arXiv subjects

Wu-Jun Li

Publications and source records attributed to Wu-Jun Li.

At least 19 recordsLinked to original sources

arXiv2026

Ordered Local Momentum for Asynchronous Distributed Learning under Arbitrary Delays

Momentum SGD (MSGD) serves as a foundational optimizer in training deep models due to momentum's key role in accelerating convergence and enhancing generalization. Meanwhile, asynchronous distributed learning is crucial for training large-scale deep models, especially when the computing capabilities of the workers in the cluster are heterogeneous. To reduce communication frequency, local updates are widely adopted in distributed learning. However, how to implement asynchronous distributed MSGD with local updates remains unexplored. To solve this problem, we propose a novel method, called \underline{or}dered \underline{lo}cal \underline{mo}mentum (OrLoMo), for asynchronous distributed learning. In OrLoMo, each worker runs MSGD locally. Then the local momentum from each worker will be aggregated by the server in order based on its global iteration index. To the best of our knowledge, OrLoMo is the first method to implement asynchronous distributed MSGD with local updates. We prove the convergence of OrLoMo for non-convex problems under arbitrary delays. Experiments validate that OrLoMo can outperform its synchronous counterpart and other asynchronous methods.

cs.LG↗

arXiv2025

RadDiff: Retrieval-Augmented Denoising Diffusion for Protein Inverse Folding

Protein inverse folding, the design of an amino acid sequence based on a target protein structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external knowledge or relying on protein language models~(PLMs). The former omits the knowledge stored in natural protein data, while the latter is parameter-inefficient and inflexible to adapt to ever-growing protein data. To overcome the above drawbacks, in this paper we propose a novel method, called $\underline{\text{r}}$etrieval-$\underline{\text{a}}$ugmented $\underline{\text{d}}$enoising $\underline{\text{diff}}$usion~($\mbox{RadDiff}$), for protein inverse folding. In RadDiff, a novel retrieval-augmentation mechanism is designed to capture the up-to-date protein knowledge. We further design a knowledge-aware diffusion model that integrates this protein knowledge into the diffusion process via a lightweight module. Experimental results on the CATH, TS50, and PDB2022 datasets show that $\mbox{RadDiff}$ consistently outperforms existing methods, improving sequence recovery rate by up to 19\%. Experimental results also demonstrate that RadDiff generates highly foldable sequences and scales effectively with database size.

q-bio.QM↗

arXiv2025

From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective optimization in protein design. Yet whether RL can push PLMs beyond their pretraining priors to uncover latent sequence-structure-function rules remains unclear. We address this by pairing RL with PLMs across four domains: antimicrobial peptide design, kinase variant optimization, antibody engineering, and inverse folding. Using diverse RL algorithms and model classes, we ask if RL improves sampling efficiency and, more importantly, if it reveals capabilities not captured by supervised learning. Across benchmarks, RL consistently boosts success rates and sample efficiency. Performance follows a three-factor interaction: task headroom, reward fidelity, and policy capacity jointly determine gains. When rewards are accurate and informative, policies have sufficient capacity, and tasks leave room beyond supervised baselines, improvements scale; when rewards are noisy or capacity is constrained, gains saturate despite exploration. This view yields practical guidance for RL in protein design: prioritize reward modeling and calibration before scaling policy size, match algorithm and regularization strength to task difficulty, and allocate capacity where marginal gains are largest. Implementation is available at https://github.com/chq1155/RL-PLM.

cs.LG↗

arXiv2025

Gated Integration of Low-Rank Adaptation for Continual Learning of Large Language Models

Continual learning (CL), which requires the model to learn multiple tasks sequentially, is crucial for large language models (LLMs). Recently, low-rank adaptation~(LoRA), one of the most representative parameter-efficient fine-tuning (PEFT) methods, has gained increasing attention in CL of LLMs. However, most existing CL methods based on LoRA typically expand a new LoRA branch to learn each new task and force the new and old LoRA branches to influence old tasks equally, potentially leading to forgetting. In this work, we propose a new method, called gated integration of low-rank adaptation (GainLoRA), for CL of LLMs. GainLoRA expands a new LoRA branch for each new task and introduces gating modules to integrate the new and old LoRA branches. Furthermore, GainLoRA leverages the new gating module to minimize the influence from the new LoRA branch to old tasks, effectively mitigating forgetting and improving the model's overall performance. Experimental results on CL benchmarks demonstrate that GainLoRA outperforms existing state-of-the-art methods.

cs.CL↗

arXiv2025

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications. Moreover, some studies involve heavy frameworks requiring extensive training, posing challenges for convenient and efficient assessment of docking methods. To fill these gaps, we design PoseX, an open-source benchmark to evaluate both self-docking and cross-docking, enabling a practical and comprehensive assessment of algorithmic advances. Specifically, we curated a novel dataset comprising 718 entries for self-docking and 1,312 entries for cross-docking; second, we incorporated 23 docking methods in three methodological categories, including physics-based methods (e.g., Schr\"odinger Glide), AI docking methods (e.g., DiffDock) and AI co-folding methods (e.g., AlphaFold3); third, we developed a relaxation method for post-processing to minimize conformational energy and refine binding poses; fourth, we built a leaderboard to rank submitted models in real-time. We derived some key insights and conclusions from extensive experiments: (1) AI approaches have consistently outperformed physics-based methods in overall docking success rate. (2) Most intra- and intermolecular clashes of AI approaches can be greatly alleviated with relaxation, which means combining AI modeling with physics-based post-processing could achieve excellent performance. (3) AI co-folding methods exhibit ligand chirality issues, except for Boltz-1x, which introduced physics-inspired potentials to fix hallucinations, suggesting modeling on stereochemistry improves the structural plausibility markedly. (4) Specifying binding pockets significantly promotes docking performance, indicating that pocket information can be leveraged adequately, particularly for AI co-folding methods, in future modeling efforts. The code, dataset, and leaderboard are released at https://github.com/CataAI/PoseX.

cs.LG↗

arXiv2025

UniAP: Unifying Inter- and Intra-Layer Automatic Parallelism by Mixed Integer Quadratic Programming

Distributed learning is commonly used for training deep learning models, especially large models. In distributed learning, manual parallelism (MP) methods demand considerable human effort and have limited flexibility. Hence, automatic parallelism (AP) methods have recently been proposed for automating the parallel strategy optimization process. Existing AP methods suffer from sub-optimal solutions because they do not jointly optimize the two categories of parallel strategies (i.e., inter-layer parallelism and intra-layer parallelism). In this paper, we propose a novel AP method called UniAP, which unifies inter- and intra-layer automatic parallelism by mixed integer quadratic programming. To the best of our knowledge, UniAP is the first parallel method that can jointly optimize the two categories of parallel strategies to find an optimal solution. Experimental results show that UniAP outperforms state-of-the-art methods by up to 3.80$\times$ in throughput and reduces strategy optimization time by up to 107$\times$ across five Transformer-based models.

cs.LG↗

arXiv2025

PIPO: Pipelined Offloading for Efficient Inference on Consumer Devices

The high memory and computation demand of large language models (LLMs) makes them challenging to be deployed on consumer devices due to limited GPU memory. Offloading can mitigate the memory constraint but often suffers from low GPU utilization, leading to low inference efficiency. In this work, we propose a novel framework, called pipelined offloading (PIPO), for efficient inference on consumer devices. PIPO designs a fine-grained offloading pipeline, complemented with optimized data transfer and computation, to achieve high concurrency and efficient scheduling for inference. Experimental results show that compared with state-of-the-art baseline, PIPO increases GPU utilization from below 40% to over 90% and achieves up to 3.1$\times$ higher throughput, running on a laptop equipped with a RTX3060 GPU of 6GB memory.

cs.DC↗

arXiv2025

LCQ: Low-Rank Codebook based Quantization for Large Language Models

Large language models~(LLMs) have recently demonstrated promising performance in many tasks. However, the high storage and computational cost of LLMs has become a challenge for deploying LLMs. Weight quantization has been widely used for model compression, which can reduce both storage and computational cost. Most existing weight quantization methods for LLMs use a rank-one codebook for quantization, which results in substantial accuracy loss when the compression ratio is high. In this paper, we propose a novel weight quantization method, called low-rank codebook based quantization~(LCQ), for LLMs. LCQ adopts a low-rank codebook, the rank of which can be larger than one, for quantization. Experiments show that LCQ can achieve better accuracy than existing methods with a negligibly extra storage cost.

cs.LG↗

arXiv2025

Ordered Momentum for Asynchronous SGD

Distributed learning is essential for training large-scale deep models. Asynchronous SGD (ASGD) and its variants are commonly used distributed learning methods, particularly in scenarios where the computing capabilities of workers in the cluster are heterogeneous. Momentum has been acknowledged for its benefits in both optimization and generalization in deep model training. However, existing works have found that naively incorporating momentum into ASGD can impede the convergence. In this paper, we propose a novel method called ordered momentum (OrMo) for ASGD. In OrMo, momentum is incorporated into ASGD by organizing the gradients in order based on their iteration indexes. We theoretically prove the convergence of OrMo with both constant and delay-adaptive learning rates for non-convex problems. To the best of our knowledge, this is the first work to establish the convergence analysis of ASGD with momentum without dependence on the maximum delay. Empirical results demonstrate that OrMo can achieve better convergence performance compared with ASGD and other asynchronous methods with momentum.

cs.LG↗

arXiv2025

TimeDP: Learning to Generate Multi-Domain Time Series with Domain Prompts

Time series generation models are crucial for applications like data augmentation and privacy preservation. Most existing time series generation models are typically designed to generate data from one specified domain. While leveraging data from other domain for better generalization is proved to work in other application areas, this approach remains challenging for time series modeling due to the large divergence in patterns among different real world time series categories. In this paper, we propose a multi-domain time series diffusion model with domain prompts, named TimeDP. In TimeDP, we utilize a time series semantic prototype module which defines time series prototypes to represent time series basis, each prototype vector serving as "word" representing some elementary time series feature. A prototype assignment module is applied to extract the extract domain specific prototype weights, for learning domain prompts as generation condition. During sampling, we extract "domain prompt" with few-shot samples from the target domain and use the domain prompts as condition to generate time series samples. Experiments demonstrate that our method outperforms baselines to provide the state-of-the-art in-domain generation quality and strong unseen domain generation capability.

cs.LG↗

arXiv2024

Hashing for Protein Structure Similarity Search

Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional alignment-based PSSS methods, which directly calculate alignment on the protein structures, are highly time-consuming with high memory cost. Recently, alignment-free methods, which represent protein structures as fixed-length real-valued vectors, are proposed for PSSS. Although these methods have lower time and memory cost than alignment-based methods, their time and memory cost is still too high for large-scale PSSS, and their accuracy is unsatisfactory. In this paper, we propose a novel method, called $\underline{\text{p}}$r$\underline{\text{o}}$tein $\underline{\text{s}}$tructure $\underline{\text{h}}$ashing (POSH), for PSSS. POSH learns a binary vector representation for each protein structure, which can dramatically reduce the time and memory cost for PSSS compared with real-valued vector representation based methods. Furthermore, in POSH we also propose expressive hand-crafted features and a structure encoder to well model both node and edge interactions in proteins. Experimental results on real datasets show that POSH can outperform other methods to achieve state-of-the-art accuracy. Furthermore, POSH achieves a memory saving of more than six times and speed improvement of more than four times, compared with other methods.

cs.LG↗

arXiv2024

Controllable Financial Market Generation with Diffusion Guided Meta Agent

Generative modeling has transformed many fields, such as language and visual modeling, while its application in financial markets remains under-explored. As the minimal unit within a financial market is an order, order-flow modeling represents a fundamental generative financial task. However, current approaches often yield unsatisfactory fidelity in generating order flow, and their generation lacks controllability, thereby limiting their practical applications. In this paper, we formulate the challenge of controllable financial market generation, and propose a Diffusion Guided Meta Agent (DigMA) model to address it. Specifically, we employ a conditional diffusion model to capture the dynamics of the market state represented by time-evolving distribution parameters of the mid-price return rate and the order arrival rate, and we define a meta agent with financial economic priors to generate orders from the corresponding distributions. Extensive experimental results show that DigMA achieves superior controllability and generation fidelity. Moreover, we validate its effectiveness as a generative environment for downstream high-frequency trading tasks and its computational efficiency.

cs.CE↗

arXiv2024

Hashing based Contrastive Learning for Virtual Screening

Virtual screening (VS) is a critical step in computer-aided drug discovery, aiming to identify molecules that bind to a specific target receptor like protein. Traditional VS methods, such as docking, are often too time-consuming for screening large-scale molecular databases. Recent advances in deep learning have demonstrated that learning vector representations for both proteins and molecules using contrastive learning can outperform traditional docking methods. However, given that target databases often contain billions of molecules, real-valued vector representations adopted by existing methods can still incur significant memory and time costs in VS. To address this problem, in this paper we propose a hashing-based contrastive learning method, called DrugHash, for VS. DrugHash treats VS as a retrieval task that uses efficient binary hash codes for retrieval. In particular, DrugHash designs a simple yet effective hashing strategy to enable end-to-end learning of binary hash codes for both protein and molecule modalities, which can dramatically reduce the memory and time costs with higher accuracy compared with existing methods. Experimental results show that DrugHash can outperform existing methods to achieve state-of-the-art accuracy, with a memory saving of 32$\times$ and a speed improvement of 3.5$\times$.

cs.AI↗

arXiv2024

Buffered Asynchronous Secure Aggregation for Cross-Device Federated Learning

Asynchronous federated learning (AFL) is an effective method to address the challenge of device heterogeneity in cross-device federated learning. However, AFL is usually incompatible with existing secure aggregation protocols used to protect user privacy in federated learning because most existing secure aggregation protocols are based on synchronous aggregation. To address this problem, we propose a novel secure aggregation protocol named buffered asynchronous secure aggregation (BASA) in this paper. Compared with existing protocols, BASA is fully compatible with AFL and provides secure aggregation under the condition that each user only needs one round of communication with the server without relying on any synchronous interaction among users. Based on BASA, we propose the first AFL method which achieves secure aggregation without extra requirements on hardware. We empirically demonstrate that BASA outperforms existing secure aggregation protocols for cross-device federated learning in terms of training efficiency and scalability.

cs.CR↗

arXiv2024

On the Evaluation Metric for Hashing

Due to its low storage cost and fast query speed, hashing has been widely used for large-scale approximate nearest neighbor (ANN) search. Bucket search, also called hash lookup, can achieve fast query speed with a sub-linear time cost based on the inverted index table constructed from hash codes. Many metrics have been adopted to evaluate hashing algorithms. However, all existing metrics are improper to evaluate the hash codes for bucket search. On one hand, all existing metrics ignore the retrieval time cost which is an important factor reflecting the performance of search. On the other hand, some of them, such as mean average precision (MAP), suffer from the uncertainty problem as the ranked list is based on integer-valued Hamming distance, and are insensitive to Hamming radius as these metrics only depend on relative Hamming distance. Other metrics, such as precision at Hamming radius R, fail to evaluate global performance as these metrics only depend on one specific Hamming radius. In this paper, we first point out the problems of existing metrics which have been ignored by the hashing community, and then propose a novel evaluation metric called radius aware mean average precision (RAMAP) to evaluate hash codes for bucket search. Furthermore, two coding strategies are also proposed to qualitatively show the problems of existing metrics. Experiments demonstrate that our proposed RAMAP can provide more proper evaluation than existing metrics.

cs.IR↗

arXiv2024

Multiple Code Hashing for Efficient Image Retrieval

Due to its low storage cost and fast query speed, hashing has been widely used in large-scale image retrieval tasks. Hash bucket search returns data points within a given Hamming radius to each query, which can enable search at a constant or sub-linear time cost. However, existing hashing methods cannot achieve satisfactory retrieval performance for hash bucket search in complex scenarios, since they learn only one hash code for each image. More specifically, by using one hash code to represent one image, existing methods might fail to put similar image pairs to the buckets with a small Hamming distance to the query when the semantic information of images is complex. As a result, a large number of hash buckets need to be visited for retrieving similar images, based on the learned codes. This will deteriorate the efficiency of hash bucket search. In this paper, we propose a novel hashing framework, called multiple code hashing (MCH), to improve the performance of hash bucket search. The main idea of MCH is to learn multiple hash codes for each image, with each code representing a different region of the image. Furthermore, we propose a deep reinforcement learning algorithm to learn the parameters in MCH. To the best of our knowledge, this is the first work that proposes to learn multiple hash codes for each image in image retrieval. Experiments demonstrate that MCH can achieve a significant improvement in hash bucket search, compared with existing methods that learn only one hash code for each image.

cs.LG↗

arXiv2024

NumLLM: Numeric-Sensitive Large Language Model for Chinese Finance

Recently, many works have proposed various financial large language models (FinLLMs) by pre-training from scratch or fine-tuning open-sourced LLMs on financial corpora. However, existing FinLLMs exhibit unsatisfactory performance in understanding financial text when numeric variables are involved in questions. In this paper, we propose a novel LLM, called numeric-sensitive large language model (NumLLM), for Chinese finance. We first construct a financial corpus from financial textbooks which is essential for improving numeric capability of LLMs during fine-tuning. After that, we train two individual low-rank adaptation (LoRA) modules by fine-tuning on our constructed financial corpus. One module is for adapting general-purpose LLMs to financial domain, and the other module is for enhancing the ability of NumLLM to understand financial text with numeric variables. Lastly, we merge the two LoRA modules into the foundation model to obtain NumLLM for inference. Experiments on financial question-answering benchmark show that NumLLM can boost the performance of the foundation model and can achieve the best overall performance compared to all baselines, on both numeric and non-numeric questions.

cs.CE↗

arXiv2024

Stochastic Normalized Gradient Descent with Momentum for Large-Batch Training

Stochastic gradient descent~(SGD) and its variants have been the dominating optimization methods in machine learning. Compared to SGD with small-batch training, SGD with large-batch training can better utilize the computational power of current multi-core systems such as graphics processing units~(GPUs) and can reduce the number of communication rounds in distributed training settings. Thus, SGD with large-batch training has attracted considerable attention. However, existing empirical results showed that large-batch training typically leads to a drop in generalization accuracy. Hence, how to guarantee the generalization ability in large-batch training becomes a challenging task. In this paper, we propose a simple yet effective method, called stochastic normalized gradient descent with momentum~(SNGM), for large-batch training. We prove that with the same number of gradient computations, SNGM can adopt a larger batch size than momentum SGD~(MSGD), which is one of the most widely used variants of SGD, to converge to an $ε$-stationary point. Empirical results on deep learning verify that when adopting the same large batch size, SNGM can achieve better test accuracy than MSGD and other state-of-the-art large-batch training methods.

stat.ML↗