Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2608.10407

FlowGRN+: Improving Gene Regulatory Network Inference by Spline Fitting and Manifold Projection in Conditional Flow Matching (Technical Report)

Tsz Pan Tong·Jun Pang
View original source ↗Read source document ↗Export metadata ↓

Abstract

Gene regulatory networks (GRNs) are fundamental in understanding cellular dynamics and underlying mechanisms during development and disease. Although scRNA-seq technologies have enabled the collection of vast numbers of gene expression profiles at single-cell resolution, inferring GRNs from scRNA-seq data remains a significant challenge due to high dimensionality and dropout. Recently, FlowGRN has shown promising results in reconstructing cell trajectories and inferring GRNs by applying conditional flow matching (CFM) to learn the cell dynamics. However, FlowGRN still faces limitations in the temporal coherence of reconstructed dynamics and relies on human inspection, which hinders downstream applications and reproducibility. In this paper, we propose FlowGRN+, an improved version of FlowGRN that integrates spline fitting into the CFM framework to generate more stable reference trajectories for training, thereby improving the temporal coherence of the learned dynamics. To address overshooting in spline fitting, we further introduce a projection scheme that projects spline tangents onto the local tangent space of the data manifold. We evaluate FlowGRN+ on the BEELINE benchmark and show improved trajectory smoothness with a competitive GRN inference performance. FlowGRN+ provides a practical framework for reconstructing cell trajectories and inferring GRNs from scRNA-seq data, and the insights from this work may also be useful for other CFM-based models of cellular dynamics.

Explore related subjects

cs.CE

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Tsz Pan Tong, Jun Pang. 2026-08-11. FlowGRN+: Improving Gene Regulatory Network Inference by Spline Fitting and Manifold Projection in Conditional Flow Matching (Technical Report). https://arxiv.org/abs/2608.10407

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Dimension Bridging for 3D RANS with Neural Network Accelerated Gaussian Functional Regression

In many computational science and engineering problems, repeatedly solving fully resolved physics-based models to design for a quantity of interest (QoI) can quickly become intractable, requiring the use of low-fidelity models to predict the same QoI but introduce errors where some features are neglected or are otherwise inaccurately resolved. We use Gaussian Functional Regression (GFR) to learn a correction to a 2D Reynolds-Averaged Navier-Stokes (RANS) model to predict the aerodynamic coefficients from a 3D RANS model. This model pair has a disparity in the governing physics from the reduced dimensionality, a previously unexplored application for GFR. Empirically, our results show that with a proper choice of low-dimensional (LD) model, the proposed kernel allows for the use of fewer high-dimensional (HD) evaluations to regress a response surface to the same level of accuracy as standard stationary kernels. Moreover, the new kernel provides more informative uncertainty quantification, which we show is advantageous when used to drive an adaptive sampling algorithm. Finally, we propose a novel neural network accelerated kernel, which we show offers predictions in good agreement while speeding up evaluations by millions of times in wall clock measurements, bringing the computational budget within the real-time regime.

cs.CE↗
arXiv2026

SabreAgent: Language Models at Design Time for Lost-Sales Inventory Control

SabreAgent uses a language model at design time to construct two components for lost-sales inventory control: a product-specific seasonal prior and a validation-selected capped base-stock policy family. During operation, statistical forecasting and inventory optimization use these frozen artifacts to determine orders, with zero language-model calls. We evaluate the approach on the $1{,}320$ instances of InventoryBench. Under the benchmark's cost assumptions, the operations-research core draws on a zero-lead-time optimality result and a projected-inventory rule for positive deterministic lead times. The latter computes replenishment shortfalls by propagating inventory using sales along simulated demand paths. The seasonal prior adds forecast variants alongside the original forecaster, and the selected policy family handles stochastic lead times with order destruction. SabreAgent scores $0.6311$, compared with $0.5380$ for the strongest published baseline, and ranks first in all six benchmark cells. Ablations attribute most of the gain to the OR core. In the paired analysis, the seasonal component adds $1.79\%$ across the three real-data cells, and the search component adds $2.3\%$ across the two stochastic-lead-time cells. These results demonstrate how model-generated priors and policy structure can improve an OR controller through design-time use.

cs.CE↗
arXiv2026

Hierarchical Multi-Task Learning with Liquidity-Aware Signals for Stock Forecasting

Stock price forecasting is a long-standing challenge in computational finance, driven by the inherent randomness of markets and complex temporal patterns. While recent deep-learning models have raised forecasting accuracy by jointly modeling inter-stock and temporal price dynamics, they conflate inter-stock relationships with intra-stock temporal dependencies and focus solely on the univariate objective of price movement. To address these limitations, we propose LiMT, a Hierarchical Multi-Task Learning framework that integrates liquidity-aware signals for stock price forecasting. LiMT employs a Market Regime Encoder (MRE) module that first extracts contemporaneous cross-stock dependencies, then models each stock's temporal dynamics, yielding a unified latent state. Building on this latent state, we introduce a Liquidity-Driven Learning (LDL) module, a mixture-of-experts architecture that features cross-task gating mechanisms to jointly predict price movement, volatility, and trading volume. We further design an Adaptive Portfolio Optimization (APO) mechanism that converts multi-task forecasts into executable portfolio weights under transaction-cost and liquidity constraints. Extensive experiments on the CSI300 and CSI500 benchmarks show that LiMT performs best among strong neural and tree-based baselines across the reported metrics. In realistic CSI300 backtests, APO improves annualized return from 3.99% to 10.01% and Sharpe ratio from 1.22 to 1.86 over equal weighting, showing that the multi-task forecasts translate into deployable portfolio gains.

cs.CE↗