arXiv subjects

Yatao Bian

Publications and source records attributed to Yatao Bian.

At least 37 records · Page 2Linked to original sources

arXiv2026

Question-Adaptive Graph Learning for Multi-hop Retrieval Augmented Generation

Retrieval-augmented generation (RAG) has demonstrated its ability to enhance Large Language Models (LLMs) by integrating external knowledge sources. However, multi-hop questions, which require the identification of multiple knowledge targets to form a synthesized answer, raise new challenges for RAG systems. Under the multi-hop settings, existing methods often struggle to fully understand the questions with complex semantic structures and are susceptible to irrelevant noise during the retrieval of multiple information targets. To address these limitations, we propose a novel graph representation learning framework for multi-hop question retrieval. We first introduce a Multi-information Level Knowledge Graph (Multi-L KG) to model various information levels for a more comprehensive understanding of multi-hop questions. Based on this, we design a Question-Adaptive Graph Neural Network (Quest-GNN) for representation learning on the Multi-L KG. Quest-GNN employs intra/inter-level message passing mechanisms, and in each message passing the information aggregation is guided by the question, which not only facilitates multi-granular information aggregation but also significantly reduces the impact of noise. To enhance its ability to learn robust representations, we further propose two synthesized data generation strategies for pre-training the Quest-GNN. Extensive experimental results demonstrate the effectiveness of our framework in multi-hop scenarios, especially in high-hop questions the improvement can reach 33.8\%. The code is available at: https://github.com/Jerry2398/QSGNN.

cs.LG↗

arXiv2026

A Survey of Reinforcement Learning for Large Language Models under Data Scarcity: Challenges and Solutions

Reinforcement learning (RL) has emerged as a powerful post-training paradigm for enhancing the reasoning capabilities of large language models (LLMs). However, reinforcement learning for LLMs faces substantial data scarcity challenges, including the limited availability of high-quality external supervision and the constrained volume of model-generated experience. These limitations make data-efficient reinforcement learning a critical research direction. In this survey, we present the first systematic review of reinforcement learning for LLMs under data scarcity. We propose a bottom-up hierarchical framework built around three complementary perspectives: the data-centric perspective, the training-centric perspective, and the framework-centric perspective. We develop a taxonomy of existing methods, summarize representative approaches in each category, and analyze their strengths and limitations. Our taxonomy aims to provide a clear conceptual foundation for understanding the design space of data-efficient RL for LLMs and to guide researchers working in this emerging area. We hope this survey offers a comprehensive roadmap for future research and inspires new directions toward more efficient and scalable reinforcement learning post-training for LLMs.

cs.LG↗

arXiv2026

ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking

Predicting the docking between proteins and ligands is a crucial and challenging task for drug discovery. However, traditional docking methods mainly rely on scoring functions, and deep learning-based docking approaches usually neglect the 3D spatial information of proteins and ligands, as well as the graph-level features of ligands, which limits their performance. To address these limitations, we propose an equivariant transformer neural network for protein-ligand docking pose prediction. Our approach involves the fusion of ligand graph-level features by feature processing, followed by the learning of ligand and protein representations using our proposed TAMformer module. Additionally, we employ an iterative optimization approach based on the predicted distance matrix to generate refined ligand poses. The experimental results on real datasets show that our model can achieve state-of-the-art performance.

q-bio.BM↗

arXiv2025

CrystalDiT: A Diffusion Transformer for Crystal Generation

We present CrystalDiT, a diffusion transformer for crystal structure generation that achieves state-of-the-art performance by challenging the trend of architectural complexity. Instead of intricate, multi-stream designs, CrystalDiT employs a unified transformer that imposes a powerful inductive bias: treating lattice and atomic properties as a single, interdependent system. Combined with a periodic table-based atomic representation and a balanced training strategy, our approach achieves 8.78% SUN (Stable, Unique, Novel) rate on MP-20, substantially outperforming recent methods including FlowMM (4.21%) and MatterGen (3.66%). Notably, CrystalDiT generates 63.28% unique and novel structures while maintaining comparable stability rates, demonstrating that architectural simplicity can be more effective than complexity for materials discovery. Our results suggest that in data-limited scientific domains, carefully designed simple architectures outperform sophisticated alternatives that are prone to overfitting.

cs.LG↗

arXiv2025

Think Consistently, Reason Efficiently: Energy-Based Calibration for Implicit Chain-of-Thought

Large Language Models (LLMs) have demonstrated strong reasoning capabilities through \emph{Chain-of-Thought} (CoT) prompting, which enables step-by-step intermediate reasoning. However, explicit CoT methods rely on discrete token-level reasoning processes that are prone to error propagation and limited by vocabulary expressiveness, often resulting in rigid and inconsistent reasoning trajectories. Recent research has explored implicit or continuous reasoning in latent spaces, allowing models to perform internal reasoning before generating explicit output. Although such approaches alleviate some limitations of discrete CoT, they generally lack explicit mechanisms to enforce consistency among reasoning steps, leading to divergent reasoning paths and unstable outcomes. To address this issue, we propose EBM-CoT, an Energy-Based Chain-of-Thought Calibration framework that refines latent thought representations through an energy-based model (EBM). Our method dynamically adjusts latent reasoning trajectories toward lower-energy, high-consistency regions in the embedding space, improving both reasoning accuracy and consistency without modifying the base language model. Extensive experiments across mathematical, commonsense, and symbolic reasoning benchmarks demonstrate that the proposed framework significantly enhances the consistency and efficiency of multi-step reasoning in LLMs.

cs.CL↗

arXiv2025

Learning to Learn with Contrastive Meta-Objective

Meta-learning enables learning systems to adapt quickly to new tasks, similar to humans. Different meta-learning approaches all work under/with the mini-batch episodic training framework. Such framework naturally gives the information about task identity, which can serve as additional supervision for meta-training to improve generalizability. We propose to exploit task identity as additional supervision in meta-training, inspired by the alignment and discrimination ability which is is intrinsic in human's fast learning. This is achieved by contrasting what meta-learners learn, i.e., model representations. The proposed ConML is evaluating and optimizing the contrastive meta-objective under a problem- and learner-agnostic meta-training framework. We demonstrate that ConML integrates seamlessly with existing meta-learners, as well as in-context learning models, and brings significant boost in performance with small implementation cost.

cs.LG↗

arXiv2025

3D-GSRD: 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding

Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL).However, extending the success of re-mask decoding from 2D to 3D MGM is non-trivial, primarily due to two conflicting challenges: avoiding 2D structure leakage to the decoder, while still providing sufficient 2D context for reconstructing re-masked atoms. To address these challenges, we propose 3D-GSRD: a 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding. The core innovation of 3D-GSRD lies in its Selective Re-mask Decoding(SRD), which re-masks only 3D-relevant information from encoder representations while preserving the 2D graph structures. This SRD is synergistically integrated with a 3D Relational-Transformer(3D-ReTrans) encoder alongside a structure-independent decoder. We analyze that SRD, combined with the structure-independent decoder, enhances the encoder's role in MRL. Extensive experiments show that 3D-GSRD achieves strong downstream performance, setting a new state-of-the-art on 7 out of 8 targets in the widely used MD17 molecular property prediction benchmark. The code is released at https://github.com/WuChang0124/3D-GSRD.

cs.LG↗

arXiv2025

Measuring Diversity in Synthetic Datasets

Large language models (LLMs) are widely adopted to generate synthetic datasets for various natural language processing (NLP) tasks, such as text classification and summarization. However, accurately measuring the diversity of these synthetic datasets-an aspect crucial for robust model performance-remains a significant challenge. In this paper, we introduce DCScore, a novel method for measuring synthetic dataset diversity from a classification perspective. Specifically, DCScore formulates diversity evaluation as a sample classification task, leveraging mutual relationships among samples. We further provide theoretical verification of the diversity-related axioms satisfied by DCScore, highlighting its role as a principled diversity evaluation method. Experimental results on synthetic datasets reveal that DCScore enjoys a stronger correlation with multiple diversity pseudo-truths of evaluated datasets, underscoring its effectiveness. Moreover, both empirical and theoretical evidence demonstrate that DCScore substantially reduces computational costs compared to existing methods. Code is available at: https://github.com/bluewhalelab/dcscore.

cs.CL↗

arXiv2025

UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation

The remarkable success of Large Language Models (LLMs) across diverse tasks has driven the research community to extend their capabilities to molecular applications. However, most molecular LLMs employ adapter-based architectures that do not treat molecule and text modalities equally and lack a supervision signal for the molecule modality. To address these issues, we introduce UniMoT, a Unified Molecule-Text LLM adopting a tokenizer-based architecture that expands the vocabulary of LLM with molecule tokens. Specifically, we introduce a Vector Quantization-driven tokenizer that incorporates a Q-Former to bridge the modality gap between molecule and text. This tokenizer transforms molecules into sequences of molecule tokens with causal dependency, encapsulating high-level molecular and textual information. Equipped with this tokenizer, UniMoT can unify molecule and text modalities under a shared token representation and an autoregressive training paradigm, enabling it to interpret molecules as a foreign language and generate them as text. Following a four-stage training scheme, UniMoT emerges as a multi-modal generalist capable of performing both molecule-to-text and text-to-molecule tasks. Extensive experiments demonstrate that UniMoT achieves state-of-the-art performance across a wide range of molecule comprehension and generation tasks.

cs.CL↗

arXiv2025

One Fits All: Learning Fair Graph Neural Networks for Various Sensitive Attributes

Recent studies have highlighted fairness issues in Graph Neural Networks (GNNs), where they produce discriminatory predictions against specific protected groups categorized by sensitive attributes such as race and age. While various efforts to enhance GNN fairness have made significant progress, these approaches are often tailored to specific sensitive attributes. Consequently, they necessitate retraining the model from scratch to accommodate changes in the sensitive attribute requirement, resulting in high computational costs. To gain deeper insights into this issue, we approach the graph fairness problem from a causal modeling perspective, where we identify the confounding effect induced by the sensitive attribute as the underlying reason. Motivated by this observation, we formulate the fairness problem in graphs from an invariant learning perspective, which aims to learn invariant representations across environments. Accordingly, we propose a graph fairness framework based on invariant learning, namely FairINV, which enables the training of fair GNNs to accommodate various sensitive attributes within a single training session. Specifically, FairINV incorporates sensitive attribute partition and trains fair GNNs by eliminating spurious correlations between the label and various sensitive attributes. Experimental results on several real-world datasets demonstrate that FairINV significantly outperforms state-of-the-art fairness approaches, underscoring its effectiveness. Our code is available via: https://github.com/ZzoomD/FairINV/.

cs.LG↗

arXiv2025

HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

cs.CL↗

arXiv2025

Right Question is Already Half the Answer: Fully Unsupervised LLM Reasoning Incentivization

Existing methods to enhance the reasoning capability of large language models predominantly rely on supervised fine-tuning (SFT) followed by reinforcement learning (RL) on reasoning-specific data. These approaches critically depend on external supervisions--such as labeled reasoning traces, verified golden answers, or pre-trained reward models. In this work, we propose Entropy Minimized Policy Optimization (\ours), which makes an early attempt at fully unsupervised LLM reasoning incentivization. By continuously minimizing the predictive entropy of LLMs on unlabeled questions in a latent semantic space, \ours achieves competitive performance compared to supervised counterparts on both mathematical and free-form natural reasoning tasks. Specifically, without any supervised signals, \ours boosts the accuracy of Qwen2.5-Math-7B Base from 30.7\% to 48.1\% on mathematical benchmarks and improves the accuracy of Qwen2.5-7B Base from 32.1\% to 50.1\% on MMLU-Pro. Primary experiments and analysis are also provided to interpret the effectiveness of \ours. Code is available at https://github.com/QingyangZhang/EMPO.

cs.LG↗

arXiv2025

InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

cs.LG↗

arXiv2024

COME: Test-time adaption by Conservatively Minimizing Entropy

Machine learning models must continuously self-adjust themselves for novel data distribution in the open world. As the predominant principle, entropy minimization (EM) has been proven to be a simple yet effective cornerstone in existing test-time adaption (TTA) methods. While unfortunately its fatal limitation (i.e., overconfidence) tends to result in model collapse. For this issue, we propose to Conservatively Minimize the Entropy (COME), which is a simple drop-in replacement of traditional EM to elegantly address the limitation. In essence, COME explicitly models the uncertainty by characterizing a Dirichlet prior distribution over model predictions during TTA. By doing so, COME naturally regularizes the model to favor conservative confidence on unreliable samples. Theoretically, we provide a preliminary analysis to reveal the ability of COME in enhancing the optimization stability by introducing a data-adaptive lower bound on the entropy. Empirically, our method achieves state-of-the-art performance on commonly used benchmarks, showing significant improvements in terms of classification accuracy and uncertainty estimation under various settings including standard, life-long and open-world TTA, i.e., up to $34.5\%$ improvement on accuracy and $15.1\%$ on false positive rate.

stat.ML↗

arXiv2024

The Best of Both Worlds: On the Dilemma of Out-of-distribution Detection

Out-of-distribution (OOD) detection is essential for model trustworthiness which aims to sensitively identify semantic OOD samples and robustly generalize for covariate-shifted OOD samples. However, we discover that the superior OOD detection performance of state-of-the-art methods is achieved by secretly sacrificing the OOD generalization ability. Specifically, the classification accuracy of these models could deteriorate dramatically when they encounter even minor noise. This phenomenon contradicts the goal of model trustworthiness and severely restricts their applicability in real-world scenarios. What is the hidden reason behind such a limitation? In this work, we theoretically demystify the ``\textit{sensitive-robust}'' dilemma that lies in many existing OOD detection methods. Consequently, a theory-inspired algorithm is induced to overcome such a dilemma. By decoupling the uncertainty learning objective from a Bayesian perspective, the conflict between OOD detection and OOD generalization is naturally harmonized and a dual-optimal performance could be expected. Empirical studies show that our method achieves superior performance on standard benchmarks. To our best knowledge, this work is the first principled OOD detection method that achieves state-of-the-art OOD detection performance without compromising OOD generalization ability. Our code is available at \href{https://github.com/QingyangZhang/DUL}{https://github.com/QingyangZhang/DUL}.

cs.LG↗

arXiv2024

Probing the Safety Response Boundary of Large Language Models via Unsafe Decoding Path Generation

Large Language Models (LLMs) are implicit troublemakers. While they provide valuable insights and assist in problem-solving, they can also potentially serve as a resource for malicious activities. Implementing safety alignment could mitigate the risk of LLMs generating harmful responses. We argue that: even when an LLM appears to successfully block harmful queries, there may still be hidden vulnerabilities that could act as ticking time bombs. To identify these underlying weaknesses, we propose to use a cost value model as both a detector and an attacker. Trained on external or self-generated harmful datasets, the cost value model could successfully influence the original safe LLM to output toxic content in decoding process. For instance, LLaMA-2-chat 7B outputs 39.18% concrete toxic content, along with only 22.16% refusals without any harmful suffixes. These potential weaknesses can then be exploited via prompt optimization such as soft prompts on images. We name this decoding strategy: Jailbreak Value Decoding (JVD), emphasizing that seemingly secure LLMs may not be as safe as we initially believe. They could be used to gather harmful data or launch covert attacks.

cs.CR↗

arXiv2024

SGFormer: Simplifying and Empowering Transformers for Large-Graph Representations

Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class of foundation encoders for graph-structured data, have shown promising performance on small graphs due to its global attention capable of capturing all-pair influence beyond neighboring nodes. Even so, existing approaches tend to inherit the spirit of Transformers in language and vision tasks, and embrace complicated models by stacking deep multi-head attentions. In this paper, we critically demonstrate that even using a one-layer attention can bring up surprisingly competitive performance across node property prediction benchmarks where node numbers range from thousand-level to billion-level. This encourages us to rethink the design philosophy for Transformers on large graphs, where the global attention is a computation overhead hindering the scalability. We frame the proposed scheme as Simplified Graph Transformers (SGFormer), which is empowered by a simple attention model that can efficiently propagate information among arbitrary nodes in one layer. SGFormer requires none of positional encodings, feature/graph pre-processing or augmented loss. Empirically, SGFormer successfully scales to the web-scale graph ogbn-papers100M and yields up to 141x inference acceleration over SOTA Transformers on medium-sized graphs. Beyond current results, we believe the proposed methodology alone enlightens a new technical path of independent interest for building Transformers on large graphs.

cs.LG↗

arXiv2024

Step-On-Feet Tuning: Scaling Self-Alignment of LLMs via Bootstrapping

Self-alignment is an effective way to reduce the cost of human annotation while ensuring promising model capability. However, most current methods complete the data collection and training steps in a single round, which may overlook the continuously improving ability of self-aligned models. This gives rise to a key query: What if we do multi-time bootstrapping self-alignment? Does this strategy enhance model performance or lead to rapid degradation? In this paper, our pioneering exploration delves into the impact of bootstrapping self-alignment on large language models. Our findings reveal that bootstrapping self-alignment markedly surpasses the single-round approach, by guaranteeing data diversity from in-context learning. To further exploit the capabilities of bootstrapping, we investigate and adjust the training order of data, which yields improved performance of the model. Drawing on these findings, we propose Step-On-Feet Tuning (SOFT) which leverages model's continuously enhanced few-shot ability to boost zero or one-shot performance. Based on easy-to-hard training recipe, we propose SOFT+ which further boost self-alignment's performance. Our experiments demonstrate the efficiency of SOFT (SOFT+) across various classification and generation tasks, highlighting the potential of bootstrapping self-alignment on continually enhancing model alignment performance.

cs.CL↗