SPARS3R: Semantic Prior Alignment and Regularization for Sparse 3D Reconstruction

Recent efforts in Gaussian-Splat-based Novel View Synthesis can achieve photorealistic rendering; however, such capability is limited in sparse-view scenarios due to sparse initialization and over-fitting floaters. Recent progress in depth estimation and alignment can provide dense point cloud with few views; however, the resulting pose accuracy is suboptimal. In this work, we present SPARS3R, which combines the advantages of accurate pose estimation from Structure-from-Motion and dense point cloud from depth estimation. To this end, SPARS3R first performs a Global Fusion Alignment process that maps a prior dense point cloud to a sparse point cloud from Structure-from-Motion based on triangulated correspondences. RANSAC is applied during this process to distinguish inliers and outliers. SPARS3R then performs a second, Semantic Outlier Alignment step, which extracts semantically coherent regions around the outliers and performs local alignment in these regions. Along with several improvements in the evaluation process, we demonstrate that SPARS3R can achieve photorealistic rendering with sparse images and significantly outperforms existing approaches.

DreamCraft3D++: Efficient Hierarchical 3D Generation with Multi-Plane Reconstruction Model

We introduce DreamCraft3D++, an extension of DreamCraft3D that enables efficient high-quality generation of complex 3D assets. DreamCraft3D++ inherits the multi-stage generation process of DreamCraft3D, but replaces the time-consuming geometry sculpting optimization with a feed-forward multi-plane based reconstruction model, speeding up the process by 1000x. For texture refinement, we propose a training-free IP-Adapter module that is conditioned on the enhanced multi-view images to enhance texture and geometry consistency, providing a 4x faster alternative to DreamCraft3D's DreamBooth fine-tuning. Experiments on diverse datasets demonstrate DreamCraft3D++'s ability to generate creative 3D assets with intricate geometry and realistic 360{\deg} textures, outperforming state-of-the-art image-to-3D methods in quality and speed. The full implementation will be open-sourced to enable new possibilities in 3D content creation.

OneGen: Efficient One-Pass Unified Generation and Retrieval for LLMs

Despite the recent advancements in Large Language Models (LLMs), which have significantly enhanced the generative capabilities for various NLP tasks, LLMs still face limitations in directly handling retrieval tasks. However, many practical applications demand the seamless integration of both retrieval and generation. This paper introduces a novel and efficient One-pass Generation and retrieval framework (OneGen), designed to improve LLMs' performance on tasks that require both generation and retrieval. The proposed framework bridges the traditionally separate training approaches for generation and retrieval by incorporating retrieval tokens generated autoregressively. This enables a single LLM to handle both tasks simultaneously in a unified forward pass. We conduct experiments on two distinct types of composite tasks, RAG and Entity Linking, to validate the pluggability, effectiveness, and efficiency of OneGen in training and inference. Furthermore, our results show that integrating generation and retrieval within the same context preserves the generative capabilities of LLMs while improving retrieval performance. To the best of our knowledge, OneGen is the first to enable LLMs to conduct vector retrieval during the generation.

Drone-assisted Road Gaussian Splatting with Cross-view Uncertainty

Robust and realistic rendering for large-scale road scenes is essential in autonomous driving simulation. Recently, 3D Gaussian Splatting (3D-GS) has made groundbreaking progress in neural rendering, but the general fidelity of large-scale road scene renderings is often limited by the input imagery, which usually has a narrow field of view and focuses mainly on the street-level local area. Intuitively, the data from the drone's perspective can provide a complementary viewpoint for the data from the ground vehicle's perspective, enhancing the completeness of scene reconstruction and rendering. However, training naively with aerial and ground images, which exhibit large view disparity, poses a significant convergence challenge for 3D-GS, and does not demonstrate remarkable improvements in performance on road views. In order to enhance the novel view synthesis of road views and to effectively use the aerial information, we design an uncertainty-aware training method that allows aerial images to assist in the synthesis of areas where ground images have poor learning outcomes instead of weighting all pixels equally in 3D-GS training like prior work did. We are the first to introduce the cross-view uncertainty to 3D-GS by matching the car-view ensemble-based rendering uncertainty to aerial images, weighting the contribution of each pixel to the training process. Additionally, to systematically quantify evaluation metrics, we assemble a high-quality synthesized dataset comprising both aerial and ground images for road scenes.

PhaGO: Protein function annotation for bacteriophages by integrating the genomic context

Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, PhaGO surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. PhaGO can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of PhaGO by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of PhaGO to extend our understanding of newly discovered phages.

UF-HOBI at "Discharge Me!": A Hybrid Solution for Discharge Summary Generation Through Prompt-based Tuning of GatorTronGPT Models

Automatic generation of discharge summaries presents significant challenges due to the length of clinical documentation, the dispersed nature of patient information, and the diverse terminology used in healthcare. This paper presents a hybrid solution for generating discharge summary sections as part of our participation in the "Discharge Me!" Challenge at the BioNLP 2024 Shared Task. We developed a two-stage generation method using both extractive and abstractive techniques, in which we first apply name entity recognition (NER) to extract key clinical concepts, which are then used as input for a prompt-tuning-based GatorTronGPT model to generate coherent text for two important sections including "Brief Hospital Course" and "Discharge Instructions". Our system was ranked 5th in this challenge, achieving an overall score of 0.284. The results demonstrate the effectiveness of our hybrid solution in improving the quality of automated discharge section generation.

Rateless Stochastic Coding for Delay-constrained Semantic Communication

We consider the problem of joint source-channel coding with distortion and perception constraints from a rateless perspective, the purpose of which is to settle the balance between reliability (distortion/perception) and effectiveness (rate) of transmission over uncertain channels. We find a new finite-blocklength bound for the achievable joint source-channel code rate with the above two constraints. To achieve a superior rateless characteristic of JSCC coding, we perform multi-level optimization on various finite-blocklength codes. Based on these two, we then propose a new JSCC coding scheme called rateless stochastic coding (RSC). We experimentally demonstrate that the proposed RSC can achieve variable rates of transmission maintaining an excellent trade-off between distortion and perception.

LP-3DGS: Learning to Prune 3D Gaussian Splatting

Recently, 3D Gaussian Splatting (3DGS) has become one of the mainstream methodologies for novel view synthesis (NVS) due to its high quality and fast rendering speed. However, as a point-based scene representation, 3DGS potentially generates a large number of Gaussians to fit the scene, leading to high memory usage. Improvements that have been proposed require either an empirical and preset pruning ratio or importance score threshold to prune the point cloud. Such hyperparamter requires multiple rounds of training to optimize and achieve the maximum pruning ratio, while maintaining the rendering quality for each scene. In this work, we propose learning-to-prune 3DGS (LP-3DGS), where a trainable binary mask is applied to the importance score that can find optimal pruning ratio automatically. Instead of using the traditional straight-through estimator (STE) method to approximate the binary mask gradient, we redesign the masking function to leverage the Gumbel-Sigmoid method, making it differentiable and compatible with the existing training process of 3DGS. Extensive experiments have shown that LP-3DGS consistently produces a good balance that is both efficient and high quality.

Improving Generalizability of Extracting Social Determinants of Health Using Large Language Models through Prompt-tuning

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.

Automatic Summarization of Doctor-Patient Encounter Dialogues Using Large Language Model through Prompt Tuning

Automatic text summarization (ATS) is an emerging technology to assist clinicians in providing continuous and coordinated care. This study presents an approach to summarize doctor-patient dialogues using generative large language models (LLMs). We developed prompt-tuning algorithms to instruct generative LLMs to summarize clinical text. We examined the prompt-tuning strategies, the size of soft prompts, and the few-short learning ability of GatorTronGPT, a generative clinical LLM developed using 277 billion clinical and general English words with up to 20 billion parameters. We compared GatorTronGPT with a previous solution based on fine-tuning of a widely used T5 model, using a clinical benchmark dataset MTS-DIALOG. The experimental results show that the GatorTronGPT- 20B model achieved the best performance on all evaluation metrics. The proposed solution has a low computing cost as the LLM parameters are not updated during prompt-tuning. This study demonstrates the efficiency of generative clinical LLMs for clinical ATS through prompt tuning.