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arXiv:2506.05628v2 Announce Type: replace Abstract: The ability to design molecules while preserving similarity to a target molecule and/or property is crucial for various applications in drug discovery, chemical design, and biology. We introduce in this paper an efficient training-free method for navigating and sampling from the molecular space with a generative Chemical Language Model (CLM), while using the molecular similarity to the target as a guide. Our method leverages the contextual representations learned from the CLM itself to estimate the molecular similarity, which is then used to adjust the autoregressive sampling strategy of the CLM. At each step of the decoding process, the method tracks the distance of the current generations from the target and updates the logits to encourage the preservation of similarity in generations. We implement the method using a recently proposed $\sim$47M parameter SMILES-based CLM, GP-MoLFormer, and therefore refer to the method as GP-MoLFormer-Sim, which enables a test-time update of the deep generative policy to reflect the contextual similarity to a set of guide molecules. The method is further integrated into a genetic algorithm (GA) and tested on a set of standard molecular optimization benchmarks involving property optimization, molecular rediscovery, and structure-based drug design. Results show that, GP-MoLFormer-Sim, combined with GA (GP-MoLFormer-Sim+GA) outperforms existing training-free baseline methods, when the oracle remains black-box. The findings in this work are a step forward in understanding and guiding the generative mechanisms of CLMs.

arXiv:2506.05178v2 Announce Type: replace Abstract: This paper shows that generative diffusion processes converge to associative memory systems at vanishing noise levels and characterizes the stability, robustness, memorization, and generation dynamics of both model classes. Morse-Smale dynamical systems are shown to be universal approximators of associative memory models, with diffusion processes as their white-noise perturbations. The universal properties of associative memory that follow are used to characterize a generic transition from generation to memory as noise diminishes. Structural stability of Morse-Smale flows -- that is, the robustness of their global critical point structure -- implies the stability of both trajectories and invariant measures for diffusions in the zero-noise limit. The learning and generation landscapes of these models appear as parameterized families of gradient flows and their stochastic perturbations, and the bifurcation theory for Morse-Smale systems implies that they are generically stable except at isolated parameter values, where enumerable sets of local and global bifurcations govern transitions between stable systems in parameter space. These landscapes are thus characterized by ordered bifurcation sequences that create, destroy, or alter connections between rest points and are robust under small stochastic or deterministic perturbations. The framework is agnostic to model formulation, which we verify with examples from energy-based models, denoising diffusion models, and classical and modern Hopfield networks. We additionally derive structural stability criteria for Hopfield-type networks and find that simple cases violate them. Collectively, our geometric approach provides insight into the classification, stability, and emergence of memory and generative landscapes.

arXiv:2505.21895v2 Announce Type: replace Abstract: Resource-constrained weight deployment is a task of immense practical importance. Recently, there has been interest in the specific task of \textit{Delta Compression}, where parties each hold a common base model and only communicate compressed weight updates. However, popular parameter efficient updates such as Low Rank Adaptation (LoRA) face inherent representation limitations - which are especially pronounced when combined with aggressive quantization. To overcome this, we build on recent work that improves LoRA representation capacity by using fixed-frequency sinusoidal functions to increase stable rank without adding additional parameters. We extend this to the quantized setting and present the first theoretical analysis showing how stable rank evolves under quantization. From this, we introduce SineLoRA$\Delta$, a principled and effective method for delta compression that improves the expressivity of quantized low-rank adapters by applying a sinusoidal activation. We validate SineLoRA$\Delta$ across a diverse variety of domains - including language modeling, vision-language tasks, and text-to-image generation - achieving up to 66% memory reduction with similar performance. We additionally provide a novel application of the canonical Bj{\o}ntegaard Delta metric to consistently compare adapter compression changes across the rate-distortion curve.

arXiv:2511.05805v2 Announce Type: replace Abstract: AI models are often evaluated based on their ability to predict the outcome of interest. However, in many AI for social impact applications, the presence of an intervention that affects the outcome can bias the evaluation. Randomized controlled trials (RCTs) randomly assign interventions, allowing data from the control group to be used for unbiased model evaluation. However, this approach is inefficient because it ignores data from the treatment group. Given the complexity and cost often associated with RCTs, making the most use of the data is essential. Thus, we investigate model evaluation strategies that leverage all data from an RCT. First, we theoretically quantify the estimation bias that arises from na\"ively aggregating performance estimates from treatment and control groups and derive the condition under which this bias leads to incorrect model selection. Leveraging these theoretical insights, we propose nuisance parameter weighting (NPW), an unbiased model evaluation approach that reweights data from the treatment group to mimic the distributions of samples that would or would not experience the outcome under no intervention. Using synthetic and real-world datasets, we demonstrate that our proposed evaluation approach consistently yields better model selection than the standard approach, which ignores data from the treatment group, across various intervention effect and sample size settings. Our contribution represents a meaningful step towards more efficient model evaluation in real-world contexts.

arXiv:2505.21020v4 Announce Type: replace Abstract: Long-term, high-fidelity simulation of slow-changing physical systems, such as the ocean and climate, presents a fundamental challenge in scientific computing. Traditional autoregressive machine learning models often fail in these tasks as minor errors accumulate and lead to rapid forecast degradation. To address this problem, we propose NeuralOM, a general neural operator framework designed for simulating complex, slow-changing dynamics. NeuralOM's core consists of two key innovations: (1) a Progressive Residual Correction Framework that decomposes the forecasting task into a series of fine-grained refinement steps, effectively suppressing long-term error accumulation; and (2) a Physics-Guided Graph Network whose built-in adaptive messaging mechanism explicitly models multi-scale physical interactions, such as gradient-driven flows and multiplicative couplings, thereby enhancing physical consistency while maintaining computational efficiency. We validate NeuralOM on the challenging task of global Subseasonal-to-Seasonal (S2S) ocean simulation. Extensive experiments demonstrate that NeuralOM not only surpasses state-of-the-art models in forecast accuracy and long-term stability, but also excels in simulating extreme events. For instance, at a 60-day lead time, NeuralOM achieves a 13.3% lower RMSE compared to the best-performing baseline, offering a stable, efficient, and physically-aware paradigm for data-driven scientific computing. Code link: https://github.com/YuanGao-YG/NeuralOM.

arXiv:2505.17708v3 Announce Type: replace Abstract: Causal reasoning and discovery, two fundamental tasks of causal analysis, often face challenges in applications due to the complexity, noisiness, and high-dimensionality of real-world data. Despite recent progress in identifying latent causal structures using causal representation learning (CRL), what makes learned representations useful for causal downstream tasks and how to evaluate them are still not well understood. In this paper, we reinterpret CRL using a measurement model framework, where the learned representations are viewed as proxy measurements of the latent causal variables. Our approach clarifies the conditions under which learned representations support downstream causal reasoning and provides a principled basis for quantitatively assessing the quality of representations using a new Test-based Measurement EXclusivity (T-MEX) score. We validate T-MEX across diverse causal inference scenarios, including numerical simulations and real-world ecological video analysis, demonstrating that the proposed framework and corresponding score effectively assess the identification of learned representations and their usefulness for causal downstream tasks.

arXiv:2505.15987v4 Announce Type: replace Abstract: We study identifiability of stochastic differential equations (SDE) under multiple interventions. Our results give the first provable bounds for unique recovery of SDE parameters given samples from their stationary distributions. We give tight bounds on the number of necessary interventions for linear SDEs, and upper bounds for nonlinear SDEs in the small noise regime. We experimentally validate the recovery of true parameters in synthetic data, and motivated by our theoretical results, demonstrate the advantage of parameterizations with learnable activation functions in application to gene regulatory dynamics.

arXiv:2505.15813v2 Announce Type: replace Abstract: Understanding functional representations within higher visual cortex is a fundamental question in computational neuroscience. While artificial neural networks pretrained on large-scale datasets exhibit striking representational alignment with human neural responses, learning image-computable models of visual cortex relies on individual-level, large-scale fMRI datasets. The necessity for expensive, time-intensive, and often impractical data acquisition limits the generalizability of encoders to new subjects and stimuli. BraInCoRL uses in-context learning to predict voxelwise neural responses from few-shot examples without any additional finetuning for novel subjects and stimuli. We leverage a transformer architecture that can flexibly condition on a variable number of in-context image stimuli, learning an inductive bias over multiple subjects. During training, we explicitly optimize the model for in-context learning. By jointly conditioning on image features and voxel activations, our model learns to directly generate better performing voxelwise models of higher visual cortex. We demonstrate that BraInCoRL consistently outperforms existing voxelwise encoder designs in a low-data regime when evaluated on entirely novel images, while also exhibiting strong test-time scaling behavior. The model also generalizes to an entirely new visual fMRI dataset, which uses different subjects and fMRI data acquisition parameters. Further, BraInCoRL facilitates better interpretability of neural signals in higher visual cortex by attending to semantically relevant stimuli. Finally, we show that our framework enables interpretable mappings from natural language queries to voxel selectivity.

arXiv:2505.11250v4 Announce Type: replace Abstract: The forecasting of irregular multivariate time series (IMTS) is crucial in key areas such as healthcare, biomechanics, climate science, and astronomy. However, achieving accurate and practical predictions is challenging due to two main factors. First, the inherent irregularity and data missingness in irregular time series make modeling difficult. Second, most existing methods are typically complex and resource-intensive. In this study, we propose a general framework called APN to address these challenges. Specifically, we design a novel Time-Aware Patch Aggregation (TAPA) module that achieves adaptive patching. By learning dynamically adjustable patch boundaries and a time-aware weighted averaging strategy, TAPA transforms the original irregular sequences into high-quality, regularized representations in a channel-independent manner. Additionally, we use a simple query module to effectively integrate historical information while maintaining the model's efficiency. Finally, predictions are made by a shallow MLP. Experimental results on multiple real-world datasets show that APN outperforms existing state-of-the-art methods in both efficiency and accuracy.

arXiv:2504.09862v2 Announce Type: replace Abstract: Millimeter-wave radar offers a privacy-preserving and environment-robust alternative to vision-based sensing, enabling human motion analysis in challenging conditions such as low light, occlusions, rain, or smoke. However, its sparse point clouds pose significant challenges for semantic understanding. We present RadarLLM, the first framework that leverages large language models (LLMs) for human motion understanding from radar signals. RadarLLM introduces two key innovations: (1) a motion-guided radar tokenizer based on our Aggregate VQ-VAE architecture, integrating deformable body templates and masked trajectory modeling to convert spatial-temporal radar sequences into compact semantic tokens; and (2) a radar-aware language model that establishes cross-modal alignment between radar and text in a shared embedding space. To overcome the scarcity of paired radar-text data, we generate a realistic radar-text dataset from motion-text datasets with a physics-aware synthesis pipeline. Extensive experiments on both synthetic and real-world benchmarks show that RadarLLM achieves state-of-the-art performance, enabling robust and interpretable motion understanding under privacy and visibility constraints, even in adverse environments. This paper has been accepted for presentation at AAAI 2026. This is an extended version with supplementary materials.

arXiv:2503.20191v2 Announce Type: replace Abstract: Training large foundation models costs hundreds of millions of dollars, making deployment optimization critical. Current approaches require machine learning engineers to manually craft training recipes through error-prone trial-and-error on expensive compute clusters. To enable efficient exploration of training configurations, researchers have developed performance modeling systems. However, these systems force users to translate their workloads into custom specification languages, introducing a fundamental semantic gap between the actual workload and its representation. This gap creates an inherent tradeoff: systems must either support a narrow set of workloads to maintain usability, require complex specifications that limit practical adoption, or compromise prediction accuracy with simplified performance models. We present Maya, a performance modeling system that eliminates these tradeoffs through transparent device emulation. By operating at the narrow interface between training frameworks and accelerator devices, Maya can capture complete workload behavior without requiring code modifications or translations. Maya intercepts device API calls from unmodified training code to directly observe low-level operations, enabling accurate performance prediction while maintaining both ease of use and generality. Our evaluation shows Maya achieves less than 5% prediction error across diverse models and optimization strategies, identifying configurations that reduce training costs by up to 56% compared to existing approaches.

arXiv:2503.20102v3 Announce Type: replace Abstract: Long-horizon planning is crucial in complex environments, but diffusion-based planners like Diffuser are limited by the trajectory lengths observed during training. This creates a dilemma: long trajectories are needed for effective planning, yet they degrade model performance. In this paper, we introduce this extendable long-horizon planning challenge and propose a two-phase solution. First, Progressive Trajectory Extension incrementally constructs longer trajectories through multi-round compositional stitching. Second, the Hierarchical Multiscale Diffuser enables efficient training and inference over long horizons by reasoning across temporal scales. To avoid the need for multiple separate models, we propose Adaptive Plan Pondering and the Recursive HM-Diffuser, which unify hierarchical planning within a single model. Experiments show our approach yields strong performance gains, advancing scalable and efficient decision-making over long-horizons.

arXiv:2503.17409v2 Announce Type: replace Abstract: In many practical reinforcement learning tasks, feedback is only provided at the end of a long horizon, leading to sparse and delayed rewards. Existing reward redistribution methods typically assume that per-step rewards are independent, thus overlooking interdependencies among state-action pairs. In this paper, we propose a Gaussian process based Likelihood Reward Redistribution (GP-LRR) framework that addresses this issue by modeling the reward function as a sample from a Gaussian process, which explicitly captures dependencies between state-action pairs through the kernel function. By maximizing the likelihood of the observed episodic return via a leave-one-out strategy that leverages the entire trajectory, our framework inherently introduces uncertainty regularization. Moreover, we show that conventional mean-squared-error (MSE) based reward redistribution arises as a special case of our GP-LRR framework when using a degenerate kernel without observation noise. When integrated with an off-policy algorithm such as Soft Actor-Critic, GP-LRR yields dense and informative reward signals, resulting in superior sample efficiency and policy performance on several MuJoCo benchmarks.

arXiv:2503.11217v3 Announce Type: replace Abstract: Universal Domain Adaptation (UniDA) aims to transfer knowledge from a labeled source domain to an unlabeled target domain, even when their classes are not fully shared. Few dedicated UniDA methods exist for Time Series (TS), which remains a challenging case. In general, UniDA approaches align common class samples and detect unknown target samples from emerging classes. Such detection often results from thresholding a discriminability metric. The threshold value is typically either a fine-tuned hyperparameter or a fixed value, which limits the ability of the model to adapt to new data. Furthermore, discriminability metrics exhibit overconfidence for unknown samples, leading to misclassifications. This paper introduces UniJDOT, an optimal-transport-based method that accounts for the unknown target samples in the transport cost. Our method also proposes a joint decision space to improve the discriminability of the detection module. In addition, we use an auto-thresholding algorithm to reduce the dependence on fixed or fine-tuned thresholds. Finally, we rely on a Fourier transform-based layer inspired by the Fourier Neural Operator for better TS representation. Experiments on TS benchmarks demonstrate the discriminability, robustness, and state-of-the-art performance of UniJDOT.

arXiv:2508.10644v2 Announce Type: replace Abstract: Multimodal sarcasm detection is a complex task that requires distinguishing subtle complementary signals across modalities while filtering out irrelevant information. Many advanced methods rely on learning shortcuts from datasets rather than extracting intended sarcasm-related features. However, our experiments show that shortcut learning impairs the model's generalization in real-world scenarios. Furthermore, we reveal the weaknesses of current modality fusion strategies for multimodal sarcasm detection through systematic experiments, highlighting the necessity of focusing on effective modality fusion for complex emotion recognition. To address these challenges, we construct MUStARD++$^{R}$ by removing shortcut signals from MUStARD++. Then, a Multimodal Conditional Information Bottleneck (MCIB) model is introduced to enable efficient multimodal fusion for sarcasm detection. Experimental results show that the MCIB achieves the best performance without relying on shortcut learning.

arXiv:2503.08305v4 Announce Type: replace Abstract: We present the Electronic Tensor Reconstruction Algorithm (ELECTRA) - an equivariant model for predicting electronic charge densities using floating orbitals. Floating orbitals are a long-standing concept in the quantum chemistry community that promises more compact and accurate representations by placing orbitals freely in space, as opposed to centering all orbitals at the position of atoms. Finding the ideal placement of these orbitals requires extensive domain knowledge, though, which thus far has prevented widespread adoption. We solve this in a data-driven manner by training a Cartesian tensor network to predict the orbital positions along with orbital coefficients. This is made possible through a symmetry-breaking mechanism that is used to learn position displacements with lower symmetry than the input molecule while preserving the rotation equivariance of the charge density itself. Inspired by recent successes of Gaussian Splatting in representing densities in space, we are using Gaussian orbitals and predicting their weights and covariance matrices. Our method achieves a state-of-the-art balance between computational efficiency and predictive accuracy on established benchmarks. Furthermore, ELECTRA is able to lower the compute time required to arrive at converged DFT solutions - initializing calculations using our predicted densities yields an average 50.72 % reduction in self-consistent field (SCF) iterations on unseen molecules.

arXiv:2503.05491v3 Announce Type: replace Abstract: Tasks are central in machine learning, as they are the most natural objects to assess the capabilities of current models. The trend is to build general models able to address any task. Even though transfer learning and multitask learning try to leverage the underlying task space, no well-founded tools are available to study its structure. This study proposes a theoretically grounded setup to define the notion of task and to compute the {\bf inclusion} between two tasks from a statistical deficiency point of view. We propose a tractable proxy as information sufficiency to estimate the degree of inclusion between tasks, show its soundness on synthetic data, and use it to reconstruct empirically the classic NLP pipeline.

arXiv:2503.02104v2 Announce Type: replace Abstract: Foundation models, first introduced in 2021, refer to large-scale pretrained models (e.g., large language models (LLMs) and vision-language models (VLMs)) that learn from extensive unlabeled datasets through unsupervised methods, enabling them to excel in diverse downstream tasks. These models, like GPT, can be adapted to various applications such as question answering and visual understanding, outperforming task-specific AI models and earning their name due to broad applicability across fields. The development of biomedical foundation models marks a significant milestone in the use of artificial intelligence (AI) to understand complex biological phenomena and advance medical research and practice. This survey explores the potential of foundation models in diverse domains within biomedical fields, including computational biology, drug discovery and development, clinical informatics, medical imaging, and public health. The purpose of this survey is to inspire ongoing research in the application of foundation models to health science.

arXiv:2502.16387v2 Announce Type: replace Abstract: Calibration is a fundamental concept that aims at ensuring the reliability of probabilistic predictions by aligning them with real-world outcomes. There is a surge of studies on new calibration measures that are easier to optimize compared to the classical $\ell_1$-Calibration while still having strong implications for downstream applications. One recent such example is the work by Fishelson et al. (2025) who show that it is possible to achieve $O(T^{1/3})$ pseudo $\ell_2$-Calibration error via minimizing pseudo swap regret of the squared loss, which in fact implies the same bound for all bounded proper losses with a smooth univariate form. In this work, we significantly generalize their result in the following ways: (a) in addition to smooth univariate forms, our algorithm also simultaneously achieves $O(T^{1/3})$ swap regret for any proper loss with a twice continuously differentiable univariate form (such as Tsallis entropy); (b) our bounds hold not only for pseudo swap regret that measures losses using the forecaster's distributions on predictions, but also hold for the actual swap regret that measures losses using the forecaster's actual realized predictions. We achieve so by introducing a new stronger notion of calibration called (pseudo) KL-Calibration, which we show is equivalent to the (pseudo) swap regret for log loss. We prove that there exists an algorithm that achieves $O(T^{1/3})$ KL-Calibration error and provide an explicit algorithm that achieves $O(T^{1/3})$ pseudo KL-Calibration error. Moreover, we show that the same algorithm achieves $O(T^{1/3}(\log T)^{-1/3}\log(T/\delta))$ swap regret w.p. $\ge 1-\delta$ for any proper loss with a smooth univariate form, which implies $O(T^{1/3})$ $\ell_2$-Calibration error. A technical contribution of our work is a new randomized rounding procedure and a non-uniform discretization scheme to minimize the swap regret for log loss.

arXiv:2502.08457v3 Announce Type: replace Abstract: Bilevel optimization has emerged as a technique for addressing a wide range of machine learning problems that involve an outer objective implicitly determined by the minimizer of an inner problem. While prior works have primarily focused on the parametric setting, a learning-theoretic foundation for bilevel optimization in the nonparametric case remains relatively unexplored. In this paper, we take a first step toward bridging this gap by studying Kernel Bilevel Optimization (KBO), where the inner objective is optimized over a reproducing kernel Hilbert space. This setting enables rich function approximation while providing a foundation for rigorous theoretical analysis. In this context, we derive novel finite-sample generalization bounds for KBO, leveraging tools from empirical process theory. These bounds further allow us to assess the statistical accuracy of gradient-based methods applied to the empirical discretization of KBO. We numerically illustrate our theoretical findings on a synthetic instrumental variable regression task.