Graph Neural Networks in Modern AI-aided Drug Discovery

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive framework for learning the complex topological and geometric features of drug-like molecules, cementing their role in modern molecular modeling. This review provides a comprehensive overview of the methodological foundations and representative applications of GNNs in drug discovery, spanning tasks such as molecular property prediction, virtual screening, molecular generation, biomedical knowledge graph construction, and synthesis planning. Particular attention is given to recent methodological advances, including geometric GNNs, interpretable models, uncertainty quantification, scalable graph architectures, and graph generative frameworks. We also discuss how these models integrate with modern deep learning approaches, such as self-supervised learning, multi-task learning, meta-learning and pre-training. Throughout this review, we highlight the practical challenges and methodological bottlenecks encountered when applying GNNs to real-world drug discovery pipelines, and conclude with a discussion on future directions.

From Real to Synthetic: Synthesizing Millions of Diversified and Complicated User Instructions with Attributed Grounding

The pursuit of diverse, complex, and large-scale instruction data is crucial for automatically aligning large language models (LLMs). While there are methods capable of generating synthetic instructions at scale, they either suffer from limited grounding sources, leading to a narrow distribution, or rely on trivial extensions that fail to produce meaningful trajectories in terms of complexity. In contrast, instructions that benefit efficient alignment are typically crafted with cognitive insights and grounded in real-world use cases. In this paper, we synthesize such instructions using attributed grounding, which involves 1) a top-down attribution process that grounds a selective set of real instructions to situated users, and 2) a bottom-up synthesis process that leverages web documents to first generate a situation, then a meaningful instruction. This framework allows us to harvest diverse and complex instructions at scale, utilizing the vast range of web documents. Specifically, we construct a dataset of 1 million instructions, called SynthQuestions, and demonstrate that models trained on it achieve leading performance on several common benchmarks, with improvements that continually scale with more web corpora. Data, models and codes will be available at https://github.com/Ignoramus0817/SynthQuestions.

MIRROR: Multi-agent Intra- and Inter-Reflection for Optimized Reasoning in Tool Learning

Complex tasks involving tool integration pose significant challenges for Large Language Models (LLMs), leading to the emergence of multi-agent workflows as a promising solution. Reflection has emerged as an effective strategy for correcting erroneous trajectories in agentic workflows. However, existing approaches only exploit such capability in the post-action stage, where the agent observes the execution outcomes. We argue that, like humans, LLMs can also engage in reflection before action execution: the agent can anticipate undesirable outcomes from its own decisions, which not only provides a necessarily complementary perspective to evaluate the decision but also prevents the propagation of errors throughout the trajectory. In this paper, we propose MIRROR, a framework that consists of both intra-reflection, which critically assesses intended actions before execution, and inter-reflection, which further adjusts the trajectory based on observations. This design systematically leverages LLM reflection capabilities to eliminate and rectify erroneous actions on a more comprehensive scope. Evaluations on both the StableToolBench and TravelPlanner benchmarks demonstrate MIRROR's superior performance, achieving state-of-the-art results compared to existing approaches.

Training LLM-Based Agents with Synthetic Self-Reflected Trajectories and Partial Masking

Autonomous agents, which perceive environments and take actions to achieve goals, have become increasingly feasible with the advancements in large language models (LLMs). However, current powerful agents often depend on sophisticated prompt engineering combined with closed-source LLMs like GPT-4. Although training open-source LLMs using expert trajectories from teacher models has yielded some improvements in agent capabilities, this approach still faces limitations such as performance plateauing and error propagation. To mitigate these challenges, we propose STeP, a novel method for improving LLM-based agent training. We synthesize self-reflected trajectories that include reflections and corrections of error steps, which enhance the effectiveness of LLM agents in learning from teacher models, enabling them to become agents capable of self-reflecting and correcting. We also introduce partial masking strategy that prevents the LLM from internalizing incorrect or suboptimal steps. Experiments demonstrate that our method improves agent performance across three representative tasks: ALFWorld, WebShop, and SciWorld. For the open-source model LLaMA2-7B-Chat, when trained using self-reflected trajectories constructed with Qwen1.5-110B-Chat as the teacher model, it achieves comprehensive improvements with less training data compared to agents trained exclusively on expert trajectories.

Automated Creativity Evaluation for Large Language Models: A Reference-Based Approach

Creative writing is a key capability of Large Language Models (LLMs), with potential applications in literature, storytelling, and various creative domains. However, evaluating the creativity of machine-generated texts remains a significant challenge, as existing methods either rely on costly manual annotations or fail to align closely with human assessments. In this paper, we propose an effective automated evaluation method based on the Torrance Test of Creative Writing (TTCW), which evaluates creativity as product. Our method employs a reference-based Likert-style approach, scoring generated creative texts relative to high-quality reference texts across various tests. Experimental results demonstrate that our method significantly improves the alignment between LLM evaluations and human assessments, achieving a pairwise accuracy of 0.75 (+15\%).

A Graph-Based Synthetic Data Pipeline for Scaling High-Quality Reasoning Instructions

Synthesizing high-quality reasoning data for continual training has been proven to be effective in enhancing the performance of Large Language Models (LLMs). However, previous synthetic approaches struggle to easily scale up data and incur high costs in the pursuit of high quality. In this paper, we propose the Graph-based Synthetic Data Pipeline (GSDP), an economical and scalable framework for high-quality reasoning data synthesis. Inspired by knowledge graphs, we extracted knowledge points from seed data and constructed a knowledge point relationships graph to explore their interconnections. By exploring the implicit relationships among knowledge, our method achieves $\times$255 data expansion. Furthermore, GSDP led by open-source models, achieves synthesis quality comparable to GPT-4-0613 while maintaining $\times$100 lower costs. To tackle the most challenging mathematical reasoning task, we present the GSDP-MATH dataset comprising over 1.91 million pairs of math problems and answers. After fine-tuning on GSDP-MATH, GSDP-7B based on Mistral-7B achieves 37.7% accuracy on MATH and 78.4% on GSM8K, demonstrating the effectiveness of our method. The dataset and models trained in this paper will be available.

Learning and Current Prediction of PMSM Drive via Differential Neural Networks

Learning models for dynamical systems in continuous time is significant for understanding complex phenomena and making accurate predictions. This study presents a novel approach utilizing differential neural networks (DNNs) to model nonlinear systems, specifically permanent magnet synchronous motors (PMSMs), and to predict their current trajectories. The efficacy of our approach is validated through experiments conducted under various load disturbances and no-load conditions. The results demonstrate that our method effectively and accurately reconstructs the original systems, showcasing strong short-term and long-term prediction capabilities and robustness. This study provides valuable insights into learning the inherent dynamics of complex dynamical data and holds potential for further applications in fields such as weather forecasting, robotics, and collective behavior analysis.

Adaptive Integral Sliding Mode Control for Attitude Tracking of Underwater Robots With Large Range Pitch Variations in Confined Space

Underwater robots play a crucial role in exploring aquatic environments. The ability to flexibly adjust their attitudes is essential for underwater robots to effectively accomplish tasks in confined space. However, the highly coupled six degrees of freedom dynamics resulting from attitude changes and the complex turbulence within limited spatial areas present significant challenges. To address the problem of attitude control of underwater robots, this letter investigates large-range pitch angle tracking during station holding as well as simultaneous roll and yaw angle control to enable versatile attitude adjustments. Based on dynamic modeling, this letter proposes an adaptive integral sliding mode controller (AISMC) that integrates an integral module into traditional sliding mode control (SMC) and adaptively adjusts the switching gain for improved tracking accuracy, reduced chattering, and enhanced robustness. The stability of the closed-loop control system is established through Lyapunov analysis. Extensive experiments and comparison studies are conducted using a commercial remotely operated vehicle (ROV), the results of which demonstrate that AISMC achieves satisfactory performance in attitude tracking control in confined space with unknown disturbances, significantly outperforming both PID and SMC.

Jointly Recognizing Speech and Singing Voices Based on Multi-Task Audio Source Separation

In short video and live broadcasts, speech, singing voice, and background music often overlap and obscure each other. This complexity creates difficulties in structuring and recognizing the audio content, which may impair subsequent ASR and music understanding applications. This paper proposes a multi-task audio source separation (MTASS) based ASR model called JRSV, which Jointly Recognizes Speech and singing Voices. Specifically, the MTASS module separates the mixed audio into distinct speech and singing voice tracks while removing background music. The CTC/attention hybrid recognition module recognizes both tracks. Online distillation is proposed to improve the robustness of recognition further. To evaluate the proposed methods, a benchmark dataset is constructed and released. Experimental results demonstrate that JRSV can significantly improve recognition accuracy on each track of the mixed audio.

Filter Pruning via Filters Similarity in Consecutive Layers

Filter pruning is widely adopted to compress and accelerate the Convolutional Neural Networks (CNNs), but most previous works ignore the relationship between filters and channels in different layers. Processing each layer independently fails to utilize the collaborative relationship across layers. In this paper, we intuitively propose a novel pruning method by explicitly leveraging the Filters Similarity in Consecutive Layers (FSCL). FSCL compresses models by pruning filters whose corresponding features are more worthless in the model. The extensive experiments demonstrate the effectiveness of FSCL, and it yields remarkable improvement over state-of-the-art on accuracy, FLOPs and parameter reduction on several benchmark models and datasets.