Author name cluster

Mengbo Wang

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4 papers

1 author row

AAAI Conference 2026 Conference Paper

RatioSketch: Towards More Accurate Frequency Estimation in Data Streams via a Lightweight Neural Network

Mengbo Wang
Zhuochen Fan
Dayu Wang
Guorui Xie
Qing Li
Zeyu Luan
Yong Jiang
Tong Yang

Sketch-based solutions are widely used to estimate item frequencies in infinite data streams.Traditional hand-crafted sketches face the bottleneck of further eliminating errors because they cannot fully utilize the data stream distribution.Although recent neural sketches represented by MetaSketch and LegoSketch have improved generalization capabilities, they face bottlenecks such as high computational overhead and parameter sensitivity.Meanwhile, they ignore load information, fail to fully utilize the local information in hand-crafted sketches, and do not focus on the frequent items that are usually more important in data streams.In this paper, we propose RatioSketch, a novel lightweight neural network correction framework that synergizes the advantages of hand-crafted sketches and neural sketches in a ``micro-correction'' paradigm.The key idea is to retain the efficient underlying data structure of the hand-crafted sketch and to build a neural correction layer in its output space. We select multiple representative hand-crafted sketches as use cases to study the correction performance of RatioSketch on them.Extensive experimental evaluations on several real-world datasets show that RatioSketch-corrected sketches achieve consistently higher estimation accuracy than their uncorrected counterparts, as well as outperforming neural baselines such as MetaSketch and LegoSketch under identical memory budgets.

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NeurIPS Conference 2025 Conference Paper

Differentiable Constraint-Based Causal Discovery

Jincheng Zhou
Mengbo Wang
Anqi He
Yumeng Zhou
Hessam Olya
Murat Kocaoglu
Bruno Ribeiro

Causal discovery from observational data is a fundamental task in artificial intelligence, with far-reaching implications for decision-making, predictions, and interventions. Despite significant advances, existing methods can be broadly categorized as constraint-based or score-based approaches. Constraint-based methods offer rigorous causal discovery but are often hindered by small sample sizes, while score-based methods provide flexible optimization but typically forgo explicit conditional independence testing. This work explores a third avenue: developing differentiable $d$-separation scores, obtained through a percolation theory using soft logic. This enables the implementation of a new type of causal discovery method: gradient-based optimization of conditional independence constraints. Empirical evaluations demonstrate the robust performance of our approach in low-sample regimes, surpassing traditional constraint-based and score-based baselines on a real-world dataset. Code implementing the proposed method is publicly available at [https: //github. com/PurdueMINDS/DAGPA](https: //github. com/PurdueMINDS/DAGPA).

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NeurIPS Conference 2025 Conference Paper

GeneFlow: Translation of Single-cell Gene Expression to Histopathological Images via Rectified Flow

Mengbo Wang
Shourya Verma
Aditya Malusare
Luopin Wang
Yiyang Lu
Vaneet Aggarwal
Mario Sola
Ananth Grama

Spatial transcriptomics technologies can be used to align transcriptomes with histopathological morphology, presenting exciting new opportunities for biomolecular discovery. Using spatial transcriptomic gene expression and corresponding histology data, we construct a novel framework, GeneFlow, to map single- and multi-cell gene expression onto paired cellular images. By combining an attention-based RNA encoder with a conditional UNet guided by rectified flow, we generate high-resolution images with different staining methods (e. g. , H&E, DAPI) to highlight various cellular/ tissue structures. Rectified flow with high-order ODE solvers creates a continuous, bijective mapping between expression and image manifolds, addressing the many-to-one relationship inherent in this problem. Our method enables the generation of realistic cellular morphology features and spatially resolved intercellular interactions under genetic or chemical perturbations. This enables minimally invasive disease diagnosis by revealing dysregulated patterns in imaging phenotypes. Our rectified flow based method outperforms diffusion methods and baselines in all experiments. Code is available at https: //github. com/wangmengbo/GeneFlow.

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NeurIPS Conference 2024 Conference Paper

A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types

Artur Szałata
Andrew Benz
Robrecht Cannoodt
Mauricio Cortes
Jason Fong
Sunil Kuppasani
Richard Lieberman
Tianyu Liu

Single-cell transcriptomics has revolutionized our understanding of cellular heterogeneity and drug perturbation effects. However, its high cost and the vast chemical space of potential drugs present barriers to experimentally characterizing the effect of chemical perturbations in all the myriad cell types of the human body. To overcome these limitations, several groups have proposed using machine learning methods to directly predict the effect of chemical perturbations either across cell contexts or chemical space. However, advances in this field have been hindered by a lack of well-designed evaluation datasets and benchmarks. To drive innovation in perturbation modeling, the Open Problems Perturbation Prediction (OP3) benchmark introduces a framework for predicting the effects of small molecule perturbations on cell type-specific gene expression. OP3 leverages the Open Problems in Single-cell Analysis benchmarking infrastructure and is enabled by a new single-cell perturbation dataset, encompassing 146 compounds tested on human blood cells. The benchmark includes diverse data representations, evaluation metrics, and winning methods from our "Single-cell perturbation prediction: generalizing experimental interventions to unseen contexts" competition at NeurIPS 2023. We envision that the OP3 benchmark and competition will drive innovation in single-cell perturbation prediction by improving the accessibility, visibility, and feasibility of this challenge, thereby promoting the impact of machine learning in drug discovery.

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