arXiv:2602.18476v1 Announce Type: cross Abstract: Protein-ligand scoring is a central component of structure-based drug design, underpinning molecular docking, virtual screening, and pose optimization. Conventional physics-based energy functions are often computationally expensive, limiting their utility in large-scale screening. In contrast, deep learning-based scoring models offer improved computational efficiency but frequently suffer from limited cross-target generalization and poor interpretability, which restrict their practical applicability. Here we present BioLM-Score, a simple yet generalizable protein-ligand scoring model that couples geometric modeling with representation learning. Specifically, it employs modality-specific and structure-aware encoders for proteins and ligands, each augmented with biomolecular language models to enrich structural and chemical representations. Subsequently, these representations are integrated through a mixture density network to predict multimodal interatomic distance distributions, from which statistically grounded likelihood-based scores are derived. Evaluations on the CASF-2016 benchmark demonstrate that BioLM-Score achieves significant improvements across docking, scoring, ranking, and screening tasks. Moreover, the proposed scoring function serves as an effective optimization objective for guiding docking protocols and conformational search. In summary, BioLM-Score provides a principled and practical alternative to existing scoring functions, combining efficiency, generalization, and interpretability for structure-based drug discovery.

arXiv:2511.20629v4 Announce Type: replace-cross Abstract: Reinforcement learning from human feedback (RLHF) with reward models has advanced alignment of generative models to human aesthetic and perceptual preferences. However, jointly optimizing multiple rewards often incurs an alignment tax, improving one dimension while degrading others. To address this, we introduce two complementary methods: MapReduce LoRA and Reward-aware Token Embedding (RaTE). MapReduce LoRA trains preference-specific LoRA experts in parallel and iteratively merges them to refine a shared base model; RaTE learns reward-specific token embeddings that compose at inference for flexible preference control. Experiments on Text-to-Image generation (Stable Diffusion 3.5 Medium and FLUX.1-dev) show improvements of 36.1%, 4.6%, and 55.7%, and 32.7%, 4.3%, and 67.1% on GenEval, PickScore, and OCR, respectively. On Text-to-Video generation (HunyuanVideo), visual and motion quality improve by 48.1% and 90.0%, respectively. On the language task, Helpful Assistant, with Llama-2 7B, helpful and harmless improve by 43.4% and 136.7%, respectively. Our framework sets a new state-of-the-art multi-preference alignment recipe across modalities.