Zehao Yu

Ruoyu Wang, Zehao Yu, Shenghua Gao

Multiple near frontal-parallel planes based depth representation demonstrated impressive results in self-supervised monocular depth estimation (MDE). Whereas, such a representation would cause the discontinuity of the ground as it is perpendicular to the frontal-parallel planes, which is detrimental to the identification of drivable space in autonomous driving. In this paper, we propose the PlaneDepth, a novel orthogonal planes based presentation, including vertical planes and ground planes. PlaneDepth estimates the depth distribution using a Laplacian Mixture Model based on orthogonal planes for an input image. These planes are used to synthesize a reference view to provide the self-supervision signal. Further, we find that the widely used resizing and cropping data augmentation breaks the orthogonality assumptions, leading to inferior plane predictions. We address this problem by explicitly constructing the resizing cropping transformation to rectify the predefined planes and predicted camera pose. Moreover, we propose an augmented self-distillation loss supervised with a bilateral occlusion mask to boost the robustness of orthogonal planes representation for occlusions. Thanks to our orthogonal planes representation, we can extract the ground plane in an unsupervised manner, which is important for autonomous driving. Extensive experiments on the KITTI dataset demonstrate the effectiveness and efficiency of our method. The code is available at https://github.com/svip-lab/PlaneDepth.

Zehao Yu, Anpei Chen, Binbin Huang et al.

Recently, 3D Gaussian Splatting has demonstrated impressive novel view synthesis results, reaching high fidelity and efficiency. However, strong artifacts can be observed when changing the sampling rate, \eg, by changing focal length or camera distance. We find that the source for this phenomenon can be attributed to the lack of 3D frequency constraints and the usage of a 2D dilation filter. To address this problem, we introduce a 3D smoothing filter which constrains the size of the 3D Gaussian primitives based on the maximal sampling frequency induced by the input views, eliminating high-frequency artifacts when zooming in. Moreover, replacing 2D dilation with a 2D Mip filter, which simulates a 2D box filter, effectively mitigates aliasing and dilation issues. Our evaluation, including scenarios such a training on single-scale images and testing on multiple scales, validates the effectiveness of our approach.

Zehao Yu, Songyou Peng, Michael Niemeyer et al.

In recent years, neural implicit surface reconstruction methods have become popular for multi-view 3D reconstruction. In contrast to traditional multi-view stereo methods, these approaches tend to produce smoother and more complete reconstructions due to the inductive smoothness bias of neural networks. State-of-the-art neural implicit methods allow for high-quality reconstructions of simple scenes from many input views. Yet, their performance drops significantly for larger and more complex scenes and scenes captured from sparse viewpoints. This is caused primarily by the inherent ambiguity in the RGB reconstruction loss that does not provide enough constraints, in particular in less-observed and textureless areas. Motivated by recent advances in the area of monocular geometry prediction, we systematically explore the utility these cues provide for improving neural implicit surface reconstruction. We demonstrate that depth and normal cues, predicted by general-purpose monocular estimators, significantly improve reconstruction quality and optimization time. Further, we analyse and investigate multiple design choices for representing neural implicit surfaces, ranging from monolithic MLP models over single-grid to multi-resolution grid representations. We observe that geometric monocular priors improve performance both for small-scale single-object as well as large-scale multi-object scenes, independent of the choice of representation.

Zehao Yu, Xi Yang, Chong Dang et al.

Objective: We aim to develop an open-source natural language processing (NLP) package, SODA (i.e., SOcial DeterminAnts), with pre-trained transformer models to extract social determinants of health (SDoH) for cancer patients, examine the generalizability of SODA to a new disease domain (i.e., opioid use), and evaluate the extraction rate of SDoH using cancer populations. Methods: We identified SDoH categories and attributes and developed an SDoH corpus using clinical notes from a general cancer cohort. We compared four transformer-based NLP models to extract SDoH, examined the generalizability of NLP models to a cohort of patients prescribed with opioids, and explored customization strategies to improve performance. We applied the best NLP model to extract 19 categories of SDoH from the breast (n=7,971), lung (n=11,804), and colorectal cancer (n=6,240) cohorts. Results and Conclusion: We developed a corpus of 629 cancer patients notes with annotations of 13,193 SDoH concepts/attributes from 19 categories of SDoH. The Bidirectional Encoder Representations from Transformers (BERT) model achieved the best strict/lenient F1 scores of 0.9216 and 0.9441 for SDoH concept extraction, 0.9617 and 0.9626 for linking attributes to SDoH concepts. Fine-tuning the NLP models using new annotations from opioid use patients improved the strict/lenient F1 scores from 0.8172/0.8502 to 0.8312/0.8679. The extraction rates among 19 categories of SDoH varied greatly, where 10 SDoH could be extracted from >70% of cancer patients, but 9 SDoH had a low extraction rate (<70% of cancer patients). The SODA package with pre-trained transformer models is publicly available at https://github.com/uf-hobiinformatics-lab/SDoH_SODA.

Kashyap Chitta, Aditya Prakash, Bernhard Jaeger et al.

How should we integrate representations from complementary sensors for autonomous driving? Geometry-based fusion has shown promise for perception (e.g. object detection, motion forecasting). However, in the context of end-to-end driving, we find that imitation learning based on existing sensor fusion methods underperforms in complex driving scenarios with a high density of dynamic agents. Therefore, we propose TransFuser, a mechanism to integrate image and LiDAR representations using self-attention. Our approach uses transformer modules at multiple resolutions to fuse perspective view and bird's eye view feature maps. We experimentally validate its efficacy on a challenging new benchmark with long routes and dense traffic, as well as the official leaderboard of the CARLA urban driving simulator. At the time of submission, TransFuser outperforms all prior work on the CARLA leaderboard in terms of driving score by a large margin. Compared to geometry-based fusion, TransFuser reduces the average collisions per kilometer by 48%.

Yuting Xiao, Jingwei Xu, Zehao Yu et al.

In recent years, the neural implicit surface has emerged as a powerful representation for multi-view surface reconstruction due to its simplicity and state-of-the-art performance. However, reconstructing smooth and detailed surfaces in indoor scenes from multi-view images presents unique challenges. Indoor scenes typically contain large texture-less regions, making the photometric loss unreliable for optimizing the implicit surface. Previous work utilizes monocular geometry priors to improve the reconstruction in indoor scenes. However, monocular priors often contain substantial errors in thin structure regions due to domain gaps and the inherent inconsistencies when derived independently from different views. This paper presents \textbf{DebSDF} to address these challenges, focusing on the utilization of uncertainty in monocular priors and the bias in SDF-based volume rendering. We propose an uncertainty modeling technique that associates larger uncertainties with larger errors in the monocular priors. High-uncertainty priors are then excluded from optimization to prevent bias. This uncertainty measure also informs an importance-guided ray sampling and adaptive smoothness regularization, enhancing the learning of fine structures. We further introduce a bias-aware signed distance function to density transformation that takes into account the curvature and the angle between the view direction and the SDF normals to reconstruct fine details better. Our approach has been validated through extensive experiments on several challenging datasets, demonstrating improved qualitative and quantitative results in reconstructing thin structures in indoor scenes, thereby outperforming previous work.

Cheng Peng, Xi Yang, Zehao Yu et al.

Objective: To develop a natural language processing system that solves both clinical concept extraction and relation extraction in a unified prompt-based machine reading comprehension (MRC) architecture with good generalizability for cross-institution applications. Methods: We formulate both clinical concept extraction and relation extraction using a unified prompt-based MRC architecture and explore state-of-the-art transformer models. We compare our MRC models with existing deep learning models for concept extraction and end-to-end relation extraction using two benchmark datasets developed by the 2018 National NLP Clinical Challenges (n2c2) challenge (medications and adverse drug events) and the 2022 n2c2 challenge (relations of social determinants of health [SDoH]). We also evaluate the transfer learning ability of the proposed MRC models in a cross-institution setting. We perform error analyses and examine how different prompting strategies affect the performance of MRC models. Results and Conclusion: The proposed MRC models achieve state-of-the-art performance for clinical concept and relation extraction on the two benchmark datasets, outperforming previous non-MRC transformer models. GatorTron-MRC achieves the best strict and lenient F1-scores for concept extraction, outperforming previous deep learning models on the two datasets by 1%~3% and 0.7%~1.3%, respectively. For end-to-end relation extraction, GatorTron-MRC and BERT-MIMIC-MRC achieve the best F1-scores, outperforming previous deep learning models by 0.9%~2.4% and 10%-11%, respectively. For cross-institution evaluation, GatorTron-MRC outperforms traditional GatorTron by 6.4% and 16% for the two datasets, respectively. The proposed method is better at handling nested/overlapped concepts, extracting relations, and has good portability for cross-institute applications.

Aman Pathak, Zehao Yu, Daniel Paredes et al.

The ultrasound characteristics of thyroid nodules guide the evaluation of thyroid cancer in patients with thyroid nodules. However, the characteristics of thyroid nodules are often documented in clinical narratives such as ultrasound reports. Previous studies have examined natural language processing (NLP) methods in extracting a limited number of characteristics (<9) using rule-based NLP systems. In this study, a multidisciplinary team of NLP experts and thyroid specialists, identified thyroid nodule characteristics that are important for clinical care, composed annotation guidelines, developed a corpus, and compared 5 state-of-the-art transformer-based NLP methods, including BERT, RoBERTa, LongFormer, DeBERTa, and GatorTron, for extraction of thyroid nodule characteristics from ultrasound reports. Our GatorTron model, a transformer-based large language model trained using over 90 billion words of text, achieved the best strict and lenient F1-score of 0.8851 and 0.9495 for the extraction of a total number of 16 thyroid nodule characteristics, and 0.9321 for linking characteristics to nodules, outperforming other clinical transformer models. To the best of our knowledge, this is the first study to systematically categorize and apply transformer-based NLP models to extract a large number of clinical relevant thyroid nodule characteristics from ultrasound reports. This study lays ground for assessing the documentation quality of thyroid ultrasound reports and examining outcomes of patients with thyroid nodules using electronic health records.

Aokun Chen, Zehao Yu, Xi Yang et al.

Objective: To develop a natural language processing (NLP) system to extract medications and contextual information that help understand drug changes. This project is part of the 2022 n2c2 challenge. Materials and methods: We developed NLP systems for medication mention extraction, event classification (indicating medication changes discussed or not), and context classification to classify medication changes context into 5 orthogonal dimensions related to drug changes. We explored 6 state-of-the-art pretrained transformer models for the three subtasks, including GatorTron, a large language model pretrained using >90 billion words of text (including >80 billion words from >290 million clinical notes identified at the University of Florida Health). We evaluated our NLP systems using annotated data and evaluation scripts provided by the 2022 n2c2 organizers. Results:Our GatorTron models achieved the best F1-scores of 0.9828 for medication extraction (ranked 3rd), 0.9379 for event classification (ranked 2nd), and the best micro-average accuracy of 0.9126 for context classification. GatorTron outperformed existing transformer models pretrained using smaller general English text and clinical text corpora, indicating the advantage of large language models. Conclusion: This study demonstrated the advantage of using large transformer models for contextual medication information extraction from clinical narratives.

Cheng Peng, Xi Yang, Kaleb E Smith et al.

Objective To develop soft prompt-based learning algorithms for large language models (LLMs), examine the shape of prompts, prompt-tuning using frozen/unfrozen LLMs, transfer learning, and few-shot learning abilities. Methods We developed a soft prompt-based LLM model and compared 4 training strategies including (1) fine-tuning without prompts; (2) hard-prompt with unfrozen LLMs; (3) soft-prompt with unfrozen LLMs; and (4) soft-prompt with frozen LLMs. We evaluated 7 pretrained LLMs using the 4 training strategies for clinical concept and relation extraction on two benchmark datasets. We evaluated the transfer learning ability of the prompt-based learning algorithms in a cross-institution setting. We also assessed the few-shot learning ability. Results and Conclusion When LLMs are unfrozen, GatorTron-3.9B with soft prompting achieves the best strict F1-scores of 0.9118 and 0.8604 for concept extraction, outperforming the traditional fine-tuning and hard prompt-based models by 0.6~3.1% and 1.2~2.9%, respectively; GatorTron-345M with soft prompting achieves the best F1-scores of 0.8332 and 0.7488 for end-to-end relation extraction, outperforming the other two models by 0.2~2% and 0.6~11.7%, respectively. When LLMs are frozen, small (i.e., 345 million parameters) LLMs have a big gap to be competitive with unfrozen models; scaling LLMs up to billions of parameters makes frozen LLMs competitive with unfrozen LLMs. For cross-institute evaluation, soft prompting with a frozen GatorTron-8.9B model achieved the best performance. This study demonstrates that (1) machines can learn soft prompts better than humans, (2) frozen LLMs have better few-shot learning ability and transfer learning ability to facilitate muti-institution applications, and (3) frozen LLMs require large models.

Aokun Chen, Daniel Paredes, Zehao Yu et al.

Delirium is an acute decline or fluctuation in attention, awareness, or other cognitive function that can lead to serious adverse outcomes. Despite the severe outcomes, delirium is frequently unrecognized and uncoded in patients' electronic health records (EHRs) due to its transient and diverse nature. Natural language processing (NLP), a key technology that extracts medical concepts from clinical narratives, has shown great potential in studies of delirium outcomes and symptoms. To assist in the diagnosis and phenotyping of delirium, we formed an expert panel to categorize diverse delirium symptoms, composed annotation guidelines, created a delirium corpus with diverse delirium symptoms, and developed NLP methods to extract delirium symptoms from clinical notes. We compared 5 state-of-the-art transformer models including 2 models (BERT and RoBERTa) from the general domain and 3 models (BERT_MIMIC, RoBERTa_MIMIC, and GatorTron) from the clinical domain. GatorTron achieved the best strict and lenient F1 scores of 0.8055 and 0.8759, respectively. We conducted an error analysis to identify challenges in annotating delirium symptoms and developing NLP systems. To the best of our knowledge, this is the first large language model-based delirium symptom extraction system. Our study lays the foundation for the future development of computable phenotypes and diagnosis methods for delirium.

Binbin Huang, Zehao Yu, Anpei Chen et al.

3D Gaussian Splatting (3DGS) has recently revolutionized radiance field reconstruction, achieving high quality novel view synthesis and fast rendering speed without baking. However, 3DGS fails to accurately represent surfaces due to the multi-view inconsistent nature of 3D Gaussians. We present 2D Gaussian Splatting (2DGS), a novel approach to model and reconstruct geometrically accurate radiance fields from multi-view images. Our key idea is to collapse the 3D volume into a set of 2D oriented planar Gaussian disks. Unlike 3D Gaussians, 2D Gaussians provide view-consistent geometry while modeling surfaces intrinsically. To accurately recover thin surfaces and achieve stable optimization, we introduce a perspective-correct 2D splatting process utilizing ray-splat intersection and rasterization. Additionally, we incorporate depth distortion and normal consistency terms to further enhance the quality of the reconstructions. We demonstrate that our differentiable renderer allows for noise-free and detailed geometry reconstruction while maintaining competitive appearance quality, fast training speed, and real-time rendering.

Zehao Yu, Torsten Sattler, Andreas Geiger

Recently, 3D Gaussian Splatting (3DGS) has demonstrated impressive novel view synthesis results, while allowing the rendering of high-resolution images in real-time. However, leveraging 3D Gaussians for surface reconstruction poses significant challenges due to the explicit and disconnected nature of 3D Gaussians. In this work, we present Gaussian Opacity Fields (GOF), a novel approach for efficient, high-quality, and adaptive surface reconstruction in unbounded scenes. Our GOF is derived from ray-tracing-based volume rendering of 3D Gaussians, enabling direct geometry extraction from 3D Gaussians by identifying its levelset, without resorting to Poisson reconstruction or TSDF fusion as in previous work. We approximate the surface normal of Gaussians as the normal of the ray-Gaussian intersection plane, enabling the application of regularization that significantly enhances geometry. Furthermore, we develop an efficient geometry extraction method utilizing Marching Tetrahedra, where the tetrahedral grids are induced from 3D Gaussians and thus adapt to the scene's complexity. Our evaluations reveal that GOF surpasses existing 3DGS-based methods in surface reconstruction and novel view synthesis. Further, it compares favorably to or even outperforms, neural implicit methods in both quality and speed.

Xi Yang, Zehao Yu, Yi Guo et al.

The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in the clinical domain. We developed a series of clinical RE models based on three transformer architectures, namely BERT, RoBERTa, and XLNet. We evaluated these models using 2 publicly available datasets from 2018 MADE1.0 and 2018 n2c2 challenges. We compared two classification strategies (binary vs. multi-class classification) and investigated two approaches to generate candidate relations in different experimental settings. In this study, we compared three transformer-based (BERT, RoBERTa, and XLNet) models for relation extraction. We demonstrated that the RoBERTa-clinical RE model achieved the best performance on the 2018 MADE1.0 dataset with an F1-score of 0.8958. On the 2018 n2c2 dataset, the XLNet-clinical model achieved the best F1-score of 0.9610. Our results indicated that the binary classification strategy consistently outperformed the multi-class classification strategy for clinical relation extraction. Our methods and models are publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction. We believe this work will improve current practice on clinical relation extraction and other related NLP tasks in the biomedical domain.

Dongze Lian, Zehao Yu, Xing Sun et al.

An Axial Shifted MLP architecture (AS-MLP) is proposed in this paper. Different from MLP-Mixer, where the global spatial feature is encoded for information flow through matrix transposition and one token-mixing MLP, we pay more attention to the local features interaction. By axially shifting channels of the feature map, AS-MLP is able to obtain the information flow from different axial directions, which captures the local dependencies. Such an operation enables us to utilize a pure MLP architecture to achieve the same local receptive field as CNN-like architecture. We can also design the receptive field size and dilation of blocks of AS-MLP, etc, in the same spirit of convolutional neural networks. With the proposed AS-MLP architecture, our model obtains 83.3% Top-1 accuracy with 88M parameters and 15.2 GFLOPs on the ImageNet-1K dataset. Such a simple yet effective architecture outperforms all MLP-based architectures and achieves competitive performance compared to the transformer-based architectures (e.g., Swin Transformer) even with slightly lower FLOPs. In addition, AS-MLP is also the first MLP-based architecture to be applied to the downstream tasks (e.g., object detection and semantic segmentation). The experimental results are also impressive. Our proposed AS-MLP obtains 51.5 mAP on the COCO validation set and 49.5 MS mIoU on the ADE20K dataset, which is competitive compared to the transformer-based architectures. Our AS-MLP establishes a strong baseline of MLP-based architecture. Code is available at https://github.com/svip-lab/AS-MLP.

Zehao Yu, Lei Jin, Shenghua Gao

This paper tackles the unsupervised depth estimation task in indoor environments. The task is extremely challenging because of the vast areas of non-texture regions in these scenes. These areas could overwhelm the optimization process in the commonly used unsupervised depth estimation framework proposed for outdoor environments. However, even when those regions are masked out, the performance is still unsatisfactory. In this paper, we argue that the poor performance suffers from the non-discriminative point-based matching. To this end, we propose P$^2$Net. We first extract points with large local gradients and adopt patches centered at each point as its representation. Multiview consistency loss is then defined over patches. This operation significantly improves the robustness of the network training. Furthermore, because those textureless regions in indoor scenes (e.g., wall, floor, roof, \etc) usually correspond to planar regions, we propose to leverage superpixels as a plane prior. We enforce the predicted depth to be well fitted by a plane within each superpixel. Extensive experiments on NYUv2 and ScanNet show that our P$^2$Net outperforms existing approaches by a large margin. Code is available at \url{https://github.com/svip-lab/Indoor-SfMLearner}.

Zehao Yu, Shenghua Gao

Almost all previous deep learning-based multi-view stereo (MVS) approaches focus on improving reconstruction quality. Besides quality, efficiency is also a desirable feature for MVS in real scenarios. Towards this end, this paper presents a Fast-MVSNet, a novel sparse-to-dense coarse-to-fine framework, for fast and accurate depth estimation in MVS. Specifically, in our Fast-MVSNet, we first construct a sparse cost volume for learning a sparse and high-resolution depth map. Then we leverage a small-scale convolutional neural network to encode the depth dependencies for pixels within a local region to densify the sparse high-resolution depth map. At last, a simple but efficient Gauss-Newton layer is proposed to further optimize the depth map. On one hand, the high-resolution depth map, the data-adaptive propagation method and the Gauss-Newton layer jointly guarantee the effectiveness of our method. On the other hand, all modules in our Fast-MVSNet are lightweight and thus guarantee the efficiency of our approach. Besides, our approach is also memory-friendly because of the sparse depth representation. Extensive experimental results show that our method is 5$\times$ and 14$\times$ faster than Point-MVSNet and R-MVSNet, respectively, while achieving comparable or even better results on the challenging Tanks and Temples dataset as well as the DTU dataset. Code is available at https://github.com/svip-lab/FastMVSNet.

Dongze Lian, Zehao Yu, Shenghua Gao

By borrowing the wisdom of human in gaze following, we propose a two-stage solution for gaze point prediction of the target persons in a scene. Specifically, in the first stage, both head image and its position are fed into a gaze direction pathway to predict the gaze direction, and then multi-scale gaze direction fields are generated to characterize the distribution of gaze points without considering the scene contents. In the second stage, the multi-scale gaze direction fields are concatenated with the image contents and fed into a heatmap pathway for heatmap regression. There are two merits for our two-stage solution based gaze following: i) our solution mimics the behavior of human in gaze following, therefore it is more psychological plausible; ii) besides using heatmap to supervise the output of our network, we can also leverage gaze direction to facilitate the training of gaze direction pathway, therefore our network can be more robustly trained. Considering that existing gaze following dataset is annotated by the third-view persons, we build a video gaze following dataset, where the ground truth is annotated by the observers in the videos. Therefore it is more reliable. The evaluation with such a dataset reflects the capacity of different methods in real scenarios better. Extensive experiments on both datasets show that our method significantly outperforms existing methods, which validates the effectiveness of our solution for gaze following. Our dataset and codes are released in https://github.com/svip-lab/GazeFollowing.

Zehao Yu, Jia Zheng, Dongze Lian et al.

Single-image piece-wise planar 3D reconstruction aims to simultaneously segment plane instances and recover 3D plane parameters from an image. Most recent approaches leverage convolutional neural networks (CNNs) and achieve promising results. However, these methods are limited to detecting a fixed number of planes with certain learned order. To tackle this problem, we propose a novel two-stage method based on associative embedding, inspired by its recent success in instance segmentation. In the first stage, we train a CNN to map each pixel to an embedding space where pixels from the same plane instance have similar embeddings. Then, the plane instances are obtained by grouping the embedding vectors in planar regions via an efficient mean shift clustering algorithm. In the second stage, we estimate the parameter for each plane instance by considering both pixel-level and instance-level consistencies. With the proposed method, we are able to detect an arbitrary number of planes. Extensive experiments on public datasets validate the effectiveness and efficiency of our method. Furthermore, our method runs at 30 fps at the testing time, thus could facilitate many real-time applications such as visual SLAM and human-robot interaction. Code is available at https://github.com/svip-lab/PlanarReconstruction.

Cheng Peng, Xi Yang, Aokun Chen et al.

Objective To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning. Methods We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (i.e., trainable vectors) with frozen LLM, where the LLM parameters were not updated (i.e., frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models. Results and Conclusion The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ~3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4~10% for clinical abbreviation disambiguation, and 5.5~9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the ``one model for all`` promise from training to deployment using a unified generative LLM.

Chong Bao, Xiyu Zhang, Zehao Yu et al.

Neural rendering has demonstrated remarkable success in high-quality 3D neural reconstruction and novel view synthesis with dense input views and accurate poses. However, applying it to extremely sparse, unposed views in unbounded 360° scenes remains a challenging problem. In this paper, we propose a novel neural rendering framework to accomplish the unposed and extremely sparse-view 3D reconstruction in unbounded 360° scenes. To resolve the spatial ambiguity inherent in unbounded scenes with sparse input views, we propose a layered Gaussian-based representation to effectively model the scene with distinct spatial layers. By employing a dense stereo reconstruction model to recover coarse geometry, we introduce a layer-specific bootstrap optimization to refine the noise and fill occluded regions in the reconstruction. Furthermore, we propose an iterative fusion of reconstruction and generation alongside an uncertainty-aware training approach to facilitate mutual conditioning and enhancement between these two processes. Comprehensive experiments show that our approach outperforms existing state-of-the-art methods in terms of rendering quality and surface reconstruction accuracy. Project page: https://zju3dv.github.io/free360/

Cheng Peng, Zehao Yu, Kaleb E Smith et al.

The progress in natural language processing (NLP) using large language models (LLMs) has greatly improved patient information extraction from clinical narratives. However, most methods based on the fine-tuning strategy have limited transfer learning ability for cross-domain applications. This study proposed a novel approach that employs a soft prompt-based learning architecture, which introduces trainable prompts to guide LLMs toward desired outputs. We examined two types of LLM architectures, including encoder-only GatorTron and decoder-only GatorTronGPT, and evaluated their performance for the extraction of social determinants of health (SDoH) using a cross-institution dataset from the 2022 n2c2 challenge and a cross-disease dataset from the University of Florida (UF) Health. The results show that decoder-only LLMs with prompt tuning achieved better performance in cross-domain applications. GatorTronGPT achieved the best F1 scores for both datasets, outperforming traditional fine-tuned GatorTron by 8.9% and 21.8% in a cross-institution setting, and 5.5% and 14.5% in a cross-disease setting.

Zehao Yu, Xi Yang, Chong Dang et al.

Social and behavioral determinants of health (SBDoH) have important roles in shaping people's health. In clinical research studies, especially comparative effectiveness studies, failure to adjust for SBDoH factors will potentially cause confounding issues and misclassification errors in either statistical analyses and machine learning-based models. However, there are limited studies to examine SBDoH factors in clinical outcomes due to the lack of structured SBDoH information in current electronic health record (EHR) systems, while much of the SBDoH information is documented in clinical narratives. Natural language processing (NLP) is thus the key technology to extract such information from unstructured clinical text. However, there is not a mature clinical NLP system focusing on SBDoH. In this study, we examined two state-of-the-art transformer-based NLP models, including BERT and RoBERTa, to extract SBDoH concepts from clinical narratives, applied the best performing model to extract SBDoH concepts on a lung cancer screening patient cohort, and examined the difference of SBDoH information between NLP extracted results and structured EHRs (SBDoH information captured in standard vocabularies such as the International Classification of Diseases codes). The experimental results show that the BERT-based NLP model achieved the best strict/lenient F1-score of 0.8791 and 0.8999, respectively. The comparison between NLP extracted SBDoH information and structured EHRs in the lung cancer patient cohort of 864 patients with 161,933 various types of clinical notes showed that much more detailed information about smoking, education, and employment were only captured in clinical narratives and that it is necessary to use both clinical narratives and structured EHRs to construct a more complete picture of patients' SBDoH factors.