arXiv subjects

Mengbo Wang

Publications and source records attributed to Mengbo Wang.

5 recordsLinked to original sources

arXiv2025

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

Spatial transcriptomics (ST) technologies can be used to align transcriptomes with histopathological morphology, presenting exciting new opportunities for biomolecular discovery. Using ST data, we construct a novel framework, GeneFlow, to map transcriptomics 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 transcriptomics 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 from observational gene expression profiles, provides potential to incorporate genetic/chemical perturbations, and enables disease diagnosis by revealing dysregulated patterns in imaging phenotypes. Our rectified flow-based method outperforms diffusion-based baseline method in all experiments. Code can be found at https://github.com/wangmengbo/GeneFlow.

q-bio.QM↗

arXiv2025

Differentiable Constraint-Based Causal Discovery

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 and data of the proposed method are publicly available at https://github$.$com/PurdueMINDS/DAGPA.

cs.LG↗

arXiv2025

RestoRect: Degraded Image Restoration via Latent Rectified Flow & Feature Distillation

Current approaches for restoration of degraded images face a trade-off: high-performance models are slow for practical use, while fast models produce poor results. Knowledge distillation transfers teacher knowledge to students, but existing static feature matching methods cannot capture how modern transformer architectures dynamically generate features. We propose a novel Latent Rectified Flow Feature Distillation method for restoring degraded images called \textbf{'RestoRect'}. We apply rectified flow to reformulate feature distillation as a generative process where students learn to synthesize teacher-quality features through learnable trajectories in latent space. Our framework combines Retinex decomposition with learnable anisotropic diffusion constraints, and trigonometric color space polarization. We introduce a Feature Layer Extraction loss for robust knowledge transfer between different network architectures through cross-normalized transformer feature alignment with percentile-based outlier detection. RestoRect achieves better training stability, and faster convergence and inference while preserving restoration quality, demonstrating superior results across 15 image restoration datasets, covering 4 tasks, on 10 metrics against baselines.

cs.CV↗

arXiv2025

Advancing AI Research Assistants with Expert-Involved Learning

Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research Assistant for Expert-in-the-Loop Learning), an open-source evaluation and optimization framework that pairs a curated multimodal biomedical corpus with expert-vetted tasks to probe two capabilities: full-length article summarization and fine-grained figure interpretation. Using uniform protocols and blinded PhD-level evaluation, we find that state-of-the-art models generate fluent but incomplete summaries, whereas LMMs struggle with detailed visual reasoning. We later observe that prompt engineering and lightweight fine-tuning substantially improve textual coverage, and a compute-scaled inference strategy enhances visual question answering. We build an ARIEL agent that integrates textual and visual cues, and we show it can propose testable mechanistic hypotheses. ARIEL delineates current strengths and limitations of foundation models, and provides a reproducible platform for advancing trustworthy AI in biomedicine.

cs.AI↗

arXiv2025

BAGEL: Adversarially Constrained Online Convex Optimization under Separation Oracle Access

In adversarial Constrained Online Convex Optimization (COCO), a learner selects actions from a fixed convex set while seeking both low regret and low cumulative constraint violation (CCV) under time-varying constraints. We ask what performance is achievable when the action set is accessed through a Separation Oracle (SO), rather than an exact Projection Oracle (PO) or a Linear Optimization Oracle (LOO). We introduce $\mathtt{BAGEL}$, which combines a Lyapunov-weighted surrogate loss, blocked adaptive online gradient descent, and an infeasible-projection procedure implemented with an SO. For convex costs and any $\beta\in(0,1/2]$, $\mathtt{BAGEL}$ achieves $\mathcal{O}(T^{1-\beta})$ regret and $\mathcal{O}(T^{1-\beta}\log T)$ cumulative violation using $\widetilde{\mathcal{O}}((D/r)^2T^{2\beta})$ SO calls. At $\beta=1/2$, this gives $\mathcal{O}(\sqrt{T})$ regret and $\mathcal{O}(\sqrt{T}\log T)$ violation with a near-linear number of SO calls. The result is an access oracle based guarantee, with computational relevance depends on the geometry of the action set and the cost of implementing its SO.

cs.LG↗