FWFang Wu

Fang Wu

*This is an algorithmically generated author record based on publicly available information.

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Fang Wu has a total of 146 co-authors. Here are the top co-authors by number of shared publications:


Latest Publications

  • Open Access

    AI for Productivity in the Age of Agentic AI

    by Zhiheng Xi, Enyu Zhou, Xinyu Fang, Zhe Sun, Baodai Huang, Jiajun Sun, Bicheng Deng, Zhihao Zhang, Wenxiang Chen, Jiazheng Zhang, et al.

    Throughout history, transformative technologies have repeatedly reshaped production systems and economic activity. In the current wave of AI development, Agentic AI systems are emerging as a new class of productive instruments capable of goal perception, multi-step planning, environmental interaction, and autonomous workflow coordination. Beyond automating routine tasks, these systems have the potential to augment knowledge work, reorganize decision-making, and reshape the relationship between human labor, organizational routines, and machine intelligence. This development gives rise to the emerging research direction of AI for Productivity (AI4Productivity), which examines how advanced AI systems affect productivity across economic and social contexts. In this paper, we conducts an in-depth investigation for explaining how Agentic AI creates productivity. We define AI4Productivity as the use of Agentic AI in real-world workflows to deliver economically valuable work with less human effort, and identify two core mechanisms of productivity gains: Efficiency, which reduces the time and labor required for existing tasks, and Expansion, which makes previously infeasible work economically viable. We further characterize the evolution of AI systems through four stages: conversational assistant, reactive operator, adaptive coordinator, and self-governing production system. Building on this framework, we review representative AI productivity tools and examine the sectoral diffusion of Agentic AI across three levels of adoption: early-stage exploration in manufacturing, agriculture, real estate, and government services; broader integration in trade, media, education, and legal services; deeper workflow orchestration in information technology, finance, and healthcare. Finally, we discuss key challenges including safety, long-horizon reliability, academia-industry gaps, adoption barriers, governance, and labor-market uncertainty. This paper provides a structured account of how Agentic AI is reshaping productivity and outlines future directions for reliable and socially beneficial AI-driven production systems. We hope this paper will serve as a foundation for advancing AI4Productivity research and guiding the design of AI systems that deliver reliable, scalable, and broadly beneficial productivity gains.

  • Open Access

    AI Scientists for Building Virtual-Cell Models

    by Mark Gerstein, Xiangru Tang, Jiapeng Chen, Yanjun Shao, Zhuoyun Yu, Yan Cui, Weixu Wang, Fang Wu, Yuxuan Liao, Yuchen Zhuang, et al.

    Autonomous agents, from virtual laboratories to biological data-analysis agents and co-scientists, have begun to turn scientific goals into hypotheses. Whether they can go further and convert real, noisy and complex biological data into executable model hypotheses and architectures that encode testable assumptions remains unclear. Predicting how cells respond to genetic and chemical perturbations (i.e., modeling virtual cells) is a natural test of this ability: it is central to decoding disease mechanisms and therapeutic discovery, yet it demands cross-disciplinary expertise rarely concentrated in a single research group. Here, we introduce CellForge, an organized team of autonomous agents for single-cell perturbation modeling. Given a dataset and a task, it surveys the literature, parses the data, identifies relevant baselines, and formulates a model hypothesis through critic-mediated discussion among agents specialized in data modeling, single-cell biology, and deep learning. It then writes the training code, runs the experiments, and returns a trained predictor including architecture, code, and validation results. The architecture itself is the hypothesis: CellForge produces it end-to-end, with no human specifying the design, loss, or training protocol. Across six perturbation datasets spanning transcriptomic, epigenomic, and proteomic contexts, CellForge yields models that are competitive with hand-crafted state-of-the-art results on established tasks and extends the same workflow to paired multiomic readouts. Blinded human evaluators rate CellForge’s research plans as more scientifically sound and innovative than those from single LLMs or deep-research systems. In summary, we show autonomous agents can complete the full hypothesis-to-validation cycle in single-cell biology, with an AI effectively building another AI, in a complex setting that currently requires a team of human experts.

  • Open Access

    The Forgetting-Learning Trade-off: Making Reinforcement Learning Work for Protein Language Models

    by Hanqun Cao, Hongrui Zhang, Junde Xu, Zhou Zhang, Lingdong Shen, Minghao Sun, Ge Liu, Jinbo Xu, Wu-Jun Li, Jinren Ni, et al.

    Reinforcement learning (RL) is increasingly applied to Protein Language Models (PLMs), yet its effectiveness varies across tasks, and standard metrics such as pass@k can rise even when the model's solvable problem set is shrinking. We introduce two capability-level diagnostics. The Expansion-Shrinkage Ratio (ESR) measures how RL shifts the set of problems a PLM can solve, separating genuine gain from probability redistribution. Dual-Reward ESR reports ESR under both the training reward and an orthogonal evaluator; the gap ΔESR quantifies reward hacking as a single observable number. Applied across four protein design tasks, three RL algorithms (DPO, PPO, GRPO), and two PLM architectures, the diagnostics reveal that RL on PLMs is governed by two reward properties: verifiability, whether the reward is a fixed environment or a learned surrogate vulnerable to distribution shift, and coverage, the fraction of sequence space giving an informative gradient. The two axes produce three regimes with distinct ΔESR signatures: well-covered verifiable rewards yield genuine expansion; sparse verifiable rewards induce a coverage bottleneck; predicted rewards induce reward hacking. Controlled analyses isolate these two factors as operative, letting practitioners predict an RL run's outcome before committing to costly fine-tuning.

  • Open Access

    SurfDesign: Effective Protein Design on Molecular Surfaces

    by Fang Wu, Shuting Jin, Xiangru Tang, Mark Gerstein, Xiangxiang Zeng, Jure Leskovec, Yejin Choi, Jinbo Xu

  • Open Access

    Deciphering Fingerprints of 3D Molecular Surfaces For Accurate Epitope Prediction

    by Fang Wu, Weihao Xuan, Jure Leskovec, Yejin Choi, Li Erran Li

  • Open Access

    Dynamics-inspired Structure Hallucination for Protein-protein Interaction Modeling

    by Fang Wu, Stan Z. Li

    Protein-protein interaction (PPI) represents a central challenge within the biology field, and accurately predicting the consequences of mutations in this context is crucial for drug design and protein engineering. Deep learning (DL) has shown promise in forecasting the effects of such mutations, but is hindered by two primary constraints. First, the structures of mutant proteins are often elusive to acquire. Secondly, PPI takes place dynamically, which is rarely integrated into the DL architecture design. To address these obstacles, we present a novel framework named Refine-PPI with two key enhancements. First, we introduce a structure refinement module trained by a mask mutation modeling (MMM) task on available wild-type structures, which is then transferred to produce the inaccessible mutant structures. Second, we employ a new kind of geometric network, called the probability density cloud network (PDC-Net), to capture 3D dynamic variations and encode the atomic uncertainty associated with PPI. Comprehensive experiments on SKEMPI.v2 substantiate the superiority of Refine-PPI over all existing tools for predicting free energy change. These findings underscore the effectiveness of our hallucination strategy and the PDC module in addressing the absence of mutant protein structure and modeling geometric uncertainty.

  • Open Access

    A Semi-supervised Molecular Learning Framework for Activity Cliff Estimation

    by Fang Wu

    Machine learning (ML) enables accurate and fast molecular property predictions, which are of interest in drug discovery and material design. Their success is based on the principle of similarity at its heart, assuming that similar molecules exhibit close properties. However, activity cliffs challenge this principle, and their presence leads to a sharp decline in the performance of existing ML algorithms, particularly graph-based methods. To overcome this obstacle under a low-data scenario, we propose a novel semi-supervised learning (SSL) method dubbed SemiMol, which employs predictions on numerous unannotated data as pseudo-signals for subsequent training. Specifically, we introduce an additional instructor model to evaluate the accuracy and trustworthiness of proxy labels because existing pseudo-labeling approaches require probabilistic outputs to reveal the model's confidence and fail to be applied in regression tasks. Moreover, we design a self-adaptive curriculum learning algorithm to progressively move the target model toward hard samples at a controllable pace. Extensive experiments on 30 activity cliff datasets demonstrate that SemiMol significantly enhances graph-based ML architectures and outpasses state-of-the-art pretraining and SSL baselines.

  • Open Access

    TeamPath: Building MultiModal Pathology Experts with Reasoning AI Copilots

    by Hongyu Zhao, Tianyu Liu, Simeng Han, Tinglin Huang, Hua Xu, Weihao Xuan, Heli Qi, Irene Li, Rui Yang, Nan Liu, et al.

    Advances in AI have introduced several strong models in computational pathology to usher it into the era of multi-modal diagnosis, analysis, and interpretation. However, the current pathology-specific visual language models still lack capacities in making diagnosis with rigorous reasoning paths as well as handling divergent tasks, and thus challenges of building AI Copilots for real scenarios still exist. Here we introduce TeamPath, an AI system powered by reinforcement learning and router-enhanced solutions based on large-scale histopathology multimodal datasets, to work as a virtual assistant for expert-level disease diagnosis, patch-level information summarization, and cross-modality generation to integrate transcriptomic information for the clinical usage. We also collaborate with pathologists from Yale School of Medicine to demonstrate that TeamPath can assist them in working more efficiently by identifying and correcting expert conclusions and reasoning paths. Overall, TeamPath can flexibly choose the best settings according to the needs, and serve as an innovative and reliable system for information communication across different modalities and experts.

  • Open Access

    BroRL: Scaling Reinforcement Learning via Broadened Exploration

    by Jian Hu, Mingjie Liu, Ximing Lu, Fang Wu, Zaid Harchaoui, Shizhe Diao, Yejin Choi, Pavlo Molchanov, Jun Yang, Jan Kautz, et al.

    Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a key ingredient for unlocking complex reasoning capabilities in large language models. Recent work ProRL has shown promise in scaling RL by increasing the number of training steps. However, performance plateaus after thousands of steps, with clear diminishing returns from allocating more computation to additional training. In this work, we investigate a complementary paradigm for scaling RL, BroR-Lincreasing the number of rollouts per example to hundreds to exhaustively Broaden exploration, which yields continuous performance gains beyond the saturation point observed in ProRL when scaling the number of training steps. Our approach is motivated by a mass balance equation analysis allowing us to characterize the rate of change in probability mass for correct and incorrect tokens during the reinforcement process. We show that under a one-step RL assumption, sampled rollout tokens always contribute to correct-mass expansion, while unsampled tokens outside rollouts may lead to gains or losses depending on their distribution and the net reward balance. Importantly, as the number of rollouts per example N increases, the effect of unsampled terms diminishes, ensuring overall correct-mass expansion. To validate our theoretical analysis, we conduct simulations under more relaxed conditions and find that a sufficiently large rollout size N-corresponding to ample exploration-guarantees an increase in the probability mass of all correct tokens. Empirically, BroRL revives models saturated after 3K ProRL training steps and demonstrates robust, continuous improvement, achieving state-of-the-art results for the 1.5B model across diverse benchmarks.