arXiv subjects

Bo Pan

Publications and source records attributed to Bo Pan.

At least 19 recordsLinked to original sources

arXiv2026

MolWorld: Molecule World Models for Actionable Molecular Optimization

Molecular optimization in drug discovery aims to discover molecules with improved target properties, but practical lead optimization often requires more than high predicted scores. A useful candidate should also be actionable: it should be reachable from known molecules through valid local structural transformations, so that it can be interpreted as a plausible revision within an evolving chemical series. Existing de novo and single-molecule optimization methods do not explicitly model such reachability, especially when both the target molecules and the intermediate molecules connecting them to known compounds are unknown. In this work, we formulate actionable molecular optimization as sequential expansion of a molecule-transfer graph, where nodes are molecules and edges encode valid local transformations. We propose MolWorld, a molecule world model-guided framework that treats the current molecule-transfer graph as an evolving search state. At each iteration, MolWorld selects local anchor contexts, generates candidate molecules conditioned on these contexts, evaluates their properties, and uses a learned world model to update the evolving molecule world by retaining admissible candidates and inserting them into the molecule-transfer graph. The expanded molecule world then guides subsequent optimization. Experiments on property optimization and docking-based tasks show that MolWorld discovers high-property molecules while maintaining substantially stronger structural connectivity, supporting actionable and sequential molecular design.

cs.LG↗

arXiv2026

LiteResearcher: A Scalable Agentic RL Training Framework for Deep Research Agent

Reinforcement Learning (RL) has emerged as a powerful training paradigm for LLM-based agents. However, scaling agentic RL for deep research remains constrained by two coupled challenges: hand-crafted synthetic data fails to elicit genuine real-world search capabilities, and real-world search dependency during RL training introduces instability and prohibitive cost, which limits the scalability of Agentic RL. LiteResearcher is a training framework that makes Agentic RL scalable: by constructing a lite virtual world that mirrors real-world search dynamics, we enable a continuously improving training recipe that empowers a tiny search agent to outperform large-scale open-source and commercial models (e.g., Tongyi DeepResearch and Claude-4.5 Sonnet). Specifically, on common benchmarks such as GAIA and Xbench, our LiteResearcher-4B achieves open-source state-of-the-art results of 71.3% and 78.0% respectively, demonstrating that scalable RL training is a key enabler for Deep Research Agents.

cs.AI↗

arXiv2026

InterDeepResearch: Enabling Human-Agent Collaborative Information Seeking through Interactive Deep Research

Deep research systems powered by LLM agents have transformed complex information seeking by automating the iterative retrieval, filtering, and synthesis of insights from massive-scale web sources. However, existing systems predominantly follow an autonomous "query-to-report" paradigm, limiting users to a passive role and failing to integrate their personal insights, contextual knowledge, and evolving research intents. This paper addresses the lack of human-in-the-loop collaboration in the agentic research process. Through a formative study, we identify that current systems hinder effective human-agent collaboration in terms of process observability, real-time steerability, and context navigation efficiency. Informed by these findings, we propose InterDeepResearch, an interactive deep research system backed by a dedicated research context management framework. The framework organizes research context into a hierarchical architecture with three levels (information, actions, and sessions), enabling dynamic context reduction to prevent LLM context exhaustion and cross-action backtracing for evidence provenance. Built upon this framework, the system interface integrates three coordinated views for visual sensemaking, and dedicated interaction mechanisms for interactive research context navigation. Evaluation on the Xbench-DeepSearch-v1 and Seal-0 benchmarks shows that InterDeepResearch achieves competitive performance compared to state-of-the-art deep research systems, while a formal user study demonstrates its effectiveness in supporting human-agent collaborative information seeking. Project page with system demo: https://github.com/bopan3/InterDeepResearch.

cs.IR↗

arXiv2026

Multi-Task Reinforcement Learning for Enhanced Multimodal LLM-as-a-Judge

Multimodal Large Language Models (MLLMs) have been widely adopted as MLLM-as-a-Judges due to their strong alignment with human judgment across various visual tasks. However, most existing judge models are optimized for single-task scenarios and struggle to generalize to diverse contexts, which is a critical requirement for reliable evaluation. To address this limitation, we propose Multi-Task Reinforcement Learning for MLLM-as-a-Judge (MT-RL-Judge), a framework that jointly optimizes the judge model across multiple tasks, leveraging the generalization capabilities of RL. Experimental results against several strong baselines demonstrate that MT-RL-Judge outperforms strong baselines in both judgment consistency and correlation with human preferences. Furthermore, our approach exhibits robust generalization on out-of-distribution tasks, further validating its effectiveness.

cs.CL↗

arXiv2026

Retrieval-Augmented Foundation Models for Matched Molecular Pair Transformations to Recapitulate Medicinal Chemistry Intuition

Matched molecular pairs (MMPs) capture the local chemical edits that medicinal chemists routinely use to design analogs, but existing ML approaches either operate at the whole-molecule level with limited edit controllability or learn MMP-style edits from restricted settings and small models. We propose a variable-to-variable formulation of analog generation and train a foundation model on large-scale MMP transformations (MMPTs) to generate diverse variables conditioned on an input variable. To enable practical control, we develop prompting mechanisms that let the users specify preferred transformation patterns during generation. We further introduce MMPT-RAG, a retrieval-augmented framework that uses external reference analogs as contextual guidance to steer generation and generalize from project-specific series. Experiments on general chemical corpora and patent-specific datasets demonstrate improved diversity, novelty, and controllability, and show that our method recovers realistic analog structures in practical discovery scenarios.

cs.LG↗

arXiv2026

Bi-Level Prompt Optimization for Multimodal LLM-as-a-Judge

Large language models (LLMs) have become widely adopted as automated judges for evaluating AI-generated content. Despite their success, aligning LLM-based evaluations with human judgments remains challenging. While supervised fine-tuning on human-labeled data can improve alignment, it is costly and inflexible, requiring new training for each task or dataset. Recent progress in auto prompt optimization (APO) offers a more efficient alternative by automatically improving the instructions that guide LLM judges. However, existing APO methods primarily target text-only evaluations and remain underexplored in multimodal settings. In this work, we study auto prompt optimization for multimodal LLM-as-a-judge, particularly for evaluating AI-generated images. We identify a key bottleneck: multimodal models can only process a limited number of visual examples due to context window constraints, which hinders effective trial-and-error prompt refinement. To overcome this, we propose BLPO, a bi-level prompt optimization framework that converts images into textual representations while preserving evaluation-relevant visual cues. Our bi-level optimization approach jointly refines the judge prompt and the I2T prompt to maintain fidelity under limited context budgets. Experiments on four datasets and three LLM judges demonstrate the effectiveness of our method.

cs.AI↗

arXiv2026

Transformer-Based Approach for Automated Functional Group Replacement in Chemical Compounds

Functional group replacement is a pivotal approach in cheminformatics to enable the design of novel chemical compounds with tailored properties. Traditional methods for functional group removal and replacement often rely on rule-based heuristics, which can be limited in their ability to generate diverse and novel chemical structures. Recently, transformer-based models have shown promise in improving the accuracy and efficiency of molecular transformations, but existing approaches typically focus on single-step modeling, lacking the guarantee of structural similarity. In this work, we seek to advance the state of the art by developing a novel two-stage transformer model for functional group removal and replacement. Unlike one-shot approaches that generate entire molecules in a single pass, our method generates the functional group to be removed and appended sequentially, ensuring strict substructure-level modifications. Using a matched molecular pairs (MMPs) dataset derived from ChEMBL, we trained an encoder-decoder transformer model with SMIRKS-based representations to capture transformation rules effectively. Extensive evaluations demonstrate our method's ability to generate chemically valid transformations, explore diverse chemical spaces, and maintain scalability across varying search sizes.

cs.LG↗

arXiv2026

IGenBench: Benchmarking the Reliability of Text-to-Infographic Generation

Infographics are composite visual artifacts that combine data visualizations with textual and illustrative elements to communicate information. While recent text-to-image (T2I) models can generate aesthetically appealing images, their reliability in generating infographics remains unclear. Generated infographics may appear correct at first glance but contain easily overlooked issues, such as distorted data encoding or incorrect textual content. We present IGENBENCH, the first benchmark for evaluating the reliability of text-to-infographic generation, comprising 600 curated test cases spanning 30 infographic types. We design an automated evaluation framework that decomposes reliability verification into atomic yes/no questions based on a taxonomy of 10 question types. We employ multimodal large language models (MLLMs) to verify each question, yielding question-level accuracy (Q-ACC) and infographic-level accuracy (I-ACC). We comprehensively evaluate 10 state-of-the-art T2I models on IGENBENCH. Our systematic analysis reveals key insights for future model development: (i) a three-tier performance hierarchy with the top model achieving Q-ACC of 0.90 but I-ACC of only 0.49; (ii) data-related dimensions emerging as universal bottlenecks (e.g., Data Completeness: 0.21); and (iii) the challenge of achieving end-to-end correctness across all models. We release IGENBENCH at https://igen-bench.vercel.app/.

cs.LG↗

arXiv2026

RelayGR: Scaling Long-Sequence Generative Recommendation via Cross-Stage Relay-Race Inference

Real-time recommender systems execute multi-stage cascades (retrieval, pre-processing, fine-grained ranking) under strict tail-latency SLOs, leaving only tens of milliseconds for ranking. Generative recommendation (GR) models can improve quality by consuming long user-behavior sequences, but in production their online sequence length is tightly capped by the ranking-stage P99 budget. We observe that the majority of GR tokens encode user behaviors that are independent of the item candidates, suggesting an opportunity to pre-infer a user-behavior prefix once and reuse it during ranking rather than recomputing it on the critical path. Realizing this idea at industrial scale is non-trivial: the prefix cache must survive across multiple pipeline stages before the final ranking instance is determined, the user population implies cache footprints far beyond a single device, and indiscriminate pre-inference would overload shared resources under high QPS. We present RelayGR, a production system that enables in-HBM relay-race inference for GR. RelayGR selectively pre-infers long-term user prefixes, keeps their KV caches resident in HBM over the request lifecycle, and ensures the subsequent ranking can consume them without remote fetches. RelayGR combines three techniques: 1) a sequence-aware trigger that admits only at-risk requests under a bounded cache footprint and pre-inference load, 2) an affinity-aware router that co-locates cache production and consumption by routing both the auxiliary pre-infer signal and the ranking request to the same instance, and 3) a memory-aware expander that uses server-local DRAM to capture short-term cross-request reuse while avoiding redundant reloads. We implement RelayGR on Huawei Ascend NPUs and evaluate it with real queries. Under a fixed P99 SLO, RelayGR supports up to 1.5$\times$ longer sequences and improves SLO-compliant throughput by up to 3.6$\times$.

cs.DC↗

arXiv2025

Toward Optimal Statistical Inference in Noisy Linear Quadratic Reinforcement Learning over a Finite Horizon

Recent developments in Reinforcement learning have significantly enhanced sequential decision-making in uncertain environments. Despite their strong performance guarantees, most existing work has focused primarily on improving the operational accuracy of learned control policies and the convergence rates of learning algorithms, with comparatively little attention to uncertainty quantification and statistical inference. Yet, these aspects are essential for assessing the reliability and variability of control policies, especially in high-stakes applications. In this paper, we study statistical inference for the policy gradient (PG) method for noisy Linear Quadratic Reinforcement learning (LQ RL) over a finite time horizon, where linear dynamics with both known and unknown drift parameters are controlled subject to a quadratic cost. We establish the theoretical foundations for statistical inference in LQ RL, deriving exact asymptotics for both the PG estimators and the corresponding objective loss. Furthermore, we introduce a principled inference framework that leverages online bootstrapping to construct confidence intervals for both the learned optimal policy and the corresponding objective losses. The method updates the PG estimates along with a set of randomly perturbed PG estimates as new observations arrive. We prove that the proposed bootstrapping procedure is distributionally consistent and that the resulting confidence intervals achieve both asymptotic and non-asymptotic validity. Notably, our results imply that the quantiles of the exact distribution can be approximated at a rate of $n^{-1/4}$, where $n$ is the number of samples used during the procedure. The proposed procedure is easy to implement and applicable to both offline and fully online settings. Numerical experiments illustrate the effectiveness of our approach across a range of noisy linear dynamical systems.

math.ST↗

arXiv2025

IntuiTF: MLLM-Guided Transfer Function Optimization for Direct Volume Rendering

Direct volume rendering (DVR) is a fundamental technique for visualizing volumetric data, where transfer functions (TFs) play a crucial role in extracting meaningful structures. However, designing effective TFs remains unintuitive due to the semantic gap between user intent and TF parameter space. Although numerous TF optimization methods have been proposed to mitigate this issue, existing approaches still face two major challenges: the vast exploration space and limited generalizability. To address these issues, we propose IntuiTF, a novel framework that leverages Multimodal Large Language Models (MLLMs) to guide TF optimization in alignment with user intent. Specifically, our method consists of two key components: (1) an evolution-driven explorer for effective exploration of the TF space, and (2) an MLLM-guided human-aligned evaluator that provides generalizable visual feedback on rendering quality. The explorer and the evaluator together establish an efficient Trial-Insight-Replanning paradigm for TF space exploration. We further extend our framework with an interactive TF design system. We demonstrate the broad applicability of our framework through three case studies and validate the effectiveness of each component through extensive experiments. We strongly recommend readers check our cases, demo video, and source code at: https://github.com/wyysteelhead/IntuiTF

cs.GR↗

arXiv2025

DreamJourney: Perpetual View Generation with Video Diffusion Models

Perpetual view generation aims to synthesize a long-term video corresponding to an arbitrary camera trajectory solely from a single input image. Recent methods commonly utilize a pre-trained text-to-image diffusion model to synthesize new content of previously unseen regions along camera movement. However, the underlying 2D diffusion model lacks 3D awareness and results in distorted artifacts. Moreover, they are limited to generating views of static 3D scenes, neglecting to capture object movements within the dynamic 4D world. To alleviate these issues, we present DreamJourney, a two-stage framework that leverages the world simulation capacity of video diffusion models to trigger a new perpetual scene view generation task with both camera movements and object dynamics. Specifically, in stage I, DreamJourney first lifts the input image to 3D point cloud and renders a sequence of partial images from a specific camera trajectory. A video diffusion model is then utilized as generative prior to complete the missing regions and enhance visual coherence across the sequence, producing a cross-view consistent video adheres to the 3D scene and camera trajectory. Meanwhile, we introduce two simple yet effective strategies (early stopping and view padding) to further stabilize the generation process and improve visual quality. Next, in stage II, DreamJourney leverages a multimodal large language model to produce a text prompt describing object movements in current view, and uses video diffusion model to animate current view with object movements. Stage I and II are repeated recurrently, enabling perpetual dynamic scene view generation. Extensive experiments demonstrate the superiority of our DreamJourney over state-of-the-art methods both quantitatively and qualitatively. Our project page: https://dream-journey.vercel.app.

cs.CV↗

arXiv2025

VIS-Shepherd: Constructing Critic for LLM-based Data Visualization Generation

Data visualization generation using Large Language Models (LLMs) has shown promising results but often produces suboptimal visualizations that require human intervention for improvement. In this work, we introduce VIS-Shepherd, a specialized Multimodal Large Language Model (MLLM)-based critic to evaluate and provide feedback for LLM-generated data visualizations. At the core of our approach is a framework to construct a high-quality visualization critique dataset, where we collect human-created visualization instances, synthesize corresponding LLM-generated instances, and construct high-quality critiques. We conduct both model-based automatic evaluation and human preference studies to evaluate the effectiveness of our approach. Our experiments show that even small (7B parameters) open-source MLLM models achieve substantial performance gains by leveraging our high-quality visualization critique dataset, reaching levels comparable to much larger open-source or even proprietary models. Our work demonstrates significant potential for MLLM-based automated visualization critique and indicates promising directions for enhancing LLM-based data visualization generation. Our project page: https://github.com/bopan3/VIS-Shepherd.

cs.CV↗

arXiv2025

XGraphRAG: Interactive Visual Analysis for Graph-based Retrieval-Augmented Generation

Graph-based Retrieval-Augmented Generation (RAG) has shown great capability in enhancing Large Language Model (LLM)'s answer with an external knowledge base. Compared to traditional RAG, it introduces a graph as an intermediate representation to capture better structured relational knowledge in the corpus, elevating the precision and comprehensiveness of generation results. However, developers usually face challenges in analyzing the effectiveness of GraphRAG on their dataset due to GraphRAG's complex information processing pipeline and the overwhelming amount of LLM invocations involved during graph construction and query, which limits GraphRAG interpretability and accessibility. This research proposes a visual analysis framework that helps RAG developers identify critical recalls of GraphRAG and trace these recalls through the GraphRAG pipeline. Based on this framework, we develop XGraphRAG, a prototype system incorporating a set of interactive visualizations to facilitate users' analysis process, boosting failure cases collection and improvement opportunities identification. Our evaluation demonstrates the effectiveness and usability of our approach. Our work is open-sourced and available at https://github.com/Gk0Wk/XGraphRAG.

cs.IR↗

arXiv2025

Multimodal DeepResearcher: Generating Text-Chart Interleaved Reports From Scratch with Agentic Framework

Visualizations play a crucial part in effective communication of concepts and information. Recent advances in reasoning and retrieval augmented generation have enabled Large Language Models (LLMs) to perform deep research and generate comprehensive reports. Despite its progress, existing deep research frameworks primarily focus on generating text-only content, leaving the automated generation of interleaved texts and visualizations underexplored. This novel task poses key challenges in designing informative visualizations and effectively integrating them with text reports. To address these challenges, we propose Formal Description of Visualization (FDV), a structured textual representation of charts that enables LLMs to learn from and generate diverse, high-quality visualizations. Building on this representation, we introduce Multimodal DeepResearcher, an agentic framework that decomposes the task into four stages: (1) researching, (2) exemplar report textualization, (3) planning, and (4) multimodal report generation. For the evaluation of generated multimodal reports, we develop MultimodalReportBench, which contains 100 diverse topics served as inputs along with 5 dedicated metrics. Extensive experiments across models and evaluation methods demonstrate the effectiveness of Multimodal DeepResearcher. Notably, utilizing the same Claude 3.7 Sonnet model, Multimodal DeepResearcher achieves an 82% overall win rate over the baseline method.

cs.CL↗

arXiv2025

Scorpio: Serving Right Requests at the Right Time for Heterogeneous SLOs in LLM Inference

Large Language Model (LLM) serving increasingly underpins online Web services such as conversational agents, Web search, and programming assistants, where requests carry heterogeneous Service Level Objectives (SLOs) such as Time to First Token (TTFT) and Time Per Output Token (TPOT). Existing LLM serving systems prioritize maximum throughput and treat all requests uniformly, which leads to suboptimal SLO attainment. This paper introduces Scorpio, an SLO-oriented LLM serving system designed to maximize system goodput and SLO attainment for workloads with heterogeneous SLOs. Our core insight is to exploit SLO heterogeneity for adaptive scheduling across admission control, queue management, and batch selection. Scorpio features a TTFT Guard, which employs least-deadline-first reordering and rejects unattainable requests, and a TPOT Guard, which utilizes a VBS-based admission control and a novel credit-based batching mechanism. Both guards are supported by a predictive module. Evaluations demonstrate that Scorpio improves system goodput by up to 14.4x and SLO adherence by up to 46.5% under high load compared to state-of-the-art baselines.

cs.LG↗

arXiv2025

Can Past Experience Accelerate LLM Reasoning?

Allocating more compute to large language models (LLMs) reasoning has generally been demonstrated to improve their effectiveness, but also results in increased inference time. In contrast, humans can perform tasks faster and better with increased experience and exposure. Hence, this paper aims to investigate the question: Can LLMs also become faster at reasoning through recurrent exposure on relevant tasks, and if so, how can it be achieved? To address these questions, we first formalize the problem setting of LLM reasoning speedup systematically in the dimensions of task relevancy and compute budget calculation. We then propose SpeedupLLM, a theoretically guaranteed framework to implement and benchmark such reasoning speedup behaviour based on adaptive compute allocation and memory mechanisms. We further conduct comprehensive experiments to benchmark such behaviour across different question similarity levels, memory methods, and reasoning methods. Results show that LLMs can generally reason faster with past experience, achieving up to a 56% reduction in compute cost when equipped with appropriate memory and reasoning methods.

cs.LG↗

arXiv2025

Exploring Multimodal Prompt for Visualization Authoring with Large Language Models

Recent advances in large language models (LLMs) have shown great potential in automating the process of visualization authoring through simple natural language utterances. However, instructing LLMs using natural language is limited in precision and expressiveness for conveying visualization intent, leading to misinterpretation and time-consuming iterations. To address these limitations, we conduct an empirical study to understand how LLMs interpret ambiguous or incomplete text prompts in the context of visualization authoring, and the conditions making LLMs misinterpret user intent. Informed by the findings, we introduce visual prompts as a complementary input modality to text prompts, which help clarify user intent and improve LLMs' interpretation abilities. To explore the potential of multimodal prompting in visualization authoring, we design VisPilot, which enables users to easily create visualizations using multimodal prompts, including text, sketches, and direct manipulations on existing visualizations. We evaluate VisPilot through a controlled user study and an expert evaluation. The results suggest that multimodal prompts facilitate users in communicating spatial constraints, local references, and design preferences while maintaining comparable task efficiency to text-only prompting. We further discuss when text, visual, and hybrid prompts are beneficial for visualization authoring, and summarize design implications for future human-AI authoring systems. All materials are available at https://osf.io/2qrak.

cs.HC↗