#01Nov 9, 2026
stat.ML
Trajectory Density Ratios under Weak Support: A Survey across the Sciences
Wei Chen, Lihao Zhuang, Yubing Wu and 1 more
Many problems across the sciences compare two stochastic processes through the sequences they generate. Reinforcement learning asks what a new policy would return from the trajectories of an old one; molecular simulation asks how much more a ligand binds from samples of the unbound state; climate attribution asks how a heat wave shifted under warming; and language-model post-training asks what a deployed agent will do from logged interactions. In every case, one quantity would answer all these questions at once: the ratio of the two probability laws over their generated sequences, the trajectory density ratio. This ratio exists only under strong conditions. When one process reaches states the other cannot, the ratio does not exist; when their overlap is thin, its variance grows without control with the sequence length; and when they concentrate on different lower-dimensional sets, the ratio is undefined altogether. Weak support of this kind is the norm for sequence data, not a sampling accident, and its price is paid in identifiability rather than in noise alone. This survey organizes the field around a three-level diagnosis of weak support and a map of the nine retreats that methods take when the full ratio is out of reach, from direct estimation and reweighting through staged decomposition, stationarization, and partial-identification bounds to smoothing, transport couplings, operator spectra, and direct estimation of a single functional. Each retreat keeps part of what the ratio offers and pays for the rest, and each application domain has standardized the retreat its data force. The survey closes with open problems: testable diagnostics at every level, partial identification at the trajectory level, a rate theory of time-amplified error, and benchmarks with ground truth.
#02Nov 9, 2026
cs.LG
Shaping Useful Noise: Energy Distributions Predict Visual Pretraining Quality
Ching Lam Choi, Antonio Torralba, Phillip Isola and 1 more
Synthetic data can scale visual pretraining, but current selection criteria only partially explain which datasets train strong representations. We propose using the energy profile of a dataset--the distribution of log-probability levels it occupies under a normalised real-image density model--as an audit and curation principle for synthetic data. To operationalise this view, we introduce Energy-Level Distribution Distance (ELD), which compares real and synthetic energy distributions. Real images span sparse high-likelihood scenes and dense low-likelihood textures, so useful synthetic data should cover this energy range rather than collapse to likely but low-variation samples. Across diverse synthetic datasets, ELD exposes mismatches missed by FID and predicts pretraining performance beyond FID, LPIPS variation, and feature-space recall, including across CNN and ViT self-supervised settings. We then use ELD to resample and mix synthetic sources, matching the real-image energy histogram while preserving diversity and improving downstream transfer.
#03Nov 9, 2026
cs.LG
MambaPD: Bidirectional Selective State Space Model for Parkinson's Disease Detection from Resting-State EEG
Ayesha Zulfiqar
Typical diagnosis of Parkinson's disease (PD) occurs only after significant dopaminergic loss, while resting-state EEG abnormalities like alpha slowing and reduced coherence occur earlier. While many published EEG-based PD detectors claim accuracy greater than 95%, many use epoch-level splits which leak subject identity. I introduce MambaPD, a bidirectional selective state space model for resting-state EEG-based PD detection, blending the channel mixing, patch tokenization and bidirectional Mamba encoder. It is compared with four baselines (TCN, BiLSTM with attention, EEGNet and a patch Transformer) in two public datasets (UNM, SanDiego) using subject-independent 5-fold cross-validation (checkpoints were selected on the held-out fold, so absolute estimates are optimistic). On UNM the accuracy is between 0.67 and 0.71, and MambaPD (0.714) is not statistically distinguishable from the Transformer (0.715), and TCN (0.708), with the highest sensitivity (0.82), while the lowest specificity (0.52). For the smaller SanDiego cohort, accuracy is in the range of 0.60 to 0.70, with the highest scores (0.703) from TCN and the lowest (0.601) from EEGNet, while MambaPD scores 0.631, with the lowest specificity (0.46) among the five models. The differences among the models on UNM are minor compared to the differences among folds. I report the whole pipeline, per-fold results, and the shortcomings of the protocol.
#04Nov 9, 2026
cs.LG
Scalable Bayesian Optimization for Efficient Exploration of Moire Patterns
Panagiotis Krokidas, Christos Lazaridis, Vassilis Sioros and 3 more
Large materials design spaces often contain rare high-performing configurations that are difficult to identify through trial-and-error exploration or purely representative machine-learning (ML) sampling. In this work, we present FruBO, a flexible Bayesian Optimization framework for accelerating the discovery of optimal configurations in computationally demanding materials design problems. As a case study, we investigate multilayer Moiré patterns generated by the superposition of six rotated hexagonal lattices, where the objective is to identify the rotational conformation that maximizes pore-size uniformity, quantified using the Jain fairness index. The resulting benchmark contains 600,000 unique configurations and exhibits a highly skewed objective distribution, making the global optimum difficult to locate by random sampling. We compare random exploration, Gaussian Process-based Bayesian Optimization, and Bayesian Optimization using a lightweight CatBoost surrogate with committee-based uncertainty estimation. Random sampling identifies the global optimum only after 533,012 evaluations, requiring approximately 31 hours, while Gaussian Process-based BO becomes impractical due to GPU memory exhaustion after 290 acquired samples. In contrast, FruBO with CatBoost identifies the global optimum after 1,470 acquired samples and approximately 1.15 hours. These results demonstrate that scalable surrogate models can substantially improve the feasibility and efficiency of BO in large nanomaterials design spaces.
#05Nov 9, 2026
cs.LG
HyPLM Technical Report
Haowei Lin, Cai Zhou, Xiangxin Zhou
Protein language models (PLMs) are standard tools for variant-effect prediction, protein annotation and design, but the compute needed to train and serve them keeps growing. We present HyPLM-Flash, an efficient and open PLM trained by Hyra 2.0, the research agent developed by our team. HyPLM-Flash is a 650-million-parameter masked language model trained on 726 billion tokens, 0.73 times the data of ESM-2 650M and a fifth to an eighth of the data of E1-600M and ESM C 600M. It runs on an inference engine with fused kernels and INT8 matrix multiplication, embedding about 130,000 residues per second on a single NVIDIA H20 GPU, 1.9 to 2.7 times faster than other 600M-class encoders. In a matched evaluation against 28 public checkpoints on 32 tasks, HyPLM-Flash reaches a ProteinGym zero-shot Spearman correlation of 0.409, statistically tied with ESM-2 650M, ESM C 600M and E1-600M, and the highest organismal-fitness score among self-supervised single-sequence models. It gives the best long-range contact precision of all models evaluated, including ESM-2 15B and ESM C 6B, and a lower masked-residue loss than ESM-2 650M, ESM C 600M and E1-600M on held-out sequences and on recently released PDB chains. Matching state-of-the-art accuracy at a fraction of the training and inference cost, HyPLM-Flash sets a new Pareto frontier for protein language models. We have released the model weights and the inference engine at https://github.com/Tencent-Hunyuan/hyra-results/tree/main.