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MoleBridge: Synthetic Space Projecting with Discrete Markov Bridges

Neural Information Processing Systems

Molecular synthetic space projecting is a critical technique in de novo molecular design, which aims to rectify molecules without synthesizability guarantee by converting them into synthetic postfix notations. However, the vast synthesizable chemical space and the discrete data modalities involved pose significant challenges to postfix notation conversion benchmarking. In this paper, we exploit conditional probability transitions in discrete state space and introduce MoleBridge, a deep generative model built on the Markov bridge approach for designing postfix notations of molecular synthesis pathways. MoleBridge consists of two iterative optimizations: i) Autoregressive extending of notation tokens from molecular graphs, and ii) generation of discrete reaction postfix notations through Markov bridge, where noisy token blocks are progressively denoised over multi-step iterations. For the challenging second iteration, which demands sensitivity to incorrect generative probability paths within intricate chemical spaces, we employ a thinking and denoising separation approach to denoise. Empirically, we find that MoleBridge is capable of accurately predicting synthesis pathways while exhibiting excellent performance in a variety of application scenarios.


Progressive Data Dropout: An Embarrassingly Simple Approach to Train Faster

Neural Information Processing Systems

The success of the machine learning field has reliably depended on training on large datasets. While effective, this trend comes at an extraordinary cost. This is due to two deeply intertwined factors: the size of models and the size of datasets. While promising research efforts focus on reducing the size of models, the other half of the equation remains fairly mysterious. Indeed, it is surprising that the standard approach to training remains to iterate over and over, uniformly sampling the training dataset.


Worse than Zero shot Checking for Evaluating the Robustness of Misleading Retrievals

Neural Information Processing Systems

Retrieval-augmented generation (RAG) has shown impressive capabilities in mitigating hallucinations in large language models (LLMs). However, LLMs struggle to maintain consistent reasoning when exposed to misleading or conflicting evidence, especially in real-world domains such as politics, where information is polarized or selectively framed. Mainstream RAG benchmarks evaluate models under clean retrieval settings, where systems generate answers from gold-standard documents, or under synthetically perturbed settings, where documents are artificially injected with noise. These assumptions fail to reflect real-world conditions, often leading to an overestimation of RAG system performance. To address this gap, we introduce RAGUARD, the first benchmark to evaluate the robustness of RAG systems against misleading retrievals.


S-Crescendo: ANested Transformer Weaving Framework for Scalable Nonlinear System in S-Domain Representation

Neural Information Processing Systems

Simulation of high-order nonlinear system requires extensive computational resources, especially in modern VLSI backend design where bifurcation-induced instability and chaos-like transient behaviors pose challenges.


STaR-Bets: Sequential Target-Recalculating Bets for Tighter Confidence Intervals

Neural Information Processing Systems

The construction of confidence intervals for the mean of a bounded random variable is a classical problem in statistics with numerous applications in machine learning and virtually all scientific fields. In particular, obtaining the tightest possible confidence intervals is vital every time the sampling of the random variables is expensive. The current state-of-the-art method to construct confidence intervals is by using betting algorithms. This is a very successful approach for deriving optimal confidence sequences, even matching the rate of law of iterated logarithms. However, in the fixed horizon setting, these approaches are either sub-optimal or based on heuristic solutions with strong empirical performance but without a finite-time guarantee.


KTAE: AModel-Free Algorithm to Key-Tokens Advantage Estimation in Mathematical Reasoning

Neural Information Processing Systems

Recent advances have demonstrated that integrating reinforcement learning with rule-based rewards can significantly enhance the reasoning capabilities of large language models, even without supervised fine-tuning. However, prevalent reinforcement learning algorithms such as GRPO and its variants like DAPO, suffer from a coarse granularity issue when computing the advantage. Specifically, they compute rollout-level advantages that assign identical values to every token within a sequence, failing to capture token-specific contributions and hindering effective learning. To address this limitation, we propose Key-token Advantage Estimation (KTAE) - a novel algorithm that estimates fine-grained, token-level advantages without introducing additional models. KTAE leverages the correctness of sampled rollouts and applies statistical analysis to quantify the importance of individual tokens within a sequence to the final outcome. This quantified token-level importance is then combined with the rollout-level advantage to obtain a more fine-grained token-level advantage estimation. Empirical results show that models trained with GRPO+KTAE and DAPO+KTAE outperform baseline methods across five mathematical reasoning benchmarks. Notably, they achieve higher accuracy with shorter responses and even surpass R1-Distill-Qwen-1.5B using the same base model.


SEMPO: Lightweight Foundation Models for Time Series Forecasting

Neural Information Processing Systems

Despite impressive performance across diverse downstream forecasting tasks, existing time series FMs possess massive network architectures and require substantial pre-training on large-scale datasets, which significantly hinders their deployment in resourceconstrained environments. In response to this growing tension between versatility and affordability, we propose SEMPO, a novel lightweight foundation model that requires pretraining on relatively small-scale data, yet exhibits strong general time series forecasting. Concretely, SEMPO comprises two key modules: 1) energyaware SpEctral decomposition module, that substantially improves the utilization of pre-training data by modeling not only the high-energy frequency signals but also the low-energy yet informative frequency signals that are ignored in current methods; and 2) Mixture-of-PrOmpts enabled Transformer, that learns heterogeneous temporal patterns through small dataset-specific prompts and adaptively routes time series tokens to prompt-based experts for parameter-efficient model adaptation across different datasets and domains. Equipped with these modules, SEMPO significantly reduces both pre-training data scale and model size, while achieving strong generalization. Extensive experiments on two large-scale benchmarks covering 16 datasets demonstrate the superior performance of SEMPO in both zero-shot and few-shot forecasting scenarios compared with state-of-the-art methods. Code and data are available at https://github.com/mala-lab/SEMPO.


Marginal-Nonuniform PACLearnability

Neural Information Processing Systems

We revisit the classical model of nonuniform PAC learning, introduced by Benedek and Itai [1994], where generalization guarantees may depend on the target concept (but not on the marginal distribution). In this work, we study a complementary variant, which we call marginal-nonuniform learning. In this setting, guarantees may depend on the marginal distribution over the domain, but must hold uniformly over all concepts. This captures the intuition that some data distributions are inherently easier to learn from than others, allowing for a flexible, distributionsensitive view of learnability. Our main result is a complete characterization of the achievable learning rates in this model, revealing a trichotomy: exponential rates of the form e n arise precisely when the hypothesis class is finite; linear rates of the form d/n are achievable when a recently introduced combinatorial parameter, the VC-eluder dimension d, is finite; and arbitrarily slow rates may occur when d = . Additionally, in the original (concept-)nonuniform model, we show that for all learnable classes linear rates are achievable. We conclude by situating marginal-nonuniform learning within the landscape of universal learning, and by discussing its relationship to other distribution-dependent learning paradigms.


AlphaBeta is not as good as you think: a simple class of synthetic games for a better analysis of deterministic game-solving algorithms

Neural Information Processing Systems

Deterministic game-solving algorithms are conventionally analyzed in the light of their average-case complexity against a distribution of random game-trees, where leaf values are independently sampled from a fixed distribution. This simplified model enables uncluttered mathematical analysis, revealing two key properties: root value distributions asymptotically collapse to a single fixed value for finitevalued trees, and all reasonable algorithms achieve global optimality. However, these findings are artifacts of the model's design: its long criticized independence assumption strips games of structural complexity, producing trivial instances where no algorithm faces meaningful challenges. To address this limitation, we introduce a class of synthetic games generated by a probabilistic model that incrementally constructs game-trees using a fixed level-wise conditional distribution. By enforcing ancestor dependencies, a critical structural feature of real-world games, our framework generates problems with adjustable difficulty while retaining some form of analytical tractability. For several algorithms, including AlphaBeta and Scout, we derive recursive formulas characterizing their average-case complexities under this model. These allow us to rigorously compare algorithms on deep gametrees, where Monte-Carlo simulations are no longer feasible. While asymptotically, all algorithms seem to converge to identical branching factor (a result analogous to that of independence-based models), deep finite trees reveal stark differences: AlphaBeta incurs a significantly larger constant multiplicative factor compared to algorithms like Scout, leading to a substantial practical slowdown. Our framework sheds new light on classical game-solving algorithms, offering rigorous evidence and analytical tools to advance the understanding of these methods under a richer, more challenging, and yet tractable model.


Shape-Informed Clustering of Multi-Dimensional Functional Data via Deep Functional Autoencoders

Neural Information Processing Systems

We introduce FAEclust, a novel functional autoencoder framework for cluster analysis of multi-dimensional functional data, data that are random realizations of vector-valued random functions. Our framework features a universal-approximator encoder that captures complex nonlinear interdependencies among component functions, and a universal-approximator decoder capable of accurately reconstructing both Euclidean and manifold-valued functional data. Stability and robustness are enhanced through innovative regularization strategies applied to functional weights and biases. Additionally, we incorporate a clustering loss into the network's training objective, promoting the learning of latent representations that are conducive to effective clustering. A key innovation is our shape-informed clustering objective, ensuring that the clustering results are resistant to phase variations in the functions. We establish the universal approximation property of our non-linear decoder and validate the effectiveness of our model through extensive experiments.