#01Nov 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.
#02Nov 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.
#03Nov 9, 2026
cs.LG
Reward-Estimated Hypergradient for Bilevel Reinforcement Learning with Black-Box Follower
Shigeki Kusaka, Mikoto Kudo, Takumi Tanabe and 2 more
Hypergradient (HG) methods for bilevel reinforcement learning (RL) typically assume a white-box follower whose reward is known. In practice, however, the leader rarely knows the follower's reward function and can only observe its trajectories. We address this black-box setting and propose Reward-Estimated Hypergradients (RE-HG), which recovers the follower's reward from these trajectories via inverse RL (IRL). Yet IRL identifies the reward only up to potential-based shaping, a transformation that leaves the follower's behavior unchanged but biases the HG. We prove that, for linear rewards, this bias cancels when IRL estimates are aggregated across sufficiently diverse dynamics, which the leader's own updates naturally supply. To handle finite samples, RE-HG truncates small eigenvalues of the aggregated feature covariance, restoring the identifiable subspace and stabilizing the estimation. Experiments show that RE-HG estimates gradients aligned with a white-box Oracle and achieves comparable performance; empirically, the truncation also suppresses HG explosions, letting RE-HG avoid local optima that trap the Oracle in sharp reward landscapes.
#04Nov 9, 2026
cs.SE
Feeling Easier, Working Harder: Cognitive Load in AI-Assisted Code Comprehension
Maryangela White, Maximilian Rose, Matthew Buckman and 3 more
Software developers spend significant time reading and understanding code, increasingly supplemented by generative AI. While these tools aim to reduce the difficulty of reading code, interacting with them introduces a dual-task environment that may impose extraneous cognitive load that is challenging to capture. This study investigates how access to generative AI affects developers' real-time cognitive workload, code comprehension performance, and self-perceived code comprehension strategies. We conducted a 3x2 within-subjects study with 20 novice CS students reviewing Java code snippets of varying lengths with or without AI assistance, followed by an AI-unassisted comprehension quiz. Cognitive workload was continuously captured using a Detection-Response Task (tDRT) during both reading and quiz phases, and compared to post-quiz NASA-TLX and SEQ scores. AI assistance significantly increased objective cognitive workload, raising tDRT reaction times by 11.2%, yet participants' perceived workload remained unchanged. Code comprehension scores were high under both conditions, with no evidence that AI assistance improved comprehension at the difficulty levels evaluated; a ceiling effect limited power to detect benefits on harder tasks. Qualitatively, participants reported trusting the AI conditionally -verifying its output against their own reading for more complex snippets, but directly trusting it for simpler code- and, while many felt their reading process was unchanged, a notable subset shifted toward skimming or reading the AI's explanations in place of the code itself. These findings reveal that developers do not accurately perceive the cognitive resources they expend when managing AI tools. This study provides evidence of added cognitive effort associated with using generative AI, pointing towards a need to account for this dual-task penalty in software engineering tools and education.
#05Nov 9, 2026
cs.RO
Thermo-VLA: A Thermal-Aware Vision-Language-Action Model with Gated Residual Modulation for Robotic Manipulation
Jingxuan Chen, Junshi Luo, Chencheng Dong and 3 more
Recent Vision-Language-Action (VLA) models have begun incorporating thermal sensing, but existing approaches typically treat thermal images as ordinary visual inputs, providing limited support for temperature-aware relational reasoning in manipulation. To address this limitation, we propose Thermo-VLA with a ThermoRes Encoder, which decomposes thermal images into cold and hot attribute representations and injects them into the RGB token through language-conditioned residual modulation, enabling temperature-driven target selection and continuous manipulation. We further construct six real-world robotic tasks on a dual-arm Unitree G1 platform, spanning basic grounding to relational reasoning. Experiments show that Thermo-VLA achieves an average success rate of 0.86 across four thermal-dependent tasks, outperforming a pi_0.5 baseline that directly incorporates RGB-thermal observations by 18 percentage points. Under unseen-object and scene variations, Thermo-VLA maintains an average success rate of 0.78, achieving the best generalisation performance among the compared methods. Beyond thermal sensing, we transfer the same residual modulation mechanism to colour attributes and observe consistent improvements in both simulation and real-robot experiments, indicating its potential to generalise beyond thermal attributes. Project website: https://j-x-chen.github.io/Thermo-VLA-web/