arXiv:2603.03312v1 Announce Type: cross Abstract: Decoding natural language from non-invasive EEG signals is a promising yet challenging task. However, current state-of-the-art models remain constrained by three fundamental limitations: Semantic Bias (mode collapse into generic templates), Signal Neglect (hallucination based on linguistic priors rather than neural inputs), and the BLEU Trap, where evaluation metrics are artificially inflated by high-frequency stopwords, masking a lack of true semantic fidelity. To address these challenges, we propose SemKey, a novel multi-stage framework that enforces signal-grounded generation through four decoupled semantic objectives: sentiment, topic, length, and surprisal. We redesign the interaction between the neural encoder and the Large Language Model (LLM) by injecting semantic prompts as Queries and EEG embeddings as Key-Value pairs, strictly forcing the model to attend to neural inputs. Furthermore, we move beyond standard translation metrics by adopting N-way Retrieval Accuracy and Fr\'echet Distance to rigorously assess diversity and alignment. Extensive experiments demonstrate that our approach effectively eliminates hallucinations on noise inputs and achieves SOTA performance on these robust protocols. Code will be released upon acceptance at https://github.com/xmed-lab/SemKey.

arXiv:2603.02406v1 Announce Type: cross Abstract: Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43\% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8\% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.