The University of California is a prominent system of 10 campuses, six academic health centers, and three affiliated national laboratories. Headquartered in Oakland, California, the Office of the President supports its campuses and students through systemwide funding and programs, embodying a commitment to public higher education and research. We collaborate with institutions across the University of California system to advance research in computer vision, optical networking, and AI model optimization. Our joint projects span fundamental and applied science, driving innovation in scalable, high-performance AI. Please read about our latest news and collaborative publications with the University of California.

Posts

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

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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

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Uncertainty Propagation on LLM Agent

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Large language models (LLMs) integrated into multi-step agent systems enable complex decision-making processes across various applications. However, their outputs often lack reliability, making uncertainty estimation crucial. Existing uncertainty estimation methods primarily focus on final-step outputs, which fail to account for cumulative uncertainty over the multi-step decision-making process and the dynamic interactions between agents and their environments. To address these limitations, we propose SAUP (Situation Awareness Uncertainty Propagation), a novel framework that propagates uncertainty through each step of an LLM-based agent’s reasoning process. SAUP incorporates situational awareness by assigning situational weights to each step’s uncertainty during the propagation. Our method, compatible with various one-step uncertainty estimation techniques, provides a comprehensive and accurate uncertainty measure. Extensive experiments on benchmark datasets demonstrate that SAUP significantly outperforms existing state-of-the-art methods, achieving up to 20% improvement in AUROC.

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National Intern Day at NEC Laboratories America: Celebrating the Next Generation of Innovators

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On National Intern Day, NEC Laboratories America celebrates the bright minds shaping tomorrow’s technology. Each summer, interns from top universities work side-by-side with our researchers on real-world challenges in AI, cybersecurity, data science, and more. From groundbreaking research to team-building events, our interns contribute fresh ideas and bold thinking that power NEC’s innovation engine.

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Position Really Matters: Towards a Holistic Approach for Prompt Tuning

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Prompt tuning is highly effective in efficiently extracting knowledge from foundation models, encompassing both language, vision, and vision-language models. However, the efficacy of employing fixed soft prompts with a predetermined position for concatenation with inputs for all instances, irrespective of their inherent disparities, remains uncertain. Variables such as the position, length, and representations of prompts across diverse instances and tasks can substantially influence the performance of prompt tuning. We first provide a theoretical analysis, revealing that optimizing the position of the prompt to encompass the input can capture additional semantic information that traditional prefix or postfix prompt tuning methods fail to capture. Then, we present a holistic parametric prompt tuning strategy that dynamically determines different factors of prompts based on specific tasks or instances. Experimental results underscore the significant performance improvement achieved by dynamic prompt tuning across a wide range of tasks, including NLP, vision recognition, and vision-language tasks. Furthermore, we establish the universal applicability of our approach under full-data, few-shot, and multitask settings.

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

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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

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State-Aware Anomaly Detection for Massive Sensor Data in Internet of Things

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With the escalating prevalence of Internet of Things (IoTs) in critical infrastructure, the requirement for efficient and effective anomaly detection solution becomes increasingly important. Unfortunately, most prior research works have largely overlooked to adapt detection criteria for different operational states, thereby rendering them inadequate when confronted with diverse and complex work states of IoTs. In this study, we address the challenges of IoT anomaly detection across various work states by introducing a novel model called Hybrid State Encoder-Decoder (HSED). HSED employs a two-step approach, beginning with identification and construction of a hybrid state for Key Performance Indicator (KPI) sensors based on their state attributes, followed by the detection of abnormal or failure events utilizing high-dimensional sensor data. Through the evaluation on real-world datasets, we demonstrate the superiority of HSED over state-of-the-art anomaly detection models. HSED can significantly enhance the efficiency, adaptability and reliability of IoTs and avoid potential risks of economic losses by IoT failures.

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Conditional Image-to-Video Generation with Latent Flow Diffusion Models

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Conditional image-to-video (cI2V) generation aims to synthesize a new plausible video starting from an image (e.g., a person’s face) and a condition (e.g., an action class label like smile). The key challenge of the cI2V task lies in the simultaneous generation of realistic spatial appearance and temporal dynamics corresponding to the given image and condition. In this paper, we propose an approach for cI2V using novel latent flow diffusion models (LFDM) that synthesize an optical flow sequence in the latent space based on the given condition to warp the given image. Compared to previous direct-synthesis-based works, our proposed LFDM can better synthesize spatial details and temporal motion by fully utilizing the spatial content of the given image and warping it in the latent space according to the generated temporally-coherent flow. The training of LFDM consists of two separate stages: (1) an unsupervised learning stage to train a latent flow auto-encoder for spatial content generation, including a flow predictor to estimate latent flow between pairs of video frames, and (2) a conditional learning stage to train a 3D-UNet-based diffusion model (DM) for temporal latent flow generation. Unlike previous DMs operating in pixel space or latent feature space that couples spatial and temporal information, the DM in our LFDM only needs to learn a low-dimensional latent flow space for motion generation, thus being more computationally efficient. We conduct comprehensive experiments on multiple datasets, where LFDM consistently outperforms prior arts. Furthermore, we show that LFDM can be easily adapted to new domains by simply finetuning the image decoder. Our code is available at https://github.com/nihaomiao/CVPR23_LFDM.

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Recommend for a Reason: Unlocking the Power of Unsupervised Aspect-Sentiment Co-Extraction

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Compliments and concerns in reviews are valuable for understanding users’ shopping interests and their opinions with respect to specific aspects of certain items. Existing review-based recommenders favor large and complex language encoders that can only learn latent and uninterpretable text representations. They lack explicit user-attention and item-property modeling, which however could provide valuable information beyond the ability to recommend items. Therefore, we propose a tightly coupled two-stage approach, including an Aspect-Sentiment Pair Extractor (ASPE) and an Attention-Property-aware Rating Estimator (APRE). Unsupervised ASPE mines Aspect-Sentiment pairs (AS-pairs) and APRE predicts ratings using AS-pairs as concrete aspect-level evidences. Extensive experiments on seven real-world Amazon Review Datasets demonstrate that ASPE can effectively extract AS-pairs which enable APRE to deliver superior accuracy over the leading baselines.

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

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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.

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Robust Graph Representation Learning via Neural Sparsification

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Graph representation learning serves as the core of important prediction tasks, ranging from product recommendation to fraud detection. Reallife graphs usually have complex information in the local neighborhood, where each node is described by a rich set of features and connects to dozens or even hundreds of neighbors. Despite the success of neighborhood aggregation in graph neural networks, task-irrelevant information is mixed into nodes’ neighborhood, making learned models suffer from sub-optimal generalization performance. In this paper, we present NeuralSparse, a supervised graph sparsification technique that improves generalization power by learning to remove potentially task-irrelevant edges from input graphs. Our method takes both structural and nonstructural information as input, utilizes deep neural networks to parameterize sparsification processes, and optimizes the parameters by feedback signals from downstream tasks. Under the NeuralSparse framework, supervised graph sparsification could seamlessly connect with existing graph neural networks for more robust performance. Experimental results on both benchmark and private datasets show that NeuralSparse can yield up to 7.2% improvement in testing accuracy when working with existing graph neural networks on node classification tasks.

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