MolTC: Towards Molecular Relational Modeling In Language Models

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge repositories and advanced logical inference capabilities, has emerged as a promising way for efficient and effective MRL. Despite their potential, these methods predominantly rely on the textual data, thus not fully harnessing the wealth of structural information inherent in molecular graphs. Moreover, the absence of a unified framework exacerbates the issue of information underutilization, as it hinders the sharing of interaction mechanism learned across diverse datasets. To address these challenges, this work proposes a novel LLM-based multi-modal framework for Molecular inTeraction prediction following Chain-of-Thought (CoT) theory, termed MolTC, which effectively integrate graphical information of two molecules in pair. For achieving a unified MRL, MolTC innovatively develops a dynamic parameter-sharing strategy for cross-dataset information sharing. Moreover, to train MolTC efficiently, we introduce a Multi-hierarchical CoT concept to refine its training paradigm, and conduct a comprehensive Molecular Interactive Instructions dataset for the development of biochemical LLMs involving MRL. Our experiments, conducted across various datasets involving over 4,000,000 molecular pairs, exhibit the superiority of our method over current GNN and LLM-based baselines. Code is available at https://github.com/MangoKiller/MolTC.

Modeling Spatio-temporal Dynamical Systems with Neural Discrete Learning and Levels-of-Experts

In this paper, we address the issue of modeling and estimating changes in the state of the spatio-temporal dynamical systems based on a sequence of observations like video frames. Traditional numerical simulation systems depend largely on the initial settings and correctness of the constructed partial differential equations (PDEs). Despite recent efforts yielding significant success in discovering data-driven PDEs with neural networks, the limitations posed by singular scenarios and the absence of local insights prevent them from performing effectively in a broader real-world context. To this end, this paper propose the universal expert module -- that is, optical flow estimation component, to capture the evolution laws of general physical processes in a data-driven fashion. To enhance local insight, we painstakingly design a finer-grained physical pipeline, since local characteristics may be influenced by various internal contextual information, which may contradict the macroscopic properties of the whole system. Further, we harness currently popular neural discrete learning to unveil the underlying important features in its latent space, this process better injects interpretability, which can help us obtain a powerful prior over these discrete random variables. We conduct extensive experiments and ablations to demonstrate that the proposed framework achieves large performance margins, compared with the existing SOTA baselines.

EXGC: Bridging Efficiency and Explainability in Graph Condensation

Graph representation learning on vast datasets, like web data, has made significant strides. However, the associated computational and storage overheads raise concerns. In sight of this, Graph condensation (GCond) has been introduced to distill these large real datasets into a more concise yet information-rich synthetic graph. Despite acceleration efforts, existing GCond methods mainly grapple with efficiency, especially on expansive web data graphs. Hence, in this work, we pinpoint two major inefficiencies of current paradigms: (1) the concurrent updating of a vast parameter set, and (2) pronounced parameter redundancy. To counteract these two limitations correspondingly, we first (1) employ the Mean-Field variational approximation for convergence acceleration, and then (2) propose the objective of Gradient Information Bottleneck (GDIB) to prune redundancy. By incorporating the leading explanation techniques (e.g., GNNExplainer and GSAT) to instantiate the GDIB, our EXGC, the Efficient and eXplainable Graph Condensation method is proposed, which can markedly boost efficiency and inject explainability. Our extensive evaluations across eight datasets underscore EXGC's superiority and relevance. Code is available at https://github.com/MangoKiller/EXGC.

Two Heads Are Better Than One: Boosting Graph Sparse Training via Semantic and Topological Awareness

Graph Neural Networks (GNNs) excel in various graph learning tasks but face computational challenges when applied to large-scale graphs. A promising solution is to remove non-essential edges to reduce the computational overheads in GNN. Previous literature generally falls into two categories: topology-guided and semantic-guided. The former maintains certain graph topological properties yet often underperforms on GNNs due to low integration with neural network training. The latter performs well at lower sparsity on GNNs but faces performance collapse at higher sparsity levels. With this in mind, we take the first step to propose a new research line and concept termed Graph Sparse Training (GST), which dynamically manipulates sparsity at the data level. Specifically, GST initially constructs a topology & semantic anchor at a low training cost, followed by performing dynamic sparse training to align the sparse graph with the anchor. We introduce the Equilibria Sparsification Principle to guide this process, effectively balancing the preservation of both topological and semantic information. Ultimately, GST produces a sparse graph with maximum topological integrity and no performance degradation. Extensive experiments on 6 datasets and 5 backbones showcase that GST (I) identifies subgraphs at higher graph sparsity levels (1.67%~15.85% $\uparrow$) than state-of-the-art sparsification methods, (II) preserves more key spectral properties, (III) achieves 1.27-3.42$\times$ speedup in GNN inference and (IV) successfully helps graph adversarial defense and graph lottery tickets.