables likelihood-guided posterior inference from sparse and noisy observations, supports variable query discretizations, and avoids explicit prior-density evaluation. Its Langevin correction uses a low-rank covariance preconditioner to exploit dominant function-space correlations across discretizations. Across Gaussian and non-Gaussian stochastic-process regression benchmarks and diverse PDE inverse problems, FAPS produces coherent posterior samples with accurate uncertainty quantification, significantly outperforming existing functional regression baselines and achieving competitive or better PDE noisy inverse performance than diffusion-based posterior samplers while reducing test-time sampling cost.

stat.ML↗
arXiv2026

Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules

Standard flow and diffusion pre-training matches the distribution of available data (e.g., molecules), which often covers only a small fraction of the valid design space. In generative discovery, however, one aims to sample valid new-to-nature designs, assigned negligible probability under, and thus inaccessible to, standard models fitted to the observed data. To overcome this limitation, we depart from data distribution matching and view a generative model through its generable set: the region it covers with non-negligible probability. This allows to introduce a new learning principle for out-of-distribution flow modeling: enlarging a model's generable set to increase coverage of the valid design space. We propose Active Flow Expansion (ActFlow), a continued pre-training method that employs verifier feedback to expand a pre-trained model over new valid regions by iteratively adapting to synthetic data generated through active exploration in the learned flow representation. Theoretically, we establish to our knowledge first-of-their-kind statistical learning guarantees for out-of-distribution flow modeling, analyzing generable set expansion as a local-to-global reachability process over a learned representation. Empirically, we assess ActFlow with suitable out-of-distribution generative modeling metrics across small organic molecules, mid-sized drug-like molecules, therapeutic peptides, and protein sequence design tasks. Results show that ActFlow expands valid coverage far beyond the region modeled by the initial pre-trained model, significantly outperforming widely adopted synthetic flow pre-training methods.

cs.LG↗
arXiv2026

Blade: A Derivative-free Bayesian Inversion Method using Diffusion Priors

Derivative-free Bayesian inversion arises in science and engineering applications, particularly when forward model is costly or infeasible to differentiate through. Existing derivative-free methods collapse the posterior to a point estimate or return severely over-confident uncertainty on high-dimensional, nonlinear problems. We introduce Blade, which produces accurate and well-calibrated posteriors using an ensemble of interacting particles. Blade leverages diffusion models as data-driven priors, and only queries the forward model through forward evaluations (i.e., derivative-free). Theoretically, we show the convergence and stability of Blade under forward model approximation and prior score estimation error. Empirically, on nonlinear fluid dynamics, Blade produces well-calibrated posterior samples that existing derivative-free methods cannot, as measured by CRPS, the spread-skill ratio, and the rank histogram. Its accuracy and calibration improve consistently with more iterations and particles, backed by our convergence and stability analysis and empirical experiments.

cs.LG↗
arXiv2026

Krause Synchronization Transformers

Self-attention in Transformers relies on globally normalized softmax weights, causing all tokens to compete for influence at every layer. When composed across depth, this interaction pattern induces strong synchronization dynamics that favor convergence toward a dominant mode, a behavior associated with representation collapse and attention sink phenomena. We introduce Krause Attention, a principled attention mechanism inspired by bounded-confidence consensus dynamics. Krause Attention replaces similarity-based global aggregation with distance-based, localized, and selectively sparse interactions, promoting structured local synchronization instead of global mixing. We relate this behavior to recent theory modeling Transformer dynamics as interacting particle systems, and show how bounded-confidence interactions naturally moderate attention concentration and alleviate attention sinks. Restricting interactions to local neighborhoods also reduces runtime complexity from quadratic to linear in sequence length. Empirically, we validate Krause Attention across diverse settings, including vision (ViT on CIFAR/ImageNet), autoregressive image generation (MNIST/CIFAR-10), large language models (Llama/Qwen), and language models trained from scratch at multiple scales (100M/200M). Across these domains, Krause Attention achieves consistent performance gains while improving computational efficiency, highlighting bounded-confidence dynamics as a scalable and effective inductive bias for attention.

cs.LG↗
arXiv2026

Escaping Plato's Cave: JAM for Aligning Independently Trained Vision and Language Models

Independently trained vision and language models inhabit disjoint representational spaces, shaped by their respective modalities, objectives, and architectures. The Platonic Representation Hypothesis (PRH) suggests these models may nonetheless converge toward a shared statistical model of reality. This raises a fundamental question: can we move beyond post-hoc detection of such alignment and explicitly optimize for it? We argue this challenge is most critical in fine-grained contextual distinctions-where multiple descriptions share global semantics but differ in subtle compositional details. We address this with the Joint Autoencoder Modulator (JAM), which aligns frozen unimodal models by jointly training modality-specific autoencoders with coordinated reconstruction and cross-modal alignment objectives. We systematically evaluate JAM across three design axes: (i) alignment objectives, introducing our multimodal Spread Loss that outperforms classic contrastive methods; (ii) the layer depth at which alignment is most effective; and (iii) the role of foundation model scale in representational convergence. Our findings show that JAM reliably induces alignment even across independently trained representations, offering both theoretical insight into the structure of shared semantics and practical guidance for transforming generalist unimodal foundations into specialist multimodal models.

cs.LG↗
arXiv2026

End-to-End Autoregressive Image Generation with 1D Semantic Tokenizer

Autoregressive image modeling relies on visual tokenizers to compress images into compact latent representations. We design an end-to-end training pipeline that jointly optimizes reconstruction and generation, enabling direct supervision from generation results to the tokenizer. This contrasts with prior two-stage approaches that train tokenizers and generative models separately. We further investigate leveraging vision foundation models to improve 1D tokenizers for autoregressive modeling. Our autoregressive generative model achieves strong empirical results, including a state-of-the-art FID score of 1.48 without guidance on ImageNet 256x256 generation.

cs.CV↗
arXiv2026

Programmatic Context Augmentation for LLM-based Symbolic Regression

Symbolic regression (SR), the task of discovering mathematical expressions that best describe a given dataset, remains a fundamental challenge in scientific discovery. Traditional approaches, primarily based on genetic algorithms and related evolutionary methods, have proven useful but suffer from scalability and expressivity limitations. Recently, large language model (LLM)-based evolutionary search methods have been introduced into SR and show promise. However, existing LLM-based approaches typically rely on scalar evaluation metrics, such as mean squared error, as the sole source of feedback during the search process, thereby overlooking the rich information embedded in the dataset. To address this limitation, we propose a novel LLM-based evolutionary search framework that incorporates programmatic context augmentation. By enabling code-based interactions with the dataset, our method can actively perform data analysis and extract informative signals, beyond aggregated evaluation scores. We evaluate our framework on advanced benchmarks, such as LLM-SRBench, and demonstrate superior efficiency and accuracy compared to strong baselines.

cs.AI↗
arXiv2026

Planetary Exploration 3.0: A Roadmap for Software-Defined, Radically Adaptive Space Systems

The surface and subsurface of worlds beyond Mars remain largely unexplored. Yet these worlds hold keys to fundamental questions in planetary science - from potentially habitable subsurface oceans on icy moons to ancient records preserved in Kuiper Belt objects. NASA's success in Mars exploration was achieved through incrementalism: 22 progressively sophisticated missions over decades. This paradigm, which we call Planetary Exploration 2.0 (PE 2.0), is untenable for the outer Solar System, where cruise times of a decade or more make iterative missions infeasible. We propose Planetary Exploration 3.0 (PE 3.0): a paradigm in which unvisited worlds are explored by a single or a few missions with radically adaptive space systems. A PE 3.0 mission conducts both initial exploratory science and follow-on hypothesis-driven science based on its own in situ data returns, evolving spacecraft capabilities to work resiliently in previously unseen environments. The key enabler of PE 3.0 is software-defined space systems (SDSSs) - systems that can adapt their functions at all levels through software updates. This paper presents findings from a Keck Institute for Space Studies (KISS) workshop on PE 3.0, covering: (1) PE 3.0 systems engineering including science definition, architecture, design methods, and verification & validation; (2) software-defined space system technologies including reconfigurable hardware, multi-functionality, and modularity; (3) onboard intelligence including autonomous science, navigation, controls, and embodied AI; and (4) three PE 3.0 mission concepts: a Neptune/Triton smart flyby, an ocean world explorer, and an Oort cloud reconnaissance mission.

astro-ph.IM↗
arXiv2026

Instructing LLMs to Negotiate using Reinforcement Learning with Verifiable Rewards

The recent advancement of Large Language Models (LLMs) has established their potential as autonomous interactive agents. However, they often struggle in strategic games of incomplete information, such as bilateral price negotiation. In this paper, we investigate if Reinforcement Learning from Verifiable Rewards (RLVR) can effectively teach LLMs to negotiate. Specifically, we explore the strategic behaviors that emerge during the learning process. We introduce a framework that trains a mid-sized buyer agent against a regulated LLM seller across a wide distribution of real-world products. By grounding reward signals directly in the maximization of economic surplus and strict adherence to private budget constraints, we reveal a novel four-phase strategic evolution. The agent progresses from naive bargaining to using aggressive starting prices, moves through a phase of deadlock, and ultimately develops sophisticated persuasive skills. Our results demonstrate that this verifiable training allows a 30B agent to significantly outperform frontier models over ten times its size in extracting surplus. Furthermore, the trained agent generalizes robustly to stronger counterparties unseen during training and remains effective even when facing hostile, adversarial seller personas.

cs.AI↗
arXiv2026

A Narwhal-Inspired Sensing-to-Control Framework for Small Fixed-Wing Aircraft

Fixed-wing unmanned aerial vehicles (UAVs) offer endurance and efficiency but lack low-speed agility due to highly coupled dynamics. We present an end-to-end sensing-to-control pipeline that combines bio-inspired hardware, physics-informed dynamics learning, and convex control allocation. Measuring airflow on a small airframe is difficult because near-body aerodynamics, propeller slipstream, control-surface actuation, and ambient gusts distort pressure signals. Inspired by the narwhal's protruding tusk, we mount in-house multi-hole probes far upstream and complement them with sparse, carefully placed wing pressure sensors for local flow measurement. A data-driven calibration maps probe pressures to airspeed and flow angles. We then learn a control-affine dynamics model using the estimated airspeed/angles and sparse sensors. A soft left/right symmetry regularizer improves identifiability under partial observability and limits confounding between wing pressures and flaperon inputs. Desired wrenches (forces and moments) are realized by a regularized least-squares allocator that yields smooth, trimmed actuation. Wind-tunnel studies across a wide operating range show that adding wing pressures reduces force-estimation error by 25-30%, the proposed model degrades less under distribution shift (about 12% versus 44% for an unstructured baseline), and force tracking improves with smoother inputs, including a 27% reduction in normal-force RMSE versus a plain affine model and 34% versus an unstructured baseline.

cs.RO↗
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↗