Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery.

However, prior work is largely empirical, and while existing routing functions work well in practice, they do not lead to theoretical guarantees on approximation ability.

When maximum likelihood estimation is infeasible, one often turns to score matching, contrastive divergence, or minimum probability flow to obtain tractable parameter estimates.

With the integration of massive distributed energy resources and the widespread participation of novel market entities, the operation of active distribution networks (ADNs) is progressively evolving into a complex multi-scenario, multi-objective problem. Although expert engineers have developed numerous domain specific models (DSMs) to address distinct technical problems, mastering, integrating, and orchestrating these heterogeneous DSMs still entail considerable overhead for ADN operators. Therefore, an intelligent approach is urgently required to unify these DSMs and enable efficient coordination. To address this challenge, this paper proposes the ADN-Agent architecture, which leverages a general large language model (LLM) to coordinate multiple DSMs, enabling adaptive intent recognition, task decomposition, and DSM invocation. Within the ADN-Agent, we design a novel communication mechanism that provides a unified and flexible interface for diverse heterogeneous DSMs. Finally, for some language-intensive subtasks, we propose an automated training pipeline for fine-tuning small language models, thereby effectively enhancing the overall problem-solving capability of the system. Comprehensive comparisons and ablation experiments validate the efficacy of the proposed method and demonstrate that the ADN-Agent architecture outperforms existing LLM application paradigms.

Our main contributions are: 1.

At the core of the Transformer, the softmax normalizes the attention matrix to be right stochastic. Previous research has shown that this often de-stabilizes training and that enforcing the attention matrix to be doubly stochastic (through Sinkhorn's algorithm) consistently improves performance across different tasks, domains and Transformer flavors. However, Sinkhorn's algorithm is iterative, approximative, non-parametric and thus inflexible w.r.t. the obtained doubly stochastic matrix (DSM). Recently, it has been proven that DSMs can be obtained with a parametric quantum circuit, yielding a novel quantum inductive bias for DSMs with no known classical analogue. Motivated by this, we demonstrate the feasibility of a hybrid classical-quantum doubly stochastic Transformer (QDSFormer) that replaces the softmax in the self-attention layer with a variational quantum circuit. We study the expressive power of the circuit and find that it yields more diverse DSMs that better preserve information than classical operators. Across multiple small-scale object recognition tasks, we find that our QDSFormer consistently surpasses both a standard ViT and other doubly stochastic Transformers. Beyond the Sinkformer, this comparison includes a novel quantum-inspired doubly stochastic Transformer (based on QR decomposition) that can be of independent interest. Our QDSFormer also shows improved training stability and lower performance variation suggesting that it may mitigate the notoriously unstable training of ViTs on small-scale data.

Multimodal protein features play a crucial role in protein function prediction. However, these features encompass a wide range of information, ranging from structural data and sequence features to protein attributes and interaction networks, making it challenging to decipher their complex interconnections. In this work, we propose a multimodal protein function prediction method (DSRPGO) by utilizing dynamic selection and reconstructive pre-training mechanisms. To acquire complex protein information, we introduce reconstructive pre-training to mine more fine-grained information with low semantic levels. Moreover, we put forward the Bidirectional Interaction Module (BInM) to facilitate interactive learning among multimodal features. Additionally, to address the difficulty of hierarchical multi-label classification in this task, a Dynamic Selection Module (DSM) is designed to select the feature representation that is most conducive to current protein function prediction. Our proposed DSRPGO model improves significantly in BPO, MFO, and CCO on human datasets, thereby outperforming other benchmark models.

In complex engineering systems, the dependencies among components or development activities are often modeled and analyzed using Design Structure Matrix (DSM). Reorganizing elements within a DSM to minimize feedback loops and enhance modularity or process efficiency constitutes a challenging combinatorial optimization (CO) problem in engineering design and operations. As problem sizes increase and dependency networks become more intricate, traditional optimization methods that rely solely on mathematical heuristics often fail to capture the contextual nuances and struggle to deliver effective solutions. In this study, we explore the potential of Large Language Models (LLMs) to address such CO problems by leveraging their capabilities for advanced reasoning and contextual understanding. We propose a novel LLM-based framework that integrates network topology with contextual domain knowledge for iterative optimization of DSM sequencing-a common CO problem. Experiments on various DSM cases demonstrate that our method consistently achieves faster convergence and superior solution quality compared to both stochastic and deterministic baselines. Notably, incorporating contextual domain knowledge significantly enhances optimization performance regardless of the chosen LLM backbone. These findings highlight the potential of LLMs to solve complex engineering CO problems by combining semantic and mathematical reasoning. This approach paves the way towards a new paradigm in LLM-based engineering design optimization.