Ling Yang

Ming Yin, Yuanhao Qu, Ling Yang et al.

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learning-friendly multiple-choice questions format, supported by 3000+ high-quality question-answer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. We fine-tune an LLM using RL with a rule-based reward signal derived from the synthetic MCQ dataset to enhance domain-specific reasoning. Our results show that reinforcement learning from scientific discussions improves model performance by over 15% compared to the base model on Genome-Bench, narrowing the gap between open-source LLMs and expert-level reasoning. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology.

Lu Ma, Zeang Sheng, Xunkai Li et al.

Graph Neural Networks (GNNs) have demonstrated effectiveness in various graph-based tasks. However, their inefficiency in training and inference presents challenges for scaling up to real-world and large-scale graph applications. To address the critical challenges, a range of algorithms have been proposed to accelerate training and inference of GNNs, attracting increasing attention from the research community. In this paper, we present a systematic review of acceleration algorithms in GNNs, which can be categorized into three main topics based on their purpose: training acceleration, inference acceleration, and execution acceleration. Specifically, we summarize and categorize the existing approaches for each main topic, and provide detailed characterizations of the approaches within each category. Additionally, we review several libraries related to acceleration algorithms in GNNs and discuss our Scalable Graph Learning (SGL) library. Finally, we propose promising directions for future research. A complete summary is presented in our GitHub repository: https://github.com/PKU-DAIR/SGL/blob/main/Awsome-GNN-Acceleration.md.

Yafei Shen, Huan-Fei Ma, Ling Yang

Understanding low-dimensional structures within high-dimensional data is crucial for visualization, interpretation, and denoising in complex datasets. Despite the advancements in manifold learning techniques, key challenges-such as limited global insight and the lack of interpretable analytical descriptions-remain unresolved. In this work, we introduce a novel framework, GAMLA (Global Analytical Manifold Learning using Auto-encoding). GAMLA employs a two-round training process within an auto-encoding framework to derive both character and complementary representations for the underlying manifold. With the character representation, the manifold is represented by a parametric function which unfold the manifold to provide a global coordinate. While with the complementary representation, an approximate explicit manifold description is developed, offering a global and analytical representation of smooth manifolds underlying high-dimensional datasets. This enables the analytical derivation of geometric properties such as curvature and normal vectors. Moreover, we find the two representations together decompose the whole latent space and can thus characterize the local spatial structure surrounding the manifold, proving particularly effective in anomaly detection and categorization. Through extensive experiments on benchmark datasets and real-world applications, GAMLA demonstrates its ability to achieve computational efficiency and interpretability while providing precise geometric and structural insights. This framework bridges the gap between data-driven manifold learning and analytical geometry, presenting a versatile tool for exploring the intrinsic properties of complex data sets.