arXiv subjects

Lijun Wu

Publications and source records attributed to Lijun Wu.

At least 91 records · Page 5Linked to original sources

arXiv2025

GRAIT: Gradient-Driven Refusal-Aware Instruction Tuning for Effective Hallucination Mitigation

Refusal-Aware Instruction Tuning (RAIT) aims to enhance Large Language Models (LLMs) by improving their ability to refuse responses to questions beyond their knowledge, thereby reducing hallucinations and improving reliability. Effective RAIT must address two key challenges: firstly, effectively reject unknown questions to minimize hallucinations; secondly, avoid over-refusal to ensure questions that can be correctly answered are not rejected, thereby maintain the helpfulness of LLM outputs. In this paper, we address the two challenges by deriving insightful observations from the gradient-based perspective, and proposing the Gradient-driven Refusal Aware Instruction Tuning Framework GRAIT: (1) employs gradient-driven sample selection to effectively minimize hallucinations and (2) introduces an adaptive weighting mechanism during fine-tuning to reduce the risk of over-refusal, achieving the balance between accurate refusals and maintaining useful responses. Experimental evaluations on open-ended and multiple-choice question answering tasks demonstrate that GRAIT significantly outperforms existing RAIT methods in the overall performance. The source code and data will be available at https://github.com/opendatalab/GRAIT .

cs.CL↗

arXiv2024

AgentMixer: Multi-Agent Correlated Policy Factorization

In multi-agent reinforcement learning, centralized training with decentralized execution (CTDE) methods typically assume that agents make decisions based on their local observations independently, which may not lead to a correlated joint policy with coordination. Coordination can be explicitly encouraged during training and individual policies can be trained to imitate the correlated joint policy. However, this may lead to an \textit{asymmetric learning failure} due to the observation mismatch between the joint and individual policies. Inspired by the concept of correlated equilibrium, we introduce a \textit{strategy modification} called AgentMixer that allows agents to correlate their policies. AgentMixer combines individual partially observable policies into a joint fully observable policy non-linearly. To enable decentralized execution, we introduce \textit{Individual-Global-Consistency} to guarantee mode consistency during joint training of the centralized and decentralized policies and prove that AgentMixer converges to an $ε$-approximate Correlated Equilibrium. In the Multi-Agent MuJoCo, SMAC-v2, Matrix Game, and Predator-Prey benchmarks, AgentMixer outperforms or matches state-of-the-art methods.

cs.MA↗

arXiv2024

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.

cs.LG↗

arXiv2024

SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in protein modeling. While traditional protein foundation models benefit from pre-training on vast unlabeled datasets, they often struggle to capture critical co-evolutionary information, which evolutionary-based methods excel at. In this study, we introduce a novel pre-training strategy for protein foundation models that emphasizes the interactions among amino acid residues to enhance the extraction of both short-range and long-range co-evolutionary features from sequence data. Trained on a large-scale protein sequence dataset, our model demonstrates superior generalization ability, outperforming established baselines of similar size, including the ESM model, across diverse downstream tasks. Experimental results confirm the model's effectiveness in integrating co-evolutionary information, marking a significant step forward in protein sequence-based modeling.

q-bio.QM↗

arXiv2024

Infusing Self-Consistency into Density Functional Theory Hamiltonian Prediction via Deep Equilibrium Models

In this study, we introduce a unified neural network architecture, the Deep Equilibrium Density Functional Theory Hamiltonian (DEQH) model, which incorporates Deep Equilibrium Models (DEQs) for predicting Density Functional Theory (DFT) Hamiltonians. The DEQH model inherently captures the self-consistency nature of Hamiltonian, a critical aspect often overlooked by traditional machine learning approaches for Hamiltonian prediction. By employing DEQ within our model architecture, we circumvent the need for DFT calculations during the training phase to introduce the Hamiltonian's self-consistency, thus addressing computational bottlenecks associated with large or complex systems. We propose a versatile framework that combines DEQ with off-the-shelf machine learning models for predicting Hamiltonians. When benchmarked on the MD17 and QH9 datasets, DEQHNet, an instantiation of the DEQH framework, has demonstrated a significant improvement in prediction accuracy. Beyond a predictor, the DEQH model is a Hamiltonian solver, in the sense that it uses the fixed-point solving capability of the deep equilibrium model to iteratively solve for the Hamiltonian. Ablation studies of DEQHNet further elucidate the network's effectiveness, offering insights into the potential of DEQ-integrated networks for Hamiltonian learning. We open source our implementation at https://github.com/Zun-Wang/DEQHNet.

cs.LG↗

arXiv2024

Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors

Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain suboptimal. In this work, inspired by the recent success of retrieval methods, we propose $k$NN-DTA, a non-parametric embedding-based retrieval method adopted on a pre-trained DTA prediction model, which can extend the power of the DTA model with no or negligible cost. Different from existing methods, we introduce two neighbor aggregation ways from both embedding space and label space that are integrated into a unified framework. Specifically, we propose a \emph{label aggregation} with \emph{pair-wise retrieval} and a \emph{representation aggregation} with \emph{point-wise retrieval} of the nearest neighbors. This method executes in the inference phase and can efficiently boost the DTA prediction performance with no training cost. In addition, we propose an extension, Ada-$k$NN-DTA, an instance-wise and adaptive aggregation with lightweight learning. Results on four benchmark datasets show that $k$NN-DTA brings significant improvements, outperforming previous state-of-the-art (SOTA) results, e.g, on BindingDB IC$_{50}$ and $K_i$ testbeds, $k$NN-DTA obtains new records of RMSE $\bf{0.684}$ and $\bf{0.750}$. The extended Ada-$k$NN-DTA further improves the performance to be $\bf{0.675}$ and $\bf{0.735}$ RMSE. These results strongly prove the effectiveness of our method. Results in other settings and comprehensive studies/analyses also show the great potential of our $k$NN-DTA approach.

q-bio.BM↗

arXiv2024

BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}.

q-bio.QM↗

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

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose $\mathbf{BioT5}$, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. $\mathbf{BioT5}$ utilizes SELFIES for $100%$ robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, $\mathbf{BioT5}$ distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at $\href{https://github.com/QizhiPei/BioT5}{Github}$.

cs.CL↗

arXiv2024

Backpropagation Through Agents

A fundamental challenge in multi-agent reinforcement learning (MARL) is to learn the joint policy in an extremely large search space, which grows exponentially with the number of agents. Moreover, fully decentralized policy factorization significantly restricts the search space, which may lead to sub-optimal policies. In contrast, the auto-regressive joint policy can represent a much richer class of joint policies by factorizing the joint policy into the product of a series of conditional individual policies. While such factorization introduces the action dependency among agents explicitly in sequential execution, it does not take full advantage of the dependency during learning. In particular, the subsequent agents do not give the preceding agents feedback about their decisions. In this paper, we propose a new framework Back-Propagation Through Agents (BPTA) that directly accounts for both agents' own policy updates and the learning of their dependent counterparts. This is achieved by propagating the feedback through action chains. With the proposed framework, our Bidirectional Proximal Policy Optimisation (BPPO) outperforms the state-of-the-art methods. Extensive experiments on matrix games, StarCraftII v2, Multi-agent MuJoCo, and Google Research Football demonstrate the effectiveness of the proposed method.

cs.MA↗

arXiv2024

FABind: Fast and Accurate Protein-Ligand Binding

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose $\mathbf{FABind}$, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. $\mathbf{FABind}$ incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed $\mathbf{FABind}$ demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

cs.LG↗

arXiv2023

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at $\href{https://github.com/QizhiPei/SSM-DTA}{Github}$.

q-bio.BM↗

arXiv2023

High efficiency spin-decoupled modulation using chiral C2-symmetric meta-atoms

Orthogonal circularly polarized light is essential for multiplexing tunable metasurfaces. Mainstream spin-decoupled metasurfaces, consisting of numerous meta-atoms with mirror symmetry, rely on the cooperative modulation of the Pancharatnam-Berry (PB) phase and the propagation phase. This paper demonstrates spin-decoupled functionality through the synergistic utilization of planar chiral meta-atom phase response and PB phase. Based on the Jones calculus, it has been found that meta-atoms with chiral C2-symmetry owns a larger geometric parameter range with high cross-polarization ratio compared to those with mirror symmetry or higher symmetries at the same aspect ratio. This characteristic is advantageous in terms of enabling high-efficiency manipulation and enhancing the signal-to-noise ratio. As an example, 10 kinds of C2-symmetry chiral meta-atoms with a H-like shape are selected by the self-adaptive genetic algorithm to attain a full 2$π$ phase span with an interval of $π$/5. To mitigate the additional propagation phase change of the guided modes originated from the arrangement alternation upon the rotation of the meta-atoms, the enantiomer of chiral meta-atoms and its PB phase delay are adopted to minimize the difference between the actual and desired target phases. A polarization-insensitive metalens and a chiral virtual-moving metalens array are designed to demonstrate the spin-decoupled function with both high efficiency and signal-to-noise ratio. The work in this paper may trigger more exciting and interesting spin-decoupled multiplexing metasurfaces and broaden the prospect of chiroptical applications.

physics.optics↗

arXiv2023

CT4Rec: Simple yet Effective Consistency Training for Sequential Recommendation

Sequential recommendation methods are increasingly important in cutting-edge recommender systems. Through leveraging historical records, the systems can capture user interests and perform recommendations accordingly. State-of-the-art sequential recommendation models proposed very recently combine contrastive learning techniques for obtaining high-quality user representations. Though effective and performing well, the models based on contrastive learning require careful selection of data augmentation methods and pretext tasks, efficient negative sampling strategies, and massive hyper-parameters validation. In this paper, we propose an ultra-simple alternative for obtaining better user representations and improving sequential recommendation performance. Specifically, we present a simple yet effective \textbf{C}onsistency \textbf{T}raining method for sequential \textbf{Rec}ommendation (CT4Rec) in which only two extra training objectives are utilized without any structural modifications and data augmentation. Experiments on three benchmark datasets and one large newly crawled industrial corpus demonstrate that our proposed method outperforms SOTA models by a large margin and with much less training time than these based on contrastive learning. Online evaluation on real-world content recommendation system also achieves 2.717\% improvement on the click-through rate and 3.679\% increase on the average click number per capita. Further exploration reveals that such a simple method has great potential for CTR prediction. Our code is available at \url{https://github.com/ct4rec/CT4Rec.git}.

cs.IR↗

arXiv2023

Polarization-insensitive dual-wavelength dispersion tunable metalens achieved by global modulation method

SF$_6$ is widely used as a gas-insulator in high-voltage power electrical system. Detecting SF$_6$ leaks using unmanned aerial vehicle (UAV)-based thermal cameras allows efficient large-scale inspections during routine maintenance. The emergence of lightweight metalenses can increase the endurance of UAVs. Simultaneously controlling dispersion and polarization properties in metalens is significant for thermal camera applications. However, via a propagation phase modulation method in which the phase is tuned locally, it is difficult and time-consuming to obtain enough different nanostructures to control multiwavelength independently while maintain the polarization-insensitive property. To this end, by using a global modulation method, a polarization-insensitive dual-wavelength achromatic and super-chromatic metalens are designed respectively. The working wavelength is set at 10.6 and 12 $\rmμ$m to match the absorption peaks of SF$_6$ and one of its decompositions (SO$_2$F$_2$), respectively. According to the operating wavelengths, only the geometric parameters of two nanofins are required to be optimized (through genetic algorithm). Then they are superimposed on each other to form cross-shaped meta-atoms. In order to control the influence between the two crossed nanofins, an additional term $Δf$ is introduced into the phase equation to modify the shape of the wavefront, whereby the phase dispersion can be easily engineered. Compared with local modulation, the number of unique nanostructures that need to be optimized can be reduced to two (operating at dual wavelengths) by the Pancharatnam-Berry (PB) phase based global modulation method. Therefore, the proposed design strategy is expected to circumvent difficulties in the local design approaches and can find widespread applications in multiwavelength imaging and spectroscopy.

physics.optics↗

arXiv2023

A Survey on Non-Autoregressive Generation for Neural Machine Translation and Beyond

Non-autoregressive (NAR) generation, which is first proposed in neural machine translation (NMT) to speed up inference, has attracted much attention in both machine learning and natural language processing communities. While NAR generation can significantly accelerate inference speed for machine translation, the speedup comes at the cost of sacrificed translation accuracy compared to its counterpart, autoregressive (AR) generation. In recent years, many new models and algorithms have been designed/proposed to bridge the accuracy gap between NAR generation and AR generation. In this paper, we conduct a systematic survey with comparisons and discussions of various non-autoregressive translation (NAT) models from different aspects. Specifically, we categorize the efforts of NAT into several groups, including data manipulation, modeling methods, training criterion, decoding algorithms, and the benefit from pre-trained models. Furthermore, we briefly review other applications of NAR models beyond machine translation, such as grammatical error correction, text summarization, text style transfer, dialogue, semantic parsing, automatic speech recognition, and so on. In addition, we also discuss potential directions for future exploration, including releasing the dependency of KD, reasonable training objectives, pre-training for NAR, and wider applications, etc. We hope this survey can help researchers capture the latest progress in NAR generation, inspire the design of advanced NAR models and algorithms, and enable industry practitioners to choose appropriate solutions for their applications. The web page of this survey is at \url{https://github.com/LitterBrother-Xiao/Overview-of-Non-autoregressive-Applications}.

cs.CL↗

arXiv2023

Retrosynthesis Prediction with Local Template Retrieval

Retrosynthesis, which predicts the reactants of a given target molecule, is an essential task for drug discovery. In recent years, the machine learing based retrosynthesis methods have achieved promising results. In this work, we introduce RetroKNN, a local reaction template retrieval method to further boost the performance of template-based systems with non-parametric retrieval. We first build an atom-template store and a bond-template store that contain the local templates in the training data, then retrieve from these templates with a k-nearest-neighbor (KNN) search during inference. The retrieved templates are combined with neural network predictions as the final output. Furthermore, we propose a lightweight adapter to adjust the weights when combing neural network and KNN predictions conditioned on the hidden representation and the retrieved templates. We conduct comprehensive experiments on two widely used benchmarks, the USPTO-50K and USPTO-MIT. Especially for the top-1 accuracy, we improved 7.1% on the USPTO-50K dataset and 12.0% on the USPTO-MIT dataset. These results demonstrate the effectiveness of our method.

cs.AI↗

arXiv2023

MolXPT: Wrapping Molecules with Text for Generative Pre-training

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

cs.CL↗