The University of California, Irvine (UCI), founded in 1965, is a public research university consistently recognized as a trailblazer across a broad range of fields. It is highly ranked among public universities for its diverse academic offerings, world-class leadership, and strong commitment to sustainability and diversity. We have collaborated with UC Irvine on advanced machine learning topics, including generative modeling and data-efficient training methods. Our work supports AI applications in vision, security, and low-resource environments. Please read about our latest news and collaborative publications with the University of California, Irvine.

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Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations

Cell fate decisions are highly coordinated processes governed bycomplex interactions among numerous regulatory genes, whiledisruptions in these mechanisms can lead to developmental abnormalitiesand disease. Traditional methods often fail to capture suchcombinatorial interactions, limiting their ability to fully model cellfate dynamics. Here, we introduce MetaVelo, a global feature explanationframework for identifying key regulatory gene sets influencingcell fate transitions. MetaVelo models these transitions as ablack-box function and employs a differentiable neural ordinary differentialequation (ODE) surrogate to enable efficient optimization.By reparameterizing the problem as a controllable data generationprocess, MetaVelo overcomes the challenges posed by the nondifferentiablenature of cell fate dynamics. Benchmarking acrossdiverse stand-alone and longitudinal single-cell RNA-seq datasetsand three black-box cell fate models demonstrates its superiorityover 12 baseline methods in predicting developmental trajectoriesand identifying combinatorial regulatory gene sets. MetaVelo furtherdistinguishes independent from synergistic regulatory genes,offering novel insights into the gene interactions governing cellfate. With the growing availability of high-resolution single-celldata, MetaVelo provides a scalable and effective framework fo

Drive-1-to-3: Enriching Diffusion Priors for Novel View Synthesis of Real Vehicles

The recent advent of large-scale 3D data, e.g. Objaverse, has led to impressive progress in training pose-conditioned diffusion models for novel view synthesis. However, due to the synthetic nature of such 3D data, their performance drops significantly when applied to real-world images. This paper consolidates a set of good practices to finetune large pretrained models for a real-world task — harvesting vehicle assets for autonomous driving applications. To this end, we delve into the discrepancies between the synthetic data and real driving data, then develop several strategies to account for them properly. Specifically, we start with a virtual camera rotation of real images to ensure geometric alignment with synthetic data and consistency with the pose manifold defined by pretrained models. We also identify important design choices in object-centric data curation to account for varying object distances in real driving scenes — learn across varying object scales with fixed camera focal length. Further, we perform occlusion-aware training in latent spaces to account for ubiquitous occlusions in real data, and handle large viewpoint changes by leveraging a symmetric prior. Our insights lead to effective finetuning that results in a 68.8% reduction in FID for novel view synthesis over prior arts.

Understanding Transcriptional Regulatory Redundancy by Learnable Global Subset Perturbations

Transcriptional regulation through cis-regulatory elements (CREs) is crucial for numerous biological functions, with its disruption potentially leading to various diseases. It is well-known that these CREs often exhibit redundancy, allowing them to compensate for each other in response to external disturbances, highlighting the need for methods to identify CRE sets that collaboratively regulate gene expression effectively. To address this, we introduce GRIDS, an in silico computational method that approaches the task as a global feature explanation challenge to dissect combinatorial CRE effects in two phases. First, GRIDS constructs a differentiable surrogate function to mirror the complex gene regulatory process, facilitating cross-translations in single-cell modalities. It then employs learnable perturbations within a state transition framework to offer global explanations, efficiently navigating the combinatorial feature landscape. Through comprehensive bench marks, GRIDS demonstrates superior explanatory capabilities compared to other leading methods. Moreover, GRIDS s global explanations reveal intricate regulatory redundancy across cell types and states, underscoring its potential to advance our understanding ofcellular regulation in biological research.

LidaRF: Delving into Lidar for Neural Radiance Field on Street Scenes

Photorealistic simulation plays a crucial role in applications such as autonomous driving, where advances in neural radiance fields (NeRFs) may allow better scalability through the automatic creation of digital 3D assets. However, reconstruction quality suffers on street scenes due to largely collinear camera motions and sparser samplings at higher speeds. On the other hand, the application often demands rendering from camera views that deviate from the inputs to accurately simulate behaviors like lane changes. In this paper, we propose several insights that allow a better utilization of Lidar data to improve NeRF quality on street scenes. First, our framework learns a geometric scene representation from Lidar, which are fused with the implicit grid-based representation for radiance decoding, thereby supplying strongergeometric information offered by explicit point cloud. Second, we put forth a robust occlusion-aware depth supervision scheme, which allows utilizing densified Lidar points by accumulation. Third, we generate augmented training views from Lidar points for further improvement. Our insights translate to largely improved novel view synthesis under real driving scenes.

Impeller: A Path-based Heterogeneous Graph Learning Method for Spatial Transcriptomic Data Imputation

Recent advances in spatial transcriptomics allow spatially resolved gene expression measurements with cellular or even sub-cellular resolution, directly characterizing the complex spatiotemporal gene expression landscape and cell-to-cell interactions in their native microenvironments. Due to technology limitations, most spatial transcriptomic technologies still yield incomplete expression measurements with excessive missing values. Therefore, gene imputation is critical to filling in missing data, enhancing resolution, and improving overall interpretability. However, existing methods either require additional matched single-cell RNA-seq data, which is rarely available, or ignore spatial proximity or expression similarity information

DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays

MotivationMapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods with limited training data. Moreover, past approaches have implemented enhancer discovery as a binary classification problem without accurate boundary detection, producing low-resolution annotations with superfluous regions and reducing the statistical power for downstream analyses (e.g. causal variant mapping and functional validations). Here, we addressed these challenges via a two-step model called Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays (DECODE). First, we employed direct enhancer-activity readouts from novel functional characterization assays, such as STARR-seq, to train a deep neural network for accurate cell-type-specific enhancer prediction. Second, to improve the annotation resolution, we implemented a weakly supervised object detection framework for enhancer localization with precise boundary detection (to a 10 bp resolution) using Gradient-weighted Class Activation Mapping.ResultsOur DECODE binary classifier outperformed a state-of-the-art enhancer prediction method by 24% in transgenic mouse validation. Furthermore, the object detection framework can condense enhancer annotations to only 13% of their original size, and these compact annotations have significantly higher conservation scores and genome-wide association study variant enrichments than the original predictions. Overall, DECODE is an effective tool for enhancer classification and precise localization.

Battery Optimal Approach to Demand Charge Reduction in Behind-The-Meter Energy Management Systems

Large monthly demand charge of commercial and industrial entities is a major problem for their economical business. Utilizing a battery by behind-the-meter Energy Management Systems (EMS) has been seen as a solution to demand charge reduction. In state-of-the-art approaches, the EMS maintains sufficient energy for the unexpected large demands and uses the battery to meet them. However, large amount of energy stored in the battery may increase the average battery State-of-Charge (SoC) and cause degradation in battery capacity. Therefore, the current approaches of demand charge reduction significantly shortens the battery lifetime which is not economical. In this paper, we propose a novel battery optimal approach to reduce the monthly demand charges. In our approach, load profile of the previous month is used by daily optimizations to shave daily power demands while considering the battery lifetime model. Evaluated daily demand thresholds and load profile are statistically analyzed to cluster different types of day. Hence, it helps the EMS to find the typical daily load profile and appropriate monthly demand threshold for the entity. The performance of our approach has been analyzed and compared to the state-of-the-arts by experimenting on multiple real-life load profiles and battery configurations. The results show significant reduction of 16% in annual average battery SoC that increases the battery lifetime from 4.1 to 5.6 years while achieving up to 13.4% demand charge reduction.