Shimin Di

Zhili Wang, Shimin Di, Lei Chen et al.

Recently, graph neural networks (GNNs) have shown its unprecedented success in many graph-related tasks. However, GNNs face the label scarcity issue as other neural networks do. Thus, recent efforts try to pre-train GNNs on a large-scale unlabeled graph and adapt the knowledge from the unlabeled graph to the target downstream task. The adaptation is generally achieved by fine-tuning the pre-trained GNNs with a limited number of labeled data. Despite the importance of fine-tuning, current GNNs pre-training works often ignore designing a good fine-tuning strategy to better leverage transferred knowledge and improve the performance on downstream tasks. Only few works start to investigate a better fine-tuning strategy for pre-trained GNNs. But their designs either have strong assumptions or overlook the data-aware issue for various downstream datasets. Therefore, we aim to design a better fine-tuning strategy for pre-trained GNNs to improve the model performance in this paper. Given a pre-trained GNN, we propose to search to fine-tune pre-trained graph neural networks for graph-level tasks (S2PGNN), which adaptively design a suitable fine-tuning framework for the given labeled data on the downstream task. To ensure the improvement brought by searching fine-tuning strategy, we carefully summarize a proper search space of fine-tuning framework that is suitable for GNNs. The empirical studies show that S2PGNN can be implemented on the top of 10 famous pre-trained GNNs and consistently improve their performance. Besides, S2PGNN achieves better performance than existing fine-tuning strategies within and outside the GNN area. Our code is publicly available at \url{https://anonymous.4open.science/r/code_icde2024-A9CB/}.

Siyu Gong, Linan Yue, Weibo Gao et al.

Tool-Integrated Reasoning (TIR) enables large language models (LLMs) to solve complex tasks by interacting with external tools, yet existing approaches depend on high-quality synthesized trajectories selected by scoring functions and sparse outcome-based rewards, providing limited and biased supervision for learning TIR. To address these challenges, in this paper, we propose AutoTraj, a two-stage framework that automatically learns TIR by repairing and rewarding tool-use trajectories. Specifically, in the supervised fine-tuning (SFT) stage, AutoTraj generates multiple candidate tool-use trajectories for each query and evaluates them along multiple dimensions. High-quality trajectories are directly retained, while low-quality ones are repaired using a LLM (i.e., LLM-as-Repairer). The resulting repaired and high-quality trajectories form a synthetic SFT dataset, while each repaired trajectory paired with its original low-quality counterpart constitutes a dataset for trajectory preference modeling. In the reinforcement learning (RL) stage, based on the preference dataset, we train a trajectory-level reward model to assess the quality of reasoning paths and combine it with outcome and format rewards, thereby explicitly guiding the optimization toward reliable TIR behaviors. Experiments on real-world benchmarks demonstrate the effectiveness of AutoTraj in TIR.

Jialiang Wang, Hanmo Liu, Shimin Di et al.

High-level automation is increasingly critical in AI, driven by rapid advances in large language models (LLMs) and AI agents. However, LLMs, despite their general reasoning power, struggle significantly in specialized, data-sensitive tasks such as designing Graph Neural Networks (GNNs). This difficulty arises from (1) the inherent knowledge gaps in modeling the intricate, varying relationships between graph properties and suitable architectures and (2) the external noise from misleading descriptive inputs, often resulting in generic or even misleading model suggestions. Achieving proficiency in designing data-aware models -- defined as the meta-level capability to systematically accumulate, interpret, and apply data-specific design knowledge -- remains challenging for existing automated approaches, due to their inefficient construction and application of meta-knowledge. To achieve meta-level proficiency, we propose DesiGNN, a knowledge-centered framework that systematically converts past model design experience into structured, fine-grained knowledge priors well-suited for meta-learning with LLMs. To account for the inherent variability and external noise, DesiGNN aligns empirical property filtering from extensive benchmarks with adaptive elicitation of literature insights via LLMs. By constructing a solid meta-knowledge between unseen graph understanding and known effective architecture patterns, DesiGNN can deliver top-5.77% initial model proposals for unseen datasets within seconds and achieve consistently superior performance with minimal search cost compared to baselines.

Yiwen Pang, Bo Zhou, Changjin Li et al.

Robotic laboratories play a critical role in autonomous scientific discovery by enabling scalable, continuous experimental execution. Recent vision-language-action (VLA) models offer a promising foundation for robotic laboratories. However, scientific experiments typically involve long-horizon tasks composed of multiple atomic tasks, posing a fundamental challenge to existing VLA models. While VLA models fine-tuned for scientific tasks can reliably execute atomic experimental actions seen during training, they often fail to perform composite tasks formed by reordering and composing these known atomic actions. This limitation arises from a distributional mismatch between training-time atomic tasks and inference-time composite tasks, which prevents VLA models from executing necessary transitional operations between atomic tasks. To address this challenge, we propose an Agentic VLA Inference Plugin for Long-Horizon Tasks in Scientific Experiments. It introduces an LLM-based agentic inference mechanism that intervenes when executing sequential manipulation tasks. By performing explicit transition inference and generating transitional robotic action code, the proposed plugin guides VLA models through missing transitional steps, enabling reliable execution of composite scientific workflows without any additional training. This inference-only intervention makes our method computationally efficient, data-efficient, and well-suited for open-ended and long-horizon robotic laboratory tasks. We build 3D assets of scientific instruments and common scientific operating scenes within an existing simulation environment. In these scenes, we have verified that our method increases the average success rate per atomic task by 42\% during inference. Furthermore, we show that our method can be easily transferred from the simulation to real scientific laboratories.

Jialiang Wang, Ning Zhang, Shimin Di et al.

Learning from Label Proportion (LLP) is a weakly supervised learning scenario in which training data is organized into predefined bags of instances, disclosing only the class label proportions per bag. This paradigm is essential for user modeling and personalization, where user privacy is paramount, offering insights into user preferences without revealing individual data. LLP faces a unique difficulty: the misalignment between bag-level supervision and the objective of instance-level prediction, primarily due to the inherent ambiguity in label proportion matching. Previous studies have demonstrated deep representation learning can generate auxiliary signals to promote the supervision level in the image domain. However, applying these techniques to tabular data presents significant challenges: 1) they rely heavily on label-invariant augmentation to establish multi-view, which is not feasible with the heterogeneous nature of tabular datasets, and 2) tabular datasets often lack sufficient semantics for perfect class distinction, making them prone to suboptimality caused by the inherent ambiguity of label proportion matching. To address these challenges, we propose an augmentation-free contrastive framework TabLLP-BDC that introduces class-aware supervision (explicitly aware of class differences) at the instance level. Our solution features a two-stage Bag Difference Contrastive (BDC) learning mechanism that establishes robust class-aware instance-level supervision by disassembling the nuance between bag label proportions, without relying on augmentations. Concurrently, our model presents a pioneering multi-task pretraining pipeline tailored for tabular-based LLP, capturing intrinsic tabular feature correlations in alignment with label proportion distribution. Extensive experiments demonstrate that TabLLP-BDC achieves state-of-the-art performance for LLP in the tabular domain.

Ran Li, Shimin Di, Yuchen Liu et al.

Previous study suggest that powerful Large Language Models (LLMs) trained with Reinforcement Learning with Verifiable Rewards (RLVR) only refines reasoning path without improving the reasoning capacity in math tasks while supervised-finetuning(SFT) with distillation can. We study this from the view of Scientific information extraction (SciIE) where LLMs and reasoning LLMs underperforms small Bert-based models. SciIE require both the reasoning and memorization. We argue that both SFT and RLVR can refine the reasoning path and improve reasoning capacity in a simple way based on SciIE. We propose two-stage training with 1. MimicSFT, using structured reasoning templates without needing high-quality chain-of-thought data, 2. R$^2$GRPO with relevance and rule-induced rewards. Experiments on scientific IE benchmarks show that both methods can improve the reasoning capacity. R$^2$GRPO with mimicSFT surpasses baseline LLMs and specialized supervised models in relation extraction. Our code is available at https://github.com/ranlislz/R2GRPO.

Jiawei Shen, Jia Zhu, Hanghui Guo et al.

Large Language Models (LLMs) have shown remarkable performance in multi-turn dialogue. However, in multi-turn dialogue, models still struggle to stay aligned with what has been established earlier, follow dependencies across many turns, and avoid drifting into incorrect facts as the interaction grows longer. Existing approaches primarily focus on extending the context window, introducing external memory, or applying context compression, yet these methods still face limitations such as \textbf{contextual inertia} and \textbf{state drift}. To address these challenges, we propose the \textbf{A}daptive \textbf{C}ontext \textbf{R}efactoring \textbf{(ACR)} Framework, which dynamically monitors and reshapes the interaction history to mitigate contextual inertia and state drift actively. ACR is built on a library of context refactoring operators and a teacher-guided self-evolving training paradigm that learns when to intervene and how to refactor, thereby decoupling context management from the reasoning process. Extensive experiments on multi-turn dialogue demonstrate that our method significantly outperforms existing baselines while reducing token consumption.

Jiachuan Wang, Shimin Di, Lei Chen et al.

Recently, emergence has received widespread attention from the research community along with the success of large-scale models. Different from the literature, we hypothesize a key factor that promotes the performance during the increase of scale: the reduction of monosemantic neurons that can only form one-to-one correlations with specific features. Monosemantic neurons tend to be sparser and have negative impacts on the performance in large models. Inspired by this insight, we propose an intuitive idea to identify monosemantic neurons and inhibit them. However, achieving this goal is a non-trivial task as there is no unified quantitative evaluation metric and simply banning monosemantic neurons does not promote polysemanticity in neural networks. Therefore, we first propose a new metric to measure the monosemanticity of neurons with the guarantee of efficiency for online computation, then introduce a theoretically supported method to suppress monosemantic neurons and proactively promote the ratios of polysemantic neurons in training neural networks. We validate our conjecture that monosemanticity brings about performance change at different model scales on a variety of neural networks and benchmark datasets in different areas, including language, image, and physics simulation tasks. Further experiments validate our analysis and theory regarding the inhibition of monosemanticity.

Yixuan Wang, Shuangyin Li, Shimin DI et al.

The single-cell RNA sequencing (scRNA-seq) technology enables researchers to study complex biological systems and diseases with high resolution. The central challenge is synthesizing enough scRNA-seq samples; insufficient samples can impede downstream analysis and reproducibility. While various methods have been attempted in past research, the resulting scRNA-seq samples were often of poor quality or limited in terms of useful specific cell subpopulations. To address these issues, we propose a novel method called Single-Cell Latent Diffusion (SCLD) based on the Diffusion Model. This method is capable of synthesizing large-scale, high-quality scRNA-seq samples, including both 'holistic' or targeted specific cellular subpopulations within a unified framework. A pre-guidance mechanism is designed for synthesizing specific cellular subpopulations, while a post-guidance mechanism aims to enhance the quality of scRNA-seq samples. The SCLD can synthesize large-scale and high-quality scRNA-seq samples for various downstream tasks. Our experimental results demonstrate state-of-the-art performance in cell classification and data distribution distances when evaluated on two scRNA-seq benchmarks. Additionally, visualization experiments show the SCLD's capability in synthesizing specific cellular subpopulations.

Hanghui Guo, Jia Zhu, Shimin Di et al.

Dynamic Retrieval-augmented Generation (RAG) has shown great success in mitigating hallucinations in large language models (LLMs) during generation. However, existing dynamic RAG methods face significant limitations in two key aspects: 1) Lack of an effective mechanism to control retrieval triggers, and 2) Lack of effective scrutiny of retrieval content. To address these limitations, we propose an innovative dynamic RAG method, DioR (Adaptive Cognitive Detection and Contextual Retrieval Optimization), which consists of two main components: adaptive cognitive detection and contextual retrieval optimization, specifically designed to determine when retrieval is needed and what to retrieve for LLMs is useful. Experimental results demonstrate that DioR achieves superior performance on all tasks, demonstrating the effectiveness of our work.

Jiawei Shen, Jia Zhu, Hanghui Guo et al.

Temporal Knowledge Graph Reasoning (TKGR) aims to complete missing factual elements along the timeline. Depending on the temporal position of the query, the task is categorized into interpolation and extrapolation. Existing interpolation methods typically embed temporal information into individual facts to complete missing historical knowledge, while extrapolation techniques often leverage sequence models over graph snapshots to identify recurring patterns for future event prediction. These methods face two critical challenges: limited contextual modeling in interpolation and cognitive generalization bias in extrapolation. To address these, we propose a unified method for TKGR, dubbed DynaGen. For interpolation, DynaGen dynamically constructs entity-centric subgraphs and processes them with a synergistic dual-branch GNN encoder to capture evolving structural context. For extrapolation, it applies a conditional diffusion process, which forces the model to learn underlying evolutionary principles rather than just superficial patterns, enhancing its ability to predict unseen future events. Extensive experiments on six benchmark datasets show DynaGen achieves state-of-the-art performance. On average, compared to the second-best models, DynaGen improves the Mean Reciprocal Rank (MRR) score by 2.61 points for interpolation and 1.45 points for extrapolation.

Hanghui Guo, Shimin Di, Pasquale De Meo et al.

As a critical task in data quality control, claim verification aims to curb the spread of misinformation by assessing the truthfulness of claims based on a wide range of evidence. However, traditional methods often overlook the complex interactions between evidence, leading to unreliable verification results. A straightforward solution represents the claim and evidence as a fully connected graph, which we define as the Claim-Evidence Graph (C-E Graph). Nevertheless, claim verification methods based on fully connected graphs face two primary confounding challenges, Data Noise and Data Biases. To address these challenges, we propose a novel framework, Multi-Path Causal Optimization (MuPlon). MuPlon integrates a dual causal intervention strategy, consisting of the back-door path and front-door path. In the back-door path, MuPlon dilutes noisy node interference by optimizing node probability weights, while simultaneously strengthening the connections between relevant evidence nodes. In the front-door path, MuPlon extracts highly relevant subgraphs and constructs reasoning paths, further applying counterfactual reasoning to eliminate data biases within these paths. The experimental results demonstrate that MuPlon outperforms existing methods and achieves state-of-the-art performance.

Jialiang Wang, Hanmo Liu, Shimin Di et al.

Database systems have recently advocated for embedding machine learning (ML) capabilities, offering declarative model queries over large, managed model repositories, thereby circumventing the huge computational overhead of traditional ML-based algorithms in automated neural network model selection. Pioneering database studies aim to organize existing benchmark repositories as model bases (MB), querying them for the model records with the highest performance estimation metrics for given tasks. However, this static model selection practice overlooks the fine-grained, evolving relational dependencies between diverse task queries and model architecture variations, resulting in suboptimal matches and failing to further refine the model effectively. To fill the model refinement gap in database research, we propose M-DESIGN, a curated model knowledge base (MKB) pipeline for mastering neural network refinement by adaptively weaving prior insights about model architecture modification. First, we propose a knowledge weaving engine that reframes model refinement as an adaptive query problem over task metadata. Given a user's task query, M-DESIGN quickly matches and iteratively refines candidate models by leveraging a graph-relational knowledge schema that explicitly encodes data properties, architecture variations, and pairwise performance deltas as joinable relations. This schema supports fine-grained relational analytics over architecture tweaks and drives a predictive query planner that can detect and adapt to out-of-distribution (OOD) tasks. We instantiate M-DESIGN for graph analytics tasks, where our model knowledge base enriches existing benchmarks with structured metadata covering 3 graph tasks and 22 graph datasets, contributing data records of 67,760 graph models. Empirical results demonstrate that M-DESIGN delivers the optimal model in 26 of 33 data-task pairs within limited budgets.

Zhili Wang, Shimin Di, Lei Chen

Recently, Graph Neural Networks (GNNs) have gained popularity in a variety of real-world scenarios. Despite the great success, the architecture design of GNNs heavily relies on manual labor. Thus, automated graph neural network (AutoGNN) has attracted interest and attention from the research community, which makes significant performance improvements in recent years. However, existing AutoGNN works mainly adopt an implicit way to model and leverage the link information in the graphs, which is not well regularized to the link prediction task on graphs, and limits the performance of AutoGNN for other graph tasks. In this paper, we present a novel AutoGNN work that explicitly models the link information, abbreviated to AutoGEL. In such a way, AutoGEL can handle the link prediction task and improve the performance of AutoGNNs on the node classification and graph classification task. Specifically, AutoGEL proposes a novel search space containing various design dimensions at both intra-layer and inter-layer designs and adopts a more robust differentiable search algorithm to further improve efficiency and effectiveness. Experimental results on benchmark data sets demonstrate the superiority of AutoGEL on several tasks.

Shimin Di, Quanming Yao, Yongqi Zhang et al.

The scoring function, which measures the plausibility of triplets in knowledge graphs (KGs), is the key to ensure the excellent performance of KG embedding, and its design is also an important problem in the literature. Automated machine learning (AutoML) techniques have recently been introduced into KG to design task-aware scoring functions, which achieve state-of-the-art performance in KG embedding. However, the effectiveness of searched scoring functions is still not as good as desired. In this paper, observing that existing scoring functions can exhibit distinct performance on different semantic patterns, we are motivated to explore such semantics by searching relation-aware scoring functions. But the relation-aware search requires a much larger search space than the previous one. Hence, we propose to encode the space as a supernet and propose an efficient alternative minimization algorithm to search through the supernet in a one-shot manner. Finally, experimental results on benchmark datasets demonstrate that the proposed method can efficiently search relation-aware scoring functions, and achieve better embedding performance than state-of-the-art methods.

Shimin Di, Quanming Yao, Lei Chen

Tensor, an extension of the vector and matrix to the multi-dimensional case, is a natural way to describe the N-ary relational data. Recently, tensor decomposition methods have been introduced into N-ary relational data and become state-of-the-art on embedding learning. However, the performance of existing tensor decomposition methods is not as good as desired. First, they suffer from the data-sparsity issue since they can only learn from the N-ary relational data with a specific arity, i.e., parts of common N-ary relational data. Besides, they are neither effective nor efficient enough to be trained due to the over-parameterization problem. In this paper, we propose a novel method, i.e., S2S, for effectively and efficiently learning from the N-ary relational data. Specifically, we propose a new tensor decomposition framework, which allows embedding sharing to learn from facts with mixed arity. Since the core tensors may still suffer from the over-parameterization, we propose to reduce parameters by sparsifying the core tensors while retaining their expressive power using neural architecture search (NAS) techniques, which can search for data-dependent architectures. As a result, the proposed S2S not only guarantees to be expressive but also efficiently learns from mixed arity. Finally, empirical results have demonstrated that S2S is efficient to train and achieves state-of-the-art performance.