Protein structure prediction has largely focused on native conformations, leaving the continuum of unfolded states, folding intermediates, and native structures difficult to access. We present FoldScape, a sequence-conditioned deep learning framework for generating protein conformational ensembles at specified folding fractions $Q$. Trained on approximately one million conformations from 10,000 protein sequences, FoldScape combines coarse-grained folding and all-atom mechanical-unfolding trajectories. It reconstructs three-dimensional $C_α$ chains through hierarchical sliding-window regressions of inter-residue distances, chain-level assembly, and a rectified-flow decoder. By conditioning on folding progress, FoldScape generates conformations from unfolded states through intermediates to native-state structures without protein-specific molecular dynamics at inference. In matched-sample comparisons, FoldScape achieves median conformational-space coverage of 0.989, 0.722, and 0.877 along radius of gyration, fraction of native contacts $Q$, and secondary-structure fraction, respectively, versus 0.05, 0.05, and 0.10 for seed-varied AlphaFold 3 ensembles. Coverage advantages are consistent across the evaluated proteins and robust to binning choices. Reconstruction accuracy remains approximately stable across the evaluated stages of a folding trajectory, and stride-one crop-and-superpose inference extends predictions to chains several times longer than the single-pass limit. Analyses of mechanical-unfolding trajectories show residue-resolved pathways, reproducible extension-conditioned observables across pulling velocities, and geometrically coherent segments in partially unfolded chains. FoldScape extends sequence-based structure prediction beyond a single folded endpoint to controllable conformational-ensemble generation across protein folding.
Junzhao Huang, Xi Wu, Zihan Wang, Zijing Wang, Ming Wang, Kang Liu, Xiaocui Yang, Shi Feng 等 12 位作者
Large language model (LLM) embeddings have been increasingly adopted in sequential recommendation to encode static item attributes and alleviate the limitations of item ID embeddings under sparse interactions. However, these embeddings typically capture only static content similarity while neglecting sequential transitions, and since their adaptation quality relies on sparse per-item updates or global geometric calibration, existing methods still struggle to explicitly transfer preceding interaction contexts from frequent to long-tail items under unevenly distributed behavioral evidence, limiting recommendation effectiveness across the catalog. To address this challenge, we propose PACERec, an ID-free progressive adaptation framework that incorporates preceding interaction contexts into semantic representation adaptation by learning a shared velocity field from items with sufficient interactions via frequency-weighted flow matching. In this way, PACERec progressively guides static LLM embeddings toward collaborative behavioral targets while preserving original item semantics, overcoming sparse per-item updates to effectively generalize sequential transition patterns to long-tail items for both user modeling and candidate scoring. Extensive experiments on three real-world datasets across three sequential backbones demonstrate the superiority of our method over competitive baselines in both overall and long-tail recommendation.
Jiahao Wu, Ning Lu, Shengcai Liu, Kun Wang, Yanting Yang, Baijiong Lin, Chen Jason Zhang, Li Qing 等 9 位作者
Reinforcement learning (RL) has become essential for post-training large language models (LLMs) in reasoning tasks. While scaling rollouts can stabilize training and enhance performance, the computational overhead is a critical issue. In algorithms like GRPO, multiple rollouts per prompt incur prohibitive costs, as a large portion of prompts provide negligible gradients and are thus of low utility. To address this problem, we investigate how to select high-utility prompts before the rollout phase. Our experimental analysis reveals that sample utility is non-uniform and evolving: the strongest learning signals concentrate at the ``learning edge", the intersection of intermediate difficulty and high uncertainty, which shifts as training proceeds. Motivated by this, we propose HIVE (History-Informed and online-VErified prompt selection), a dual-stage framework for data-efficient RL. HIVE utilizes historical reward trajectories for coarse selection and employs prompt entropy as a real-time proxy to prune instances with stale utility. By evaluating HIVE across multiple math reasoning benchmarks and models, we show that HIVE yields significant rollout efficiency without compromising performance.