Yue Yu

Wenqi Shi, Ran Xu, Yuchen Zhuang et al. · gatech

Despite their improved capabilities in generation and reasoning, adapting large language models (LLMs) to the biomedical domain remains challenging due to their immense size and corporate privacy. In this work, we propose MedAdapter, a unified post-hoc adapter for test-time adaptation of LLMs towards biomedical applications. Instead of fine-tuning the entire LLM, MedAdapter effectively adapts the original model by fine-tuning only a small BERT-sized adapter to rank candidate solutions generated by LLMs. Experiments demonstrate that MedAdapter effectively adapts both white-box and black-box LLMs in biomedical reasoning, achieving average performance improvements of 25.48% and 11.31%, respectively, without requiring extensive computational resources or sharing data with third parties. MedAdapter also yields superior performance when combined with train-time adaptation, highlighting a flexible and complementary solution to existing adaptation methods. Faced with the challenges of balancing model performance, computational resources, and data privacy, MedAdapter provides an efficient, privacy-preserving, cost-effective, and transparent solution for adapting LLMs to the biomedical domain.

Hasi Hays, Yue Yu, William Richardson

Cellular signaling networks represent complex information processing systems that have been modeled via traditional mathematical or statistical approaches. However, these methods often struggle to capture context-dependent signaling, pathway cross-talk, and temporal dynamics across multiple biological scales. Here, we introduce hierarchical molecular language models (HMLMs), a novel architecture that proposes a molecular network-specific large language model (LLM) to use in intracellular communication as a specialized molecular language, which includes molecules as tokens, protein interactions, post-translational modifications, and regulatory events modeled as semantic relationships within an adapted transformer architecture. HMLMs employ graph-structured attention mechanisms to accommodate signaling network topology while integrating information across the molecular, pathway, and cellular scales through hierarchical attention patterns. We demonstrate HMLM superiority using a cardiac fibroblast signaling network comprising over 100 molecular species across functional modules connected by regulatory edges. HMLM achieved a mean squared error (MSE) of 0.058 for temporal signaling predictions, representing 30% improvement over graph neural networks (GNNs: 0.083) and 52% improvement over ordinary differential equation models (ODEs: 0.121), with particular advantages under sparse temporal sampling conditions where HMLM maintained MSE = 0.041 with only 4 time-points. The HMLMs offer a foundation for AI-driven biology and medicine with predictable scaling characteristics suitable for interactive applications. By bridging molecular mechanisms with cellular phenotypes through AI-driven molecular language representation, HMLMs provide a powerful paradigm for systems biology that advances precision medicine applications and therapeutic discovery in the era of AI.

Chenglu Pan, Jiarong Xu, Yue Yu et al.

Graph federated learning (FL) has emerged as a pivotal paradigm enabling multiple agents to collaboratively train a graph model while preserving local data privacy. Yet, current efforts overlook a key issue: agents are self-interested and would hesitant to share data without fair and satisfactory incentives. This paper is the first endeavor to address this issue by studying the incentive mechanism for graph federated learning. We identify a unique phenomenon in graph federated learning: the presence of agents posing potential harm to the federation and agents contributing with delays. This stands in contrast to previous FL incentive mechanisms that assume all agents contribute positively and in a timely manner. In view of this, this paper presents a novel incentive mechanism tailored for fair graph federated learning, integrating incentives derived from both model gradient and payoff. To achieve this, we first introduce an agent valuation function aimed at quantifying agent contributions through the introduction of two criteria: gradient alignment and graph diversity. Moreover, due to the high heterogeneity in graph federated learning, striking a balance between accuracy and fairness becomes particularly crucial. We introduce motif prototypes to enhance accuracy, communicated between the server and agents, enhancing global model aggregation and aiding agents in local model optimization. Extensive experiments show that our model achieves the best trade-off between accuracy and the fairness of model gradient, as well as superior payoff fairness.

Yuanzhao Zhai, Zhuo Zhang, Kele Xu et al.

Aligning with human preference datasets has been critical to the success of large language models (LLMs). Reinforcement learning from human feedback (RLHF) employs a costly reward model to provide feedback for on-policy sampling responses. Recently, offline methods that directly fit responses with binary preferences in the dataset have emerged as alternatives. However, existing methods do not explicitly model preference strength information, which is crucial for distinguishing different response pairs. To overcome this limitation, we propose Online Self-Preferring (OSP) language models to learn from self-generated response pairs and self-judged preference strengths. For each prompt and corresponding self-generated responses, we introduce a ranked pairing method to construct multiple response pairs with preference strength information. We then propose the soft-preference cross-entropy loss to leverage such information. Empirically, we demonstrate that leveraging preference strength is crucial for avoiding overfitting and enhancing alignment performance. OSP achieves state-of-the-art alignment performance across various metrics in two widely used human preference datasets. OSP is parameter-efficient and more robust than the dominant online method, RLHF when limited offline data are available and generalizing to out-of-domain tasks. Moreover, OSP language models established by LLMs with proficiency in self-preferring can efficiently self-improve without external supervision.

Yue Yu, Siyao Peng, Grace Hui Yang

In dialogues, an utterance is a chain of consecutive sentences produced by one speaker which ranges from a short sentence to a thousand-word post. When studying dialogues at the utterance level, it is not uncommon that an utterance would serve multiple functions. For instance, "Thank you. It works great." expresses both gratitude and positive feedback in the same utterance. Multiple dialogue acts (DA) for one utterance breeds complex dependencies across dialogue turns. Therefore, DA recognition challenges a model's predictive power over long utterances and complex DA context. We term this problem Concurrent Dialogue Acts (CDA) recognition. Previous work on DA recognition either assumes one DA per utterance or fails to realize the sequential nature of dialogues. In this paper, we present an adapted Convolutional Recurrent Neural Network (CRNN) which models the interactions between utterances of long-range context. Our model significantly outperforms existing work on CDA recognition on a tech forum dataset.