arXiv subjects

Dan Luo

Publications and source records attributed to Dan Luo.

At least 19 recordsLinked to original sources

arXiv2026

A Systematic Evaluation of Molecule Generation Models for De Novo Drug Design: From Benchmarks to Practical Insights

Molecule generation has emerged as a powerful computational tool for de novo drug design, enabling the exploration of chemical space beyond the limits of conventional virtual screening. The field has progressed rapidly, driven by advances in molecular representations, generative architectures, and target-aware modeling strategies. However, existing reviews typically address specific model families or application scenarios in isolation, rather than offering an integrated perspective on how these components collectively form a coherent generation workflow. In this review, we present a comprehensive evaluation of molecule generation models for de novo drug design, covering 82 methods across five deep generative frameworks, including recurrent neural network (RNN)- and Transformer-based models, variational autoencoders (VAEs), generative adversarial networks (GANs), flow-based models, and diffusion models. We first summarize widely used benchmarks and molecular representations, and then examine the methodological principles underlying both general and pocket-conditioned generation. A central contribution of this work is a systematic synthesis and comparative analysis of reported performance across commonly used benchmarks and evaluation metrics. We also summarize representative experimentally validated case studies. Looking ahead, we discuss future directions in standardized 3D data, interaction-aware generation, receptor flexibility, and multi-objective molecular design, with the aim of improving the reliability and experimental relevance of molecule generation. All collected benchmark resources, evaluation metrics, and model references are provided in a publicly accessible repository at https://github.com/JacklinGroup/molecule-generation-review.

cs.LG↗

arXiv2026

A Single-Loop Minorized Dual Decomposition Method for Nonsmooth Multi-Stage Stochastic Programming

In this paper, we study multi-stage stochastic programming (MSP) problems with nonsmooth composite objectives. Tailored to their intrinsic stage-wise and scenario-wise structure, we develop a single-loop minorized dual decomposition method, in which each iteration constructs a minorized problem and its restricted Wolfe dual, and then performs \textit{one iteration} of the symmetric Gauss--Seidel based inexact alternating direction method of multipliers on the resulting dual problem to generate the next iterate. A key feature of the proposed optimization framework is that the resulting updates preserve the stage-wise and scenario-wise decomposable structure of the MSP problem and are suitable for parallel implementation. We establish global convergence of the generated iterates for the three-stage case and further establish the corresponding global convergence theorem for the general multi-stage setting. Numerical experiments illustrate the computational viability of the proposed framework and its favorable scaling behavior with respect to the stage-wise and scenario-wise structure.

math.OC↗

arXiv2026

CryoProt: A Protein Pretraining Framework with Cross-Box Interactions on Cryo-EM Density Maps

Despite the growing availability of cryo-electron microscopy (cryo-EM) density maps, effectively leveraging them for protein representation remains challenging. First, current methods lack a general-purpose protein pretraining framework tailored for cryo-EM density maps, designed for protein-related property prediction. Second, existing approaches typically partition density maps into local box regions and model them independently, overlooking interactions across boxes which are essential for capturing global structural context in cryo-EM density map. To address these challenges, we propose CryoProt, a protein pretraining framework designed for cryo-EM density maps. CryoProt introduces a Map Encoder based on multi-head latent attention (MLA), where box-level representations interact through a shared latent space, enabling explicit modeling of cross-box dependencies within the density map. Furthermore, we adopt a multi-task pretraining strategy to learn generalizable representations that can be effectively transferred to diverse downstream tasks, such as protein flexibility prediction, where cryo-EM density maps are not required and can be inferred implicitly by the pretrained model. Experimental results demonstrate that CryoProt consistently outperforms existing state-of-the-art methods across multiple benchmarks, achieving up to 12% improvement over the best-performing baselines, highlighting the importance of modeling cross-box interactions in cryo-EM data. The source code is publicly available at https://anonymous.4open.science/r/CryoProt.

cs.LG↗

arXiv2026

A Triple-Modal Contrastive Learning Framework with Sequence, Graph, and 3D Features for Drug-Target Interaction Prediction

Accurate prediction of drug-target interactions (DTI) is critical for drug discovery. Existing methods often rely on single-modal representations (e.g., sequences or graphs) or combine only two modalities, overlooking 3D structural features. To address this challenge, we propose TriMod-DTI, a triple-modal contrastive learning framework that incorporates 1D sequences, 2D graphs, and 3D structures of drugs and proteins, obtaining the universal and complementary feature representations for DTI prediction. We design a Feature Extractor to capture drug and target features across the three modalities, thereby enriching their representations. We further propose a triple-modal contrastive learning strategy to align different modal representations of the same drug or protein in the latent space. By constructing cross-modal positive and negative sample pairs, this approach enhances the model's discriminative ability. Experiments on three benchmark datasets demonstrate that TriMod-DTI outperforms state-of-the-art methods. The ablation studies validate the contributions of each modality. Moreover, case studies highlight its practical potential for DTI prediction and drug discovery.

cs.LG↗

arXiv2026

Multimodal Insights into Credit Risk Modelling: Integrating Climate and Text Data for Default Prediction

Credit risk assessment increasingly relies on diverse sources of information beyond traditional structured financial data, particularly for micro and small enterprises (mSEs) with limited financial histories. This study proposes a multimodal framework that integrates structured credit variables, climate panel data, and unstructured textual narratives within a unified learning architecture. Specifically, we use long short-term memory (LSTM), the gated recurrent unit (GRU), and transformer models to analyse the interplay between these data modalities. The empirical results demonstrate that unimodal models based on climate or text data outperform those relying solely on structured data, while the integration of multiple data modalities yields significant improvements in credit default prediction. Using SHAP-based explainability methods, we find that physical climate risks play an important role in default prediction, with water-logging by rain emerging as the most influential factor. Overall, this study demonstrates the potential of multimodal approaches in AI-enabled decision-making, which provides robust tools for credit risk assessment while contributing to the broader integration of environmental and textual insights into predictive analytics.

q-fin.RM↗

arXiv2025

Adobe Summit Concierge Evaluation with Human in the Loop

Generative AI assistants offer significant potential to enhance productivity, streamline information access, and improve user experience in enterprise contexts. In this work, we present Summit Concierge, a domain-specific AI assistant developed for Adobe Summit. The assistant handles a wide range of event-related queries and operates under real-world constraints such as data sparsity, quality assurance, and rapid deployment. To address these challenges, we adopt a human-in-the-loop development workflow that combines prompt engineering, retrieval grounding, and lightweight human validation. We describe the system architecture, development process, and real-world deployment outcomes. Our experience shows that agile, feedback-driven development enables scalable and reliable AI assistants, even in cold-start scenarios.

cs.AI↗

arXiv2025

LFD: Layer Fused Decoding to Exploit External Knowledge in Retrieval-Augmented Generation

Retrieval-augmented generation (RAG) incorporates external knowledge into large language models (LLMs), improving their adaptability to downstream tasks and enabling information updates. Surprisingly, recent empirical evidence demonstrates that injecting noise into retrieved relevant documents paradoxically facilitates exploitation of external knowledge and improves generation quality. Although counterintuitive and challenging to apply in practice, this phenomenon enables granular control and rigorous analysis of how LLMs integrate external knowledge. Therefore, in this paper, we intervene on noise injection and establish a layer-specific functional demarcation within the LLM: shallow layers specialize in local context modeling, intermediate layers focus on integrating long-range external factual knowledge, and deeper layers primarily rely on parametric internal knowledge. Building on this insight, we propose Layer Fused Decoding (LFD), a simple decoding strategy that directly combines representations from an intermediate layer with final-layer decoding outputs to fully exploit the external factual knowledge. To identify the optimal intermediate layer, we introduce an internal knowledge score (IKS) criterion that selects the layer with the lowest IKS value in the latter half of layers. Experimental results across multiple benchmarks demonstrate that LFD helps RAG systems more effectively surface retrieved context knowledge with minimal cost.

cs.CL↗

arXiv2025

DAFMSVC: One-Shot Singing Voice Conversion with Dual Attention Mechanism and Flow Matching

Singing Voice Conversion (SVC) transfers a source singer's timbre to a target while keeping melody and lyrics. The key challenge in any-to-any SVC is adapting unseen speaker timbres to source audio without quality degradation. Existing methods either face timbre leakage or fail to achieve satisfactory timbre similarity and quality in the generated audio. To address these challenges, we propose DAFMSVC, where the self-supervised learning (SSL) features from the source audio are replaced with the most similar SSL features from the target audio to prevent timbre leakage. It also incorporates a dual cross-attention mechanism for the adaptive fusion of speaker embeddings, melody, and linguistic content. Additionally, we introduce a flow matching module for high quality audio generation from the fused features. Experimental results show that DAFMSVC significantly enhances timbre similarity and naturalness, outperforming state-of-the-art methods in both subjective and objective evaluations.

cs.SD↗

arXiv2025

NTIRE 2025 XGC Quality Assessment Challenge: Methods and Results

This paper reports on the NTIRE 2025 XGC Quality Assessment Challenge, which will be held in conjunction with the New Trends in Image Restoration and Enhancement Workshop (NTIRE) at CVPR 2025. This challenge is to address a major challenge in the field of video and talking head processing. The challenge is divided into three tracks, including user generated video, AI generated video and talking head. The user-generated video track uses the FineVD-GC, which contains 6,284 user generated videos. The user-generated video track has a total of 125 registered participants. A total of 242 submissions are received in the development phase, and 136 submissions are received in the test phase. Finally, 5 participating teams submitted their models and fact sheets. The AI generated video track uses the Q-Eval-Video, which contains 34,029 AI-Generated Videos (AIGVs) generated by 11 popular Text-to-Video (T2V) models. A total of 133 participants have registered in this track. A total of 396 submissions are received in the development phase, and 226 submissions are received in the test phase. Finally, 6 participating teams submitted their models and fact sheets. The talking head track uses the THQA-NTIRE, which contains 12,247 2D and 3D talking heads. A total of 89 participants have registered in this track. A total of 225 submissions are received in the development phase, and 118 submissions are received in the test phase. Finally, 8 participating teams submitted their models and fact sheets. Each participating team in every track has proposed a method that outperforms the baseline, which has contributed to the development of fields in three tracks.

cs.CV↗

arXiv2025

From Aggregation to Selection: User-Validated Distributed Social Recommendation

Social recommender systems facilitate social connections by identifying potential friends for users. Each user maintains a local social network centered around themselves, resulting in a naturally distributed social structure. Recent research on distributed modeling for social recommender systems has gained increasing attention, as it naturally aligns with the user-centric structure of user interactions. Current distributed social recommender systems rely on automatically combining predictions from multiple models, often overlooking the user's active role in validating whether suggested connections are appropriate. Moreover, recommendation decisions are validated by individual users rather than derived from a single global ordering of candidates. As a result, standard ranking-based evaluation metrics make it difficult to evaluate whether a user-confirmed recommendation decision is actually correct. To address these limitations, we propose DeSocial, a distributed social recommendation framework with user-validation. DeSocial enables users to select recommendation algorithms to validate their potential connections, and the verification is processed through majority consensus among multiple independent user validators. To evaluate the distributed recommender system with user validator, we formulate this setting as a link prediction and verification task and introduce Acc@K, a consensus-based evaluation metric that measures whether user-approved recommendations are correct. Experiments on 4 real-world social networks shows that DeSocial improves decision correctness and robustness compared to single-point and distributed baselines. These findings highlight the potential of user-validated distributed recommender systems as a practical approach to social recommendation, with broader applicability to distributed and decentralized recommendations. Code: https://github.com/agiresearch/DeSocial.

cs.SI↗

arXiv2025

Flow Matching based Sequential Recommender Model

Generative models, particularly diffusion model, have emerged as powerful tools for sequential recommendation. However, accurately modeling user preferences remains challenging due to the noise perturbations inherent in the forward and reverse processes of diffusion-based methods. Towards this end, this study introduces FMRec, a Flow Matching based model that employs a straight flow trajectory and a modified loss tailored for the recommendation task. Additionally, from the diffusion-model perspective, we integrate a reconstruction loss to improve robustness against noise perturbations, thereby retaining user preferences during the forward process. In the reverse process, we employ a deterministic reverse sampler, specifically an ODE-based updating function, to eliminate unnecessary randomness, thereby ensuring that the generated recommendations closely align with user needs. Extensive evaluations on four benchmark datasets reveal that FMRec achieves an average improvement of 6.53% over state-of-the-art methods. The replication code is available at https://github.com/FengLiu-1/FMRec.

cs.IR↗

arXiv2025

DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representation

Predicting drug-target binding affinity (DTA) is essential for identifying potential therapeutic candidates in drug discovery. However, most existing models rely heavily on static protein structures, often overlooking the dynamic nature of proteins, which is crucial for capturing conformational flexibility that will be beneficial for protein binding interactions. We introduce DynamicDTA, an innovative deep learning framework that incorporates static and dynamic protein features to enhance DTA prediction. The proposed DynamicDTA takes three types of inputs, including drug sequence, protein sequence, and dynamic descriptors. A molecular graph representation of the drug sequence is generated and subsequently processed through graph convolutional network, while the protein sequence is encoded using dilated convolutions. Dynamic descriptors, such as root mean square fluctuation, are processed through a multi-layer perceptron. These embedding features are fused with static protein features using cross-attention, and a tensor fusion network integrates all three modalities for DTA prediction. Extensive experiments on three datasets demonstrate that DynamicDTA achieves by at least 3.4% improvement in RMSE score with comparison to seven state-of-the-art baseline methods. Additionally, predicting novel drugs for Human Immunodeficiency Virus Type 1 and visualizing the docking complexes further demonstrates the reliability and biological relevance of DynamicDTA.

cs.RO↗

arXiv2025

AutoStyle-TTS: Retrieval-Augmented Generation based Automatic Style Matching Text-to-Speech Synthesis

With the advancement of speech synthesis technology, users have higher expectations for the naturalness and expressiveness of synthesized speech. But previous research ignores the importance of prompt selection. This study proposes a text-to-speech (TTS) framework based on Retrieval-Augmented Generation (RAG) technology, which can dynamically adjust the speech style according to the text content to achieve more natural and vivid communication effects. We have constructed a speech style knowledge database containing high-quality speech samples in various contexts and developed a style matching scheme. This scheme uses embeddings, extracted by Llama, PER-LLM-Embedder,and Moka, to match with samples in the knowledge database, selecting the most appropriate speech style for synthesis. Furthermore, our empirical research validates the effectiveness of the proposed method. Our demo can be viewed at: https://thuhcsi.github.io/icme2025-AutoStyle-TTS

cs.SD↗

arXiv2025

UniSep: Universal Target Audio Separation with Language Models at Scale

We propose Universal target audio Separation (UniSep), addressing the separation task on arbitrary mixtures of different types of audio. Distinguished from previous studies, UniSep is performed on unlimited source domains and unlimited source numbers. We formulate the separation task as a sequence-to-sequence problem, and a large language model (LLM) is used to model the audio sequence in the discrete latent space, leveraging the power of LLM in handling complex mixture audios with large-scale data. Moreover, a novel pre-training strategy is proposed to utilize audio-only data, which reduces the efforts of large-scale data simulation and enhances the ability of LLMs to understand the consistency and correlation of information within audio sequences. We also demonstrate the effectiveness of scaling datasets in an audio separation task: we use large-scale data (36.5k hours), including speech, music, and sound, to train a universal target audio separation model that is not limited to a specific domain. Experiments show that UniSep achieves competitive subjective and objective evaluation results compared with single-task models.

cs.SD↗

arXiv2025

From Documents to Dialogue: Building KG-RAG Enhanced AI Assistants

The Adobe Experience Platform AI Assistant is a conversational tool that enables organizations to interact seamlessly with proprietary enterprise data through a chatbot. However, due to access restrictions, Large Language Models (LLMs) cannot retrieve these internal documents, limiting their ability to generate accurate zero-shot responses. To overcome this limitation, we use a Retrieval-Augmented Generation (RAG) framework powered by a Knowledge Graph (KG) to retrieve relevant information from external knowledge sources, enabling LLMs to answer questions over private or previously unseen document collections. In this paper, we propose a novel approach for building a high-quality, low-noise KG. We apply several techniques, including incremental entity resolution using seed concepts, similarity-based filtering to deduplicate entries, assigning confidence scores to entity-relation pairs to filter for high-confidence pairs, and linking facts to source documents for provenance. Our KG-RAG system retrieves relevant tuples, which are added to the user prompts context before being sent to the LLM generating the response. Our evaluation demonstrates that this approach significantly enhances response relevance, reducing irrelevant answers by over 50% and increasing fully relevant answers by 88% compared to the existing production system.

cs.IR↗

arXiv2025

Federated Retrieval Augmented Generation for Multi-Product Question Answering

Recent advancements in Large Language Models and Retrieval-Augmented Generation have boosted interest in domain-specific question-answering for enterprise products. However, AI Assistants often face challenges in multi-product QA settings, requiring accurate responses across diverse domains. Existing multi-domain RAG-QA approaches either query all domains indiscriminately, increasing computational costs and LLM hallucinations, or rely on rigid resource selection, which can limit search results. We introduce MKP-QA, a novel multi-product knowledge-augmented QA framework with probabilistic federated search across domains and relevant knowledge. This method enhances multi-domain search quality by aggregating query-domain and query-passage probabilistic relevance. To address the lack of suitable benchmarks for multi-product QAs, we also present new datasets focused on three Adobe products: Adobe Experience Platform, Target, and Customer Journey Analytics. Our experiments show that MKP-QA significantly boosts multi-product RAG-QA performance in terms of both retrieval accuracy and response quality.

cs.CL↗

arXiv2025

Generating Negative Samples for Multi-Modal Recommendation

Multi-modal recommender systems (MMRS) have gained significant attention due to their ability to leverage information from various modalities to enhance recommendation quality. However, existing negative sampling techniques often struggle to effectively utilize the multi-modal data, leading to suboptimal performance. In this paper, we identify two key challenges in negative sampling for MMRS: (1) producing cohesive negative samples contrasting with positive samples and (2) maintaining a balanced influence across different modalities. To address these challenges, we propose NegGen, a novel framework that utilizes multi-modal large language models (MLLMs) to generate balanced and contrastive negative samples. We design three different prompt templates to enable NegGen to analyze and manipulate item attributes across multiple modalities, and then generate negative samples that introduce better supervision signals and ensure modality balance. Furthermore, NegGen employs a causal learning module to disentangle the effect of intervened key features and irrelevant item attributes, enabling fine-grained learning of user preferences. Extensive experiments on real-world datasets demonstrate the superior performance of NegGen compared to state-of-the-art methods in both negative sampling and multi-modal recommendation.

cs.IR↗

arXiv2024

How Does Topology Bias Distort Message Passing? A Dirichlet Energy Perspective

Graph-based recommender systems have achieved remarkable effectiveness by modeling high-order interactions between users and items. However, such approaches are significantly undermined by popularity bias, which distorts the interaction graph's structure, referred to as topology bias. This leads to overrepresentation of popular items, thereby reinforcing biases and fairness issues through the user-system feedback loop. Despite attempts to study this effect, most prior work focuses on the embedding or gradient level bias, overlooking how topology bias fundamentally distorts the message passing process itself. We bridge this gap by providing an empirical and theoretical analysis from a Dirichlet energy perspective, revealing that graph message passing inherently amplifies topology bias and consistently benefits highly connected nodes. To address these limitations, we propose Test-time Simplicial Propagation (TSP), which extends message passing to higher-order simplicial complexes. By incorporating richer structures beyond pairwise connections, TSP mitigates harmful topology bias and substantially improves the representation and recommendation of long-tail items during inference. Extensive experiments across five real-world datasets demonstrate the superiority of our approach in mitigating topology bias and enhancing recommendation quality.

cs.IR↗