Multimodal protein language models (pLMs) learn joint protein sequence-structure distributions, and their generation performance should also depend critically on inference-time sampling strategies. Yet prior work has focused more on model training than on how inference-time strategies behave. In this paper, we establish a three-stage investigation framework to empirically study the inference design space of multimodal pLMs across three representative pLMs and four fundamental tasks. We evaluate vanilla sampling, task-specific classifier-free guidance, and reward-guided beam search on multimodal pLMs, corresponding to controls over sampling distributions, per-step logits, and parallel trajectories. Throughout the complementary advancements centered on exploration-exploitation trade-off, we (1) reveal the suboptimality of default inference protocols and identify task-oriented sampling preferences; (2) observe substantial quantitative gains across tasks, consistently boosting the upper bound performance of multimodal pLMs without updating model parameters; (3) derive conclusions about base models that differ from prior consensus. Our code is available at: https://github.com/EchoChou990919/mplm_inference.

Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further exploration in integrating protein structural information. We argue that the structural information of proteins is not only limited to their 3D information but also encompasses information from amino acid molecules (local information) to protein-protein structure similarity (global information). To address this, we propose GLProtein, the first framework in protein pre-training that incorporates both global structural similarity and local amino acid details to enhance prediction accuracy and functional insights. GLProtein innovatively combines protein-masked modelling with triplet structure similarity scoring, protein 3D distance encoding and substructure-based amino acid molecule encoding. Experimental results demonstrate that GLProtein outperforms previous methods in several bioinformatics tasks, including predicting protein-protein interactions, contact prediction, and so on.

In this work we study user controlled table-to-text generation where users explore the content in a table by selecting cells and reading a natural language description thereof automatically produce by a natural language generator. Such generation models usually learn from carefully selected cell combinations (clean cell selections); however, in practice users may select unexpected, redundant, or incoherent cell combinations (noisy cell selections). In experiments, we find that models perform well on test sets coming from the same distribution as the train data but their performance drops when evaluated on realistic noisy user inputs. We propose a fine-tuning regime with additional user-simulated noisy cell selections. Models fine-tuned with the proposed regime gain 4.85 BLEU points on user noisy test cases and 1.4 on clean test cases; and achieve comparable state-of-the-art performance on the ToTTo dataset.