arXiv subjects

Guoqing Liu

Publications and source records attributed to Guoqing Liu.

At least 37 records · Page 2Linked to original sources

arXiv2025

EvoPrompt: Connecting LLMs with Evolutionary Algorithms Yields Powerful Prompt Optimizers

Large Language Models (LLMs) excel in various tasks, but they rely on carefully crafted prompts that often demand substantial human effort. To automate this process, in this paper, we propose a novel framework for discrete prompt optimization, called EvoPrompt, which borrows the idea of evolutionary algorithms (EAs) as they exhibit good performance and fast convergence. To enable EAs to work on discrete prompts, which are natural language expressions that need to be coherent and human-readable, we connect LLMs with EAs. This approach allows us to simultaneously leverage the powerful language processing capabilities of LLMs and the efficient optimization performance of EAs. Specifically, abstaining from any gradients or parameters, EvoPrompt starts from a population of prompts and iteratively generates new prompts with LLMs based on the evolutionary operators, improving the population based on the development set. We optimize prompts for both closed- and open-source LLMs including GPT-3.5 and Alpaca, on 31 datasets covering language understanding, generation tasks, as well as BIG-Bench Hard (BBH) tasks. EvoPrompt significantly outperforms human-engineered prompts and existing methods for automatic prompt generation (e.g., up to 25% on BBH). Furthermore, EvoPrompt demonstrates that connecting LLMs with EAs creates synergies, which could inspire further research on the combination of LLMs and conventional algorithms.

cs.CL↗

arXiv2025

TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design

Structure-based drug design (SBDD) is a critical task in drug discovery, requiring the generation of molecular information across two distinct modalities: discrete molecular graphs and continuous 3D coordinates. However, existing SBDD methods often overlook two key challenges: (1) the multi-modal nature of this task and (2) the causal relationship between these modalities, limiting their plausibility and performance. To address both challenges, we propose TransDiffSBDD, an integrated framework combining autoregressive transformers and diffusion models for SBDD. Specifically, the autoregressive transformer models discrete molecular information, while the diffusion model samples continuous distributions, effectively resolving the first challenge. To address the second challenge, we design a hybrid-modal sequence for protein-ligand complexes that explicitly respects the causality between modalities. Experiments on the CrossDocked2020 benchmark demonstrate that TransDiffSBDD outperforms existing baselines.

cs.CE↗

arXiv2025

HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

cs.LG↗

arXiv2025

3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformer-based framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. The code is available at: https://github.com/HXYfighter/3DMolFormer .

cs.CE↗

arXiv2024

Theoretically Guaranteed Distribution Adaptable Learning

In many open environment applications, data are collected in the form of a stream, which exhibits an evolving distribution over time. How to design algorithms to track these evolving data distributions with provable guarantees, particularly in terms of the generalization ability, remains a formidable challenge. To handle this crucial but rarely studied problem and take a further step toward robust artificial intelligence, we propose a novel framework called Distribution Adaptable Learning (DAL). It enables the model to effectively track the evolving data distributions. By Encoding Feature Marginal Distribution Information (EFMDI), we broke the limitations of optimal transport to characterize the environmental changes and enable model reuse across diverse data distributions. It can enhance the reusable and evolvable properties of DAL in accommodating evolving distributions. Furthermore, to obtain the model interpretability, we not only analyze the generalization error bound of the local step in the evolution process, but also investigate the generalization error bound associated with the entire classifier trajectory of the evolution based on the Fisher-Rao distance. For demonstration, we also present two special cases within the framework, together with their optimizations and convergence analyses. Experimental results over both synthetic and real-world data distribution evolving tasks validate the effectiveness and practical utility of the proposed framework.

cs.LG↗

arXiv2024

Reinforcement Learning from Bagged Reward

In Reinforcement Learning (RL), it is commonly assumed that an immediate reward signal is generated for each action taken by the agent, helping the agent maximize cumulative rewards to obtain the optimal policy. However, in many real-world scenarios, designing immediate reward signals is difficult; instead, agents receive a single reward that is contingent upon a partial sequence or a complete trajectory. In this work, we define this challenging problem as RL from Bagged Reward (RLBR), where sequences of data are treated as bags with non-Markovian bagged rewards, leading to the formulation of Bagged Reward Markov Decision Processes (BRMDPs). Theoretically, we demonstrate that RLBR can be addressed by solving a standard MDP with properly redistributed bagged rewards allocated to each instance within a bag. Empirically, we find that reward redistribution becomes more challenging as the bag length increases, due to reduced informational granularity. Existing reward redistribution methods are insufficient to address these challenges. Therefore, we propose a novel reward redistribution method equipped with a bidirectional attention mechanism, enabling the accurate interpretation of contextual nuances and temporal dependencies within each bag. We experimentally demonstrate that our proposed method consistently outperforms existing approaches.

cs.LG↗

arXiv2024

EPContrast: Effective Point-level Contrastive Learning for Large-scale Point Cloud Understanding

The acquisition of inductive bias through point-level contrastive learning holds paramount significance in point cloud pre-training. However, the square growth in computational requirements with the scale of the point cloud poses a substantial impediment to the practical deployment and execution. To address this challenge, this paper proposes an Effective Point-level Contrastive Learning method for large-scale point cloud understanding dubbed \textbf{EPContrast}, which consists of AGContrast and ChannelContrast. In practice, AGContrast constructs positive and negative pairs based on asymmetric granularity embedding, while ChannelContrast imposes contrastive supervision between channel feature maps. EPContrast offers point-level contrastive loss while concurrently mitigating the computational resource burden. The efficacy of EPContrast is substantiated through comprehensive validation on S3DIS and ScanNetV2, encompassing tasks such as semantic segmentation, instance segmentation, and object detection. In addition, rich ablation experiments demonstrate remarkable bias induction capabilities under label-efficient and one-epoch training settings.

cs.CV↗

arXiv2024

Differentially Private Multimodal Laplacian Dropout (DP-MLD) for EEG Representative Learning

Recently, multimodal electroencephalogram (EEG) learning has shown great promise in disease detection. At the same time, ensuring privacy in clinical studies has become increasingly crucial due to legal and ethical concerns. One widely adopted scheme for privacy protection is differential privacy (DP) because of its clear interpretation and ease of implementation. Although numerous methods have been proposed under DP, it has not been extensively studied for multimodal EEG data due to the complexities of models and signal data considered there. In this paper, we propose a novel Differentially Private Multimodal Laplacian Dropout (DP-MLD) scheme for multimodal EEG learning. Our approach proposes a novel multimodal representative learning model that processes EEG data by language models as text and other modal data by vision transformers as images, incorporating well-designed cross-attention mechanisms to effectively extract and integrate cross-modal features. To achieve DP, we design a novel adaptive feature-level Laplacian dropout scheme, where randomness allocation and performance are dynamically optimized within given privacy budgets. In the experiment on an open-source multimodal dataset of Freezing of Gait (FoG) in Parkinson's Disease (PD), our proposed method demonstrates an approximate 4\% improvement in classification accuracy, and achieves state-of-the-art performance in multimodal EEG learning under DP.

eess.SP↗

arXiv2024

Learning-based Traversability Costmap for Autonomous Off-road Navigation

Traversability estimation in off-road terrains is an essential procedure for autonomous navigation. However, creating reliable labels for complex interactions between the robot and the surface is still a challenging problem in learning-based costmap generation. To address this, we propose a method that predicts traversability costmaps by leveraging both visual and geometric information of the environment. To quantify the surface properties like roughness and bumpiness, we introduce a novel way of risk-aware labelling with proprioceptive information for network training. We validate our method in costmap prediction and navigation tasks for complex off-road scenarios. Our results demonstrate that our costmap prediction method excels in terms of average accuracy and MSE. The navigation results indicate that using our learned costmaps leads to safer and smoother driving, outperforming previous methods in terms of the highest success rate, lowest normalized trajectory length, lowest time cost, and highest mean stability across two scenarios.

cs.RO↗

arXiv2024

Re-evaluating Retrosynthesis Algorithms with Syntheseus

Automated Synthesis Planning has recently re-emerged as a research area at the intersection of chemistry and machine learning. Despite the appearance of steady progress, we argue that imperfect benchmarks and inconsistent comparisons mask systematic shortcomings of existing techniques, and unnecessarily hamper progress. To remedy this, we present a synthesis planning library with an extensive benchmarking framework, called syntheseus, which promotes best practice by default, enabling consistent meaningful evaluation of single-step models and multi-step planning algorithms. We demonstrate the capabilities of syntheseus by re-evaluating several previous retrosynthesis algorithms, and find that the ranking of state-of-the-art models changes in controlled evaluation experiments. We end with guidance for future works in this area, and call the community to engage in the discussion on how to improve benchmarks for synthesis planning.

cs.LG↗

arXiv2024

Token-level Direct Preference Optimization

Fine-tuning pre-trained Large Language Models (LLMs) is essential to align them with human values and intentions. This process often utilizes methods like pairwise comparisons and KL divergence against a reference LLM, focusing on the evaluation of full answers generated by the models. However, the generation of these responses occurs in a token level, following a sequential, auto-regressive fashion. In this paper, we introduce Token-level Direct Preference Optimization (TDPO), a novel approach to align LLMs with human preferences by optimizing policy at the token level. Unlike previous methods, which face challenges in divergence efficiency, TDPO incorporates forward KL divergence constraints for each token, improving alignment and diversity. Utilizing the Bradley-Terry model for a token-based reward system, TDPO enhances the regulation of KL divergence, while preserving simplicity without the need for explicit reward modeling. Experimental results across various text tasks demonstrate TDPO's superior performance in balancing alignment with generation diversity. Notably, fine-tuning with TDPO strikes a better balance than DPO in the controlled sentiment generation and single-turn dialogue datasets, and significantly improves the quality of generated responses compared to both DPO and PPO-based RLHF methods. Our code is open-sourced at https://github.com/Vance0124/Token-level-Direct-Preference-Optimization.

cs.CL↗

arXiv2024

SE3Set: Harnessing equivariant hypergraph neural networks for molecular representation learning

In this paper, we develop SE3Set, an SE(3) equivariant hypergraph neural network architecture tailored for advanced molecular representation learning. Hypergraphs are not merely an extension of traditional graphs; they are pivotal for modeling high-order relationships, a capability that conventional equivariant graph-based methods lack due to their inherent limitations in representing intricate many-body interactions. To achieve this, we first construct hypergraphs via proposing a new fragmentation method that considers both chemical and three-dimensional spatial information of molecular system. We then design SE3Set, which incorporates equivariance into the hypergragh neural network. This ensures that the learned molecular representations are invariant to spatial transformations, thereby providing robustness essential for accurate prediction of molecular properties. SE3Set has shown performance on par with state-of-the-art (SOTA) models for small molecule datasets like QM9 and MD17. It excels on the MD22 dataset, achieving a notable improvement of approximately 20% in accuracy across all molecules, which highlights the prevalence of complex many-body interactions in larger molecules. This exceptional performance of SE3Set across diverse molecular structures underscores its transformative potential in computational chemistry, offering a route to more accurate and physically nuanced modeling.

cs.LG↗

arXiv2024

Unveiling the Impact of B-site Distribution on the Frustration Effect in Double Perovskite Ca2FeReO6 Using Monte Carlo Simulation and Molecular Field Theory

This work systematically investigates the spin glass behavior of the double perovskite Ca2FeReO6. Building on previous studies, we have developed a formula to quantify the ions distribution at B-site, incorporating the next-nearest neighbor interactions. Employing molecular field theory and Monte Carlo simulations, the influence of various arrangements of two B-site ions on frustration effects was uncovered. B-site is segmented into a and b-site, defining the number of nearest neighbors from Fea to Feb (and vice versa) as Zx(Zy). The significant frustration effects occur when 1<Zx(or Zy)<3, with Zx is not equal to Zy and also when Zx(or Zy) ~ 3 while Zy(or Zx) ~ 4. All of these are reflected in the variations observed in ground state magnetization and the Thermal Energy Step relation to Zx and Zy. The model proposed in this work can be applied to most B-site disordered in perovskite systems and even to other chemically disordered in frustrated systems.

cond-mat.mtrl-sci↗

arXiv2024

Elastic Interaction Energy-Informed Real-Time Traffic Scene Perception

Urban segmentation and lane detection are two important tasks for traffic scene perception. Accuracy and fast inference speed of visual perception are crucial for autonomous driving safety. Fine and complex geometric objects are the most challenging but important recognition targets in traffic scene, such as pedestrians, traffic signs and lanes. In this paper, a simple and efficient topology-aware energy loss function-based network training strategy named EIEGSeg is proposed. EIEGSeg is designed for multi-class segmentation on real-time traffic scene perception. To be specific, the convolutional neural network (CNN) extracts image features and produces multiple outputs, and the elastic interaction energy loss function (EIEL) drives the predictions moving toward the ground truth until they are completely overlapped. Our strategy performs well especially on fine-scale structure, \textit{i.e.} small or irregularly shaped objects can be identified more accurately, and discontinuity issues on slender objects can be improved. We quantitatively and qualitatively analyze our method on three traffic datasets, including urban scene segmentation data Cityscapes and lane detection data TuSimple and CULane. Our results demonstrate that EIEGSeg consistently improves the performance, especially on real-time, lightweight networks that are better suited for autonomous driving.

cs.CV↗

arXiv2024

TON-VIO: Online Time Offset Modeling Networks for Robust Temporal Alignment in High Dynamic Motion VIO

Temporal misalignment (time offset) between sensors is common in low cost visual-inertial odometry (VIO) systems. Such temporal misalignment introduces inconsistent constraints for state estimation, leading to a significant positioning drift especially in high dynamic motion scenarios. In this article, we focus on online temporal calibration to reduce the positioning drift caused by the time offset for high dynamic motion VIO. For the time offset observation model, most existing methods rely on accurate state estimation or stable visual tracking. For the prediction model, current methods oversimplify the time offset as a constant value with white Gaussian noise. However, these ideal conditions are seldom satisfied in real high dynamic scenarios, resulting in the poor performance. In this paper, we introduce online time offset modeling networks (TON) to enhance real-time temporal calibration. TON improves the accuracy of time offset observation and prediction modeling. Specifically, for observation modeling, we propose feature velocity observation networks to enhance velocity computation for features in unstable visual tracking conditions. For prediction modeling, we present time offset prediction networks to learn its evolution pattern. To highlight the effectiveness of our method, we integrate the proposed TON into both optimization-based and filter-based VIO systems. Simulation and real-world experiments are conducted to demonstrate the enhanced performance of our approach. Additionally, to contribute to the VIO community, we will open-source the code of our method on: https://github.com/Franky-X/FVON-TPN.

cs.RO↗

arXiv2024

Thermal-NeRF: Neural Radiance Fields from an Infrared Camera

In recent years, Neural Radiance Fields (NeRFs) have demonstrated significant potential in encoding highly-detailed 3D geometry and environmental appearance, positioning themselves as a promising alternative to traditional explicit representation for 3D scene reconstruction. However, the predominant reliance on RGB imaging presupposes ideal lighting conditions: a premise frequently unmet in robotic applications plagued by poor lighting or visual obstructions. This limitation overlooks the capabilities of infrared (IR) cameras, which excel in low-light detection and present a robust alternative under such adverse scenarios. To tackle these issues, we introduce Thermal-NeRF, the first method that estimates a volumetric scene representation in the form of a NeRF solely from IR imaging. By leveraging a thermal mapping and structural thermal constraint derived from the thermal characteristics of IR imaging, our method showcasing unparalleled proficiency in recovering NeRFs in visually degraded scenes where RGB-based methods fall short. We conduct extensive experiments to demonstrate that Thermal-NeRF can achieve superior quality compared to existing methods. Furthermore, we contribute a dataset for IR-based NeRF applications, paving the way for future research in IR NeRF reconstruction.

cs.CV↗

arXiv2024

Retrosynthetic Planning with Dual Value Networks

Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro*, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro*, and from 5.63 to 4.78 for RetroGraph). Our code is available at \url{https://github.com/DiXue98/PDVN}.

cs.AI↗

arXiv2024

Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs

AI for drug discovery has been a research hotspot in recent years, and SMILES-based language models has been increasingly applied in drug molecular design. However, no work has explored whether and how language models understand the chemical spatial structure from 1D sequences. In this work, we pre-train a transformer model on chemical language and fine-tune it toward drug design objectives, and investigate the correspondence between high-frequency SMILES substrings and molecular fragments. The results indicate that language models can understand chemical structures from the perspective of molecular fragments, and the structural knowledge learned through fine-tuning is reflected in the high-frequency SMILES substrings generated by the model.

cs.LG↗