arXiv subjects

Yuangang Pan

Publications and source records attributed to Yuangang Pan.

At least 19 recordsLinked to original sources

arXiv2026

Sequence-Informed Geometric Evaluation of RNA 3D Structures

Computational RNA structure pipelines generate many candidate conformations for the same sequence. Reliable evaluation therefore requires more than recognising plausible geometry, it requires determining whether that geometry is compatible with the sequence. We introduce SIRGE, a sequence-informed geometric evaluator that conditions structural representations on nucleotide embeddings from a pretrained RNA language model. Early results show that SIRGE outperforms established evaluators in Kendall--$\tau$ alignment, Top-1 selection, and Top-3 ranking. Controlled comparisons further show that sequence conditioning corrects errors made by an otherwise matched geometric model and improves target-level rank structure. These findings provide initial evidence that pretrained sequence representations supply ranking information that complements geometric reasoning.

q-bio.BM↗

arXiv2026

Reliable Neural Collapse Approximation for Open-World Test-Time Adaptation

Test-Time Adaptation (TTA) methods aim to bridge the domain gap between the source and target domains. However, traditional TTA methods become ineffective when the label distribution shift occurs, a challenge commonly referred to as an open-world scenario. In this paper, we introduce a new method named Reliable Neural Collapse approximation (ReNC) for Open-World Test-Time Adaptation (OWTTA). Specifically, we leverage neural collapse as a structural prior for reliable target-domain adaptation. Guided by this prior, we justify that the pre-trained classifier weights can serve as the prototypes of the source domain. By measuring the similarity between samples and prototypes, we filter out the Out-Of-Distribution~(OOD) samples for reliable updates. Furthermore, we propose a neural collapse approximation mechanism to refine these prototypes, ensuring they can gradually adapt to the target domain while maintaining the neural collapse structure. Extensive experiments on several open-world benchmarks demonstrate the superiority of the proposed method. Our empirical analysis suggests that ReNC better preserves NC-related properties in the target domain, providing useful evidence for explaining reliable OWTTA and offering new insights for model design. Code is available at https://github.com/JiaqiLin-AI/ReNC.

cs.LG↗

arXiv2026

PETA:Parameter-Efficient Test-Time Adaptation for Virtual Screening

Accurately ranking active ligands for a target protein pocket from massive chemical libraries remains a central challenge in virtual screening. DrugCLIP and its recent extensions substantially accelerate this process by encoding protein pockets and molecules into a shared embedding space. Despite this progress, further performance improvements typically require retraining the entire model, incurring substantial computational overhead and making target-specific customization inefficient. In this work, we formulate the specialization of pretrained virtual screening models to individual pockets as a test-time adaptation problem and propose PETA, a parameter-efficient framework that directly adapts pretrained model at test time. Given a target pocket, PETA constructs pocket-specific negatives through molecular diffusion and chemical validity filtering, and further moves them toward the reference ligand retrieved from structural databases via embedding-space mixup to create more challenging ranking tasks. A ranking objective then places greater emphasis on suppressing high-scoring invalid candidates that could contaminate the top-ranked screening results, providing structured supervision for lightweight adaptation. Experiments across diverse benchmarks demonstrate that this lightweight, pocket-specific adaptation outperforms both pretrained and fully retrained baselines while updating only the LayerNorm parameters, which account for approximately $0.03\%$ of the full model.

cs.LG↗

arXiv2026

Mastering PokeGym: Graph-Guided Multimodal Evolution at Test Time

While artificial intelligence has mastered structured games like chess and Go, vision-language agents still struggle in visually-driven 3D games without access to game states. Existing game environments typically evaluate a fixed agent configuration, rather than an agent's ability to improve its configuration across consecutive episodes of the same task---a paradigm known as test-time learning (TTL). Furthermore, current TTL methods typically optimize single modalities---such as text prompts or actions---in isolation, ignoring the synergy between perception, reasoning, and control. To bridge these gaps, we first introduce \textbf{PokeGym}, a long-horizon benchmark built upon the 3D open-world game Pok\'emon Legends: Z-A, where agents act from visual observations without access to game states, designed to evaluate an agent's ability to learn and adapt across consecutive episodes of the task. To tackle this challenging environment, we propose Graph-Guided Evolutionary Multimodal Agent Configuration (\textbf{G-EvoMAC}), a graph-guided framework that jointly optimizes visual perception, strategy, and action set synergistically. Extensive experiments show that G-EvoMAC achieves a 60.18\% average success rate on PokeGym, outperforming the strongest baseline by over 11 percentage points, validating the power of cross-modal co-evolution.

cs.CV↗

arXiv2025

The Reward Model Selection Crisis in Personalized Alignment

Personalized alignment from preference data has focused primarily on improving personal reward model (RM) accuracy, with the implicit assumption that better preference ranking translates to better personalized behavior. However, in deployment, computational constraints necessitate inference-time adaptation such as reward-guided decoding (RGD) rather than per-user policy fine-tuning. This creates a critical but overlooked requirement: reward models must not only rank preferences accurately but also effectively guide generation. We demonstrate that standard RM accuracy fails catastrophically as a selection criterion for deployment-ready personalized rewards. We introduce policy accuracy; a metric quantifying whether RGD-adapted LLMs correctly discriminate between preferred and dispreferred responses and show that upstream RM accuracy correlates only weakly with downstream policy accuracy (Kendall's tau = 0.08--0.31). More critically, we introduce Pref-LaMP the first personalized alignment benchmark with ground-truth user completions, enabling direct behavioural evaluation. On Pref-LaMP, we expose a complete decoupling between discriminative ranking and generation metrics: methods with 20-point RM accuracy differences produce almost identical output quality, and methods with high ranking accuracy can fail to generate behaviorally aligned responses. These findings reveal that the field has been optimizing for proxy metrics that do not predict deployment performance, and that current personalized alignment methods fail to operationalize preferences into behavioral adaptation under realistic deployment constraints. In contrast, we find simple in-context learning (ICL) to be highly effective - dominating all reward-guided methods for models $\geq$3B parameters, achieving $\sim$3 point ROUGE-1 gains over the best reward method at 7B scale.

cs.AI↗

arXiv2025

Leveraging Scene Context with Dual Networks for Sequential User Behavior Modeling

Modeling sequential user behaviors for future behavior prediction is crucial in improving user's information retrieval experience. Recent studies highlight the importance of incorporating contextual information to enhance prediction performance. One crucial but usually neglected contextual information is the scene feature which we define as sub-interfaces within an app, created by developers to provide specific functionalities, such as ``text2product search" and ``live" modules in e-commence apps. Different scenes exhibit distinct functionalities and usage habits, leading to significant distribution gap in user engagement across them. Popular sequential behavior models either ignore the scene feature or merely use it as attribute embeddings, which cannot effectively capture the dynamic interests and interplay between scenes and items when modeling user sequences. In this work, we propose a novel Dual Sequence Prediction networks (DSPnet) to effectively capture the dynamic interests and interplay between scenes and items for future behavior prediction. DSPnet consists of two parallel networks dedicated to learn users' dynamic interests over items and scenes, and a sequence feature enhancement module to capture the interplay for enhanced future behavior prediction. Further, we introduce a Conditional Contrastive Regularization (CCR) loss to capture the invariance of similar historical sequences. Theoretical analysis suggests that DSPnet is a principled way to learn the joint relationships between scene and item sequences. Extensive experiments are conducted on one public benchmark and two collected industrial datasets. The method has been deployed online in our system, bringing a 0.04 point increase in CTR, 0.78\% growth in deals, and 0.64\% rise in GMV. The codes are available at this anonymous github: \textcolor{blue}{https://anonymous.4open.science/r/DSPNet-ForPublish-2506/}.

cs.IR↗

arXiv2025

Generative Co-Design of Antibody Sequences and Structures via Black-Box Guidance in a Shared Latent Space

Advancements in deep generative models have enabled the joint modeling of antibody sequence and structure, given the antigen-antibody complex as context. However, existing approaches for optimizing complementarity-determining regions (CDRs) to improve developability properties operate in the raw data space, leading to excessively costly evaluations due to the inefficient search process. To address this, we propose LatEnt blAck-box Design (LEAD), a sequence-structure co-design framework that optimizes both sequence and structure within their shared latent space. Optimizing shared latent codes can not only break through the limitations of existing methods, but also ensure synchronization of different modality designs. Particularly, we design a black-box guidance strategy to accommodate real-world scenarios where many property evaluators are non-differentiable. Experimental results demonstrate that our LEAD achieves superior optimization performance for both single and multi-property objectives. Notably, LEAD reduces query consumption by a half while surpassing baseline methods in property optimization. The code is available at https://github.com/EvaFlower/LatEnt-blAck-box-Design.

cs.LG↗

arXiv2024

Learning Multi-Branch Cooperation for Enhanced Click-Through Rate Prediction at Taobao

Existing click-through rate (CTR) prediction works have studied the role of feature interaction through a variety of techniques. Each interaction technique exhibits its own strength, and solely using one type usually constrains the model's capability to capture the complex feature relationships, especially for industrial data with enormous input feature fields. Recent research shows that effective CTR models often combine an MLP network with a dedicated feature interaction network in a two-parallel structure. However, the interplay and cooperative dynamics between different streams or branches remain under-researched. In this work, we introduce a novel Multi-Branch Cooperation Network (MBCnet) which enables multiple branch networks to collaborate with each other for better complex feature interaction modeling. Specifically, MBCnet consists of three branches: the Extensible Feature Grouping and Crossing (EFGC) branch that promotes the model's memorization ability of specific feature fields, the low rank Cross Net branch and Deep branch to enhance explicit and implicit feature crossing for improved generalization. Among these branches, a novel cooperation scheme is proposed based on two principles: Branch co-teaching and moderate differentiation. Branch co-teaching encourages well-learned branches to support poorly-learned ones on specific training samples. Moderate differentiation advocates branches to maintain a reasonable level of difference in their feature representations on the same inputs. This cooperation strategy improves learning through mutual knowledge sharing and boosts the discovery of diverse feature interactions across branches. Experiments on large-scale industrial datasets and online A/B test at Taobao app demonstrate MBCnet's superior performance, delivering a 0.09 point increase in CTR, 1.49% growth in deals, and 1.62% rise in GMV. Core codes are available online.

cs.IR↗

arXiv2024

Alpha and Prejudice: Improving $\alpha$-sized Worst-case Fairness via Intrinsic Reweighting

Worst-case fairness with off-the-shelf demographics achieves group parity by maximizing the model utility of the worst-off group. Nevertheless, demographic information is often unavailable in practical scenarios, which impedes the use of such a direct max-min formulation. Recent advances have reframed this learning problem by introducing the lower bound of minimal partition ratio, denoted as $\alpha$, as side information, referred to as ``$\alpha$-sized worst-case fairness'' in this paper. We first justify the practical significance of this setting by presenting noteworthy evidence from the data privacy perspective, which has been overlooked by existing research. Without imposing specific requirements on loss functions, we propose reweighting the training samples based on their intrinsic importance to fairness. Given the global nature of the worst-case formulation, we further develop a stochastic learning scheme to simplify the training process without compromising model performance. Additionally, we address the issue of outliers and provide a robust variant to handle potential outliers during model training. Our theoretical analysis and experimental observations reveal the connections between the proposed approaches and existing ``fairness-through-reweighting'' studies, with extensive experimental results on fairness benchmarks demonstrating the superiority of our methods.

cs.LG↗

arXiv2024

PROUD: PaRetO-gUided Diffusion Model for Multi-objective Generation

Recent advancements in the realm of deep generative models focus on generating samples that satisfy multiple desired properties. However, prevalent approaches optimize these property functions independently, thus omitting the trade-offs among them. In addition, the property optimization is often improperly integrated into the generative models, resulting in an unnecessary compromise on generation quality (i.e., the quality of generated samples). To address these issues, we formulate a constrained optimization problem. It seeks to optimize generation quality while ensuring that generated samples reside at the Pareto front of multiple property objectives. Such a formulation enables the generation of samples that cannot be further improved simultaneously on the conflicting property functions and preserves good quality of generated samples. Building upon this formulation, we introduce the PaRetO-gUided Diffusion model (PROUD), wherein the gradients in the denoising process are dynamically adjusted to enhance generation quality while the generated samples adhere to Pareto optimality. Experimental evaluations on image generation and protein generation tasks demonstrate that our PROUD consistently maintains superior generation quality while approaching Pareto optimality across multiple property functions compared to various baselines.

cs.LG↗

arXiv2023

Sanitized Clustering against Confounding Bias

Real-world datasets inevitably contain biases that arise from different sources or conditions during data collection. Consequently, such inconsistency itself acts as a confounding factor that disturbs the cluster analysis. Existing methods eliminate the biases by projecting data onto the orthogonal complement of the subspace expanded by the confounding factor before clustering. Therein, the interested clustering factor and the confounding factor are coarsely considered in the raw feature space, where the correlation between the data and the confounding factor is ideally assumed to be linear for convenient solutions. These approaches are thus limited in scope as the data in real applications is usually complex and non-linearly correlated with the confounding factor. This paper presents a new clustering framework named Sanitized Clustering Against confounding Bias (SCAB), which removes the confounding factor in the semantic latent space of complex data through a non-linear dependence measure. To be specific, we eliminate the bias information in the latent space by minimizing the mutual information between the confounding factor and the latent representation delivered by Variational Auto-Encoder (VAE). Meanwhile, a clustering module is introduced to cluster over the purified latent representations. Extensive experiments on complex datasets demonstrate that our SCAB achieves a significant gain in clustering performance by removing the confounding bias. The code is available at \url{https://github.com/EvaFlower/SCAB}.

cs.LG↗

arXiv2023

Earning Extra Performance from Restrictive Feedbacks

Many machine learning applications encounter a situation where model providers are required to further refine the previously trained model so as to gratify the specific need of local users. This problem is reduced to the standard model tuning paradigm if the target data is permissibly fed to the model. However, it is rather difficult in a wide range of practical cases where target data is not shared with model providers but commonly some evaluations about the model are accessible. In this paper, we formally set up a challenge named \emph{Earning eXtra PerformancE from restriCTive feEDdbacks} (EXPECTED) to describe this form of model tuning problems. Concretely, EXPECTED admits a model provider to access the operational performance of the candidate model multiple times via feedback from a local user (or a group of users). The goal of the model provider is to eventually deliver a satisfactory model to the local user(s) by utilizing the feedbacks. Unlike existing model tuning methods where the target data is always ready for calculating model gradients, the model providers in EXPECTED only see some feedbacks which could be as simple as scalars, such as inference accuracy or usage rate. To enable tuning in this restrictive circumstance, we propose to characterize the geometry of the model performance with regard to model parameters through exploring the parameters' distribution. In particular, for the deep models whose parameters distribute across multiple layers, a more query-efficient algorithm is further tailor-designed that conducts layerwise tuning with more attention to those layers which pay off better. Extensive experiments on different applications demonstrate that our work forges a sound solution to the EXPECTED problem. Code is available via https://github.com/kylejingli/EXPECTED.

cs.LG↗

arXiv2022

Coarse-to-Fine Contrastive Learning on Graphs

Inspired by the impressive success of contrastive learning (CL), a variety of graph augmentation strategies have been employed to learn node representations in a self-supervised manner. Existing methods construct the contrastive samples by adding perturbations to the graph structure or node attributes. Although impressive results are achieved, it is rather blind to the wealth of prior information assumed: with the increase of the perturbation degree applied on the original graph, 1) the similarity between the original graph and the generated augmented graph gradually decreases; 2) the discrimination between all nodes within each augmented view gradually increases. In this paper, we argue that both such prior information can be incorporated (differently) into the contrastive learning paradigm following our general ranking framework. In particular, we first interpret CL as a special case of learning to rank (L2R), which inspires us to leverage the ranking order among positive augmented views. Meanwhile, we introduce a self-ranking paradigm to ensure that the discriminative information among different nodes can be maintained and also be less altered to the perturbations of different degrees. Experiment results on various benchmark datasets verify the effectiveness of our algorithm compared with the supervised and unsupervised models.

cs.LG↗

arXiv2021

Taming Overconfident Prediction on Unlabeled Data from Hindsight

Minimizing prediction uncertainty on unlabeled data is a key factor to achieve good performance in semi-supervised learning (SSL). The prediction uncertainty is typically expressed as the \emph{entropy} computed by the transformed probabilities in output space. Most existing works distill low-entropy prediction by either accepting the determining class (with the largest probability) as the true label or suppressing subtle predictions (with the smaller probabilities). Unarguably, these distillation strategies are usually heuristic and less informative for model training. From this discernment, this paper proposes a dual mechanism, named ADaptive Sharpening (\ADS), which first applies a soft-threshold to adaptively mask out determinate and negligible predictions, and then seamlessly sharpens the informed predictions, distilling certain predictions with the informed ones only. More importantly, we theoretically analyze the traits of \ADS by comparing with various distillation strategies. Numerous experiments verify that \ADS significantly improves the state-of-the-art SSL methods by making it a plug-in. Our proposed \ADS forges a cornerstone for future distillation-based SSL research.

cs.LG↗

arXiv2021

TRIP: Refining Image-to-Image Translation via Rival Preferences

Relative attribute (RA), referring to the preference over two images on the strength of a specific attribute, can enable fine-grained image-to-image translation due to its rich semantic information. Existing work based on RAs however failed to reconcile the goal for fine-grained translation and the goal for high-quality generation. We propose a new model TRIP to coordinate these two goals for high-quality fine-grained translation. In particular, we simultaneously train two modules: a generator that translates an input image to the desired image with smooth subtle changes with respect to the interested attributes; and a ranker that ranks rival preferences consisting of the input image and the desired image. Rival preferences refer to the adversarial ranking process: (1) the ranker thinks no difference between the desired image and the input image in terms of the desired attributes; (2) the generator fools the ranker to believe that the desired image changes the attributes over the input image as desired. RAs over pairs of real images are introduced to guide the ranker to rank image pairs regarding the interested attributes only. With an effective ranker, the generator would "win" the adversarial game by producing high-quality images that present desired changes over the attributes compared to the input image. The experiments on two face image datasets and one shoe image dataset demonstrate that our TRIP achieves state-of-art results in generating high-fidelity images which exhibit smooth changes over the interested attributes.

cs.LG↗

arXiv2021

Differential-Critic GAN: Generating What You Want by a Cue of Preferences

This paper proposes Differential-Critic Generative Adversarial Network (DiCGAN) to learn the distribution of user-desired data when only partial instead of the entire dataset possesses the desired property. DiCGAN generates desired data that meets the user's expectations and can assist in designing biological products with desired properties. Existing approaches select the desired samples first and train regular GANs on the selected samples to derive the user-desired data distribution. However, the selection of the desired data relies on global knowledge and supervision over the entire dataset. DiCGAN introduces a differential critic that learns from pairwise preferences, which are local knowledge and can be defined on a part of training data. The critic is built by defining an additional ranking loss over the Wasserstein GAN's critic. It endows the difference of critic values between each pair of samples with the user preference and guides the generation of the desired data instead of the whole data. For a more efficient solution to ensure data quality, we further reformulate DiCGAN as a constrained optimization problem, based on which we theoretically prove the convergence of our DiCGAN. Extensive experiments on a diverse set of datasets with various applications demonstrate that our DiCGAN achieves state-of-the-art performance in learning the user-desired data distributions, especially in the cases of insufficient desired data and limited supervision.

cs.LG↗

arXiv2020

Towards Equivalent Transformation of User Preferences in Cross Domain Recommendation

Cross domain recommendation (CDR) is one popular research topic in recommender systems. This paper focuses on a popular scenario for CDR where different domains share the same set of users but no overlapping items. The majority of recent methods have explored the shared-user representation to transfer knowledge across domains. However, the idea of shared-user representation resorts to learn the overlapped features of user preferences and suppresses the domain-specific features. Other works try to capture the domain-specific features by an MLP mapping but require heuristic human knowledge of choosing samples to train the mapping. In this paper, we attempt to learn both features of user preferences in a more principled way. We assume that each user's preferences in one domain can be expressed by the other one, and these preferences can be mutually converted to each other with the so-called equivalent transformation. Based on this assumption, we propose an equivalent transformation learner (ETL) which models the joint distribution of user behaviors across domains. The equivalent transformation in ETL relaxes the idea of shared-user representation and allows the learned preferences in different domains to preserve the domain-specific features as well as the overlapped features. Extensive experiments on three public benchmarks demonstrate the effectiveness of ETL compared with recent state-of-the-art methods. Codes and data are available online:~\url{https://github.com/xuChenSJTU/ETL-master}

cs.IR↗

arXiv2020

Learning Node Representations against Perturbations

Recent graph neural networks (GNN) has achieved remarkable performance in node representation learning. One key factor of GNN's success is the \emph{smoothness} property on node representations. Despite this, most GNN models are fragile to the perturbations on graph inputs and could learn unreliable node representations. In this paper, we study how to learn node representations against perturbations in GNN. Specifically, we consider that a node representation should remain stable under slight perturbations on the input, and node representations from different structures should be identifiable, which two are termed as the \emph{stability} and \emph{identifiability} on node representations, respectively. To this end, we propose a novel model called Stability-Identifiability GNN Against Perturbations (SIGNNAP) that learns reliable node representations in an unsupervised manner. SIGNNAP formalizes the \emph{stability} and \emph{identifiability} by a contrastive objective and preserves the \emph{smoothness} with existing GNN backbones. The proposed method is a generic framework that can be equipped with many other backbone models (e.g. GCN, GraphSage and GAT). Extensive experiments on six benchmarks under both transductive and inductive learning setups of node classification demonstrate the effectiveness of our method. Codes and data are available online:~\url{https://github.com/xuChenSJTU/SIGNNAP-master-online}

cs.LG↗