OpenRaiser/Intern-Atlas huggingface dataset:
ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
Venue: arXiv cs.LG 2024
Year: 2024

Deep learning approaches achieved significant progress in predicting protein structures. These methods are often applied to protein-protein interactions (PPIs) yet require Multiple Sequence Alignment (MSA) which is unavailable for various interactions, such as antibody-antigen. Computational docking methods are capable of sampling accurate complex models, but also produce thousands of invalid configurations. The design of scoring functions for identifying accurate models is a long-standing challenge. We develop a novel attention-based Graph Neural Network (GNN), ContactNet, for classifying PPI models obtained from docking algorithms into accurate and incorrect ones. When trained on docked antigen and modeled antibody structures, ContactNet doubles the accuracy of current state-of-the-art scoring functions, achieving accurate models among its Top-10 at 43% of the test cases. When applied to unbound antibodies, its Top-10 accuracy increases to 65%. This performance is achieved without MSA and the approach is applicable to other types of interactions, such as host-pathogens or general PPIs.
The Effects of Data Split Strategies on the Offline Experiments for CTR Prediction
Venue: arXiv cs.IR 2024
Year: 2024

Click-through rate (CTR) prediction is a crucial task in online advertising to recommend products that users are likely to be interested in. To identify the best-performing models, rigorous model evaluation is necessary. Offline experimentation plays a significant role in selecting models for live user-item interactions, despite the value of online experimentation like A/B testing, which has its own limitations and risks. Often, the correlation between offline performance metrics and actual online model performance is inadequate. One main reason for this discrepancy is the common practice of using random splits to create training, validation, and test datasets in CTR prediction. In contrast, real-world CTR prediction follows a temporal order. Therefore, the methodology used in offline evaluation, particularly the data splitting strategy, is crucial. This study aims to address the inconsistency between current offline evaluation methods and real-world use cases, by focusing on data splitting strategies. To examine the impact of different data split strategies on offline performance, we conduct extensive experiments using both random and temporal splits on a large open benchmark dataset, Criteo.
Themis: A Reference-free NLG Evaluation Language Model with Flexibility and Interpretability
Venue: arXiv cs.CL 2024
Year: 2024

The evaluation of natural language generation (NLG) tasks is a significant and longstanding research area. With the recent emergence of powerful large language models (LLMs), some studies have turned to LLM-based automatic evaluation methods, which demonstrate great potential to become a new evaluation paradigm following traditional string-based and model-based metrics. However, despite the improved performance of existing methods, they still possess some deficiencies, such as dependency on references and limited evaluation flexibility. Therefore, in this paper, we meticulously construct a large-scale NLG evaluation corpus NLG-Eval with annotations from both human and GPT-4 to alleviate the lack of relevant data in this field. Furthermore, we propose Themis, an LLM dedicated to NLG evaluation, which has been trained with our designed multi-perspective consistency verification and rating-oriented preference alignment methods. Themis can conduct flexible and interpretable evaluations without references, and it exhibits superior evaluation performance on various NLG tasks, simultaneously generalizing well to unseen tasks and surpassing other evaluation models, including GPT-4.
Blockchain Based Zero-Knowledge Proof of Location in IoT
Venue: arXiv cs.CR 2024
Year: 2024

With the development of precise positioning technology, a growing number of location-based services (LBSs) facilitate people's life. Most LBSs require proof of location (PoL) to prove that the user satisfies the service requirement, which exposes the user's privacy. In this paper, we propose a zero-knowledge proof of location (zk-PoL) protocol to better protect the user's privacy. With the zk-PoL protocol, the user can choose necessary information to expose to the server, so that hierarchical privacy protection can be achieved. The evaluation shows that the zk-PoL has excellent security to resist main attacks, moreover the computational efficiency is independent of input parameters and the zk-PoL is appropriate to delay-tolerant LBSs.
Repeat and Concatenate: 2D to 3D Image Translation with 3D to 3D Generative Modeling
Venue: arXiv cs.CV 2024
Year: 2024

This paper investigates a 2D to 3D image translation method with a straightforward technique, enabling correlated 2D X-ray to 3D CT-like reconstruction. We observe that existing approaches, which integrate information across multiple 2D views in the latent space, lose valuable signal information during latent encoding. Instead, we simply repeat and concatenate the 2D views into higher-channel 3D volumes and approach the 3D reconstruction challenge as a straightforward 3D to 3D generative modeling problem, sidestepping several complex modeling issues. This method enables the reconstructed 3D volume to retain valuable information from the 2D inputs, which are passed between channel states in a Swin UNETR backbone. Our approach applies neural optimal transport, which is fast and stable to train, effectively integrating signal information across multiple views without the requirement for precise alignment; it produces non-collapsed reconstructions that are highly faithful to the 2D views, even after limited training. We demonstrate correlated results, both qualitatively and quantitatively, having trained our model on a single dataset and evaluated its generalization ability across six datasets, including out-of-distribution samples.
Sum-of-Squares Lower Bounds for Independent Set in Ultra-Sparse Random Graphs
Venue: arXiv cs.DS 2024
Year: 2024

We prove that for every $D \in \N$, and large enough constant $d \in \N$, with high probability over the choice of $G \sim G(n,d/n)$, the \Erdos-\Renyi random graph distribution, the canonical degree $2D$ Sum-of-Squares relaxation fails to certify that the largest independent set in $G$ is of size $o(\frac{n}{\sqrt{d} D^4})$. In particular, degree $D$ sum-of-squares strengthening can reduce the integrality gap of the classical \Lovasz theta SDP relaxation by at most a $O(D^4)$ factor. This is the first lower bound for $>4$-degree Sum-of-Squares (SoS) relaxation for any problems on \emph{ultra sparse} random graphs (i.e. average degree of an absolute constant). Such ultra-sparse graphs were a known barrier for previous methods and explicitly identified as a major open direction (e.g.,~\cite{deshpande2019threshold, kothari2021stressfree}). Indeed, the only other example of an SoS lower bound on ultra-sparse random graphs was a degree-4 lower bound for Max-Cut. Our main technical result is a new method to obtain spectral norm estimates on graph matrices (a class of low-degree matrix-valued polynomials in $G(n,d/n)$) that are accurate to within an absolute constant factor. All prior works lose $\poly log n$ factors that trivialize any lower bound on $o(\log n)$-degree random graphs. We combine these new bounds with several upgrades on the machinery for analyzing lower-bound witnesses constructed by pseudo-calibration so that our analysis does not lose any $ω(1)$-factors that would trivialize our results. In addition to other SoS lower bounds, we believe that our methods for establishing spectral norm estimates on graph matrices will be useful in the analyses of numerical algorithms on average-case inputs.
GaussianDreamerPro: Text to Manipulable 3D Gaussians with Highly Enhanced Quality
Venue: arXiv cs.CV 2024
Year: 2024

Recently, 3D Gaussian splatting (3D-GS) has achieved great success in reconstructing and rendering real-world scenes. To transfer the high rendering quality to generation tasks, a series of research works attempt to generate 3D-Gaussian assets from text. However, the generated assets have not achieved the same quality as those in reconstruction tasks. We observe that Gaussians tend to grow without control as the generation process may cause indeterminacy. Aiming at highly enhancing the generation quality, we propose a novel framework named GaussianDreamerPro. The main idea is to bind Gaussians to reasonable geometry, which evolves over the whole generation process. Along different stages of our framework, both the geometry and appearance can be enriched progressively. The final output asset is constructed with 3D Gaussians bound to mesh, which shows significantly enhanced details and quality compared with previous methods. Notably, the generated asset can also be seamlessly integrated into downstream manipulation pipelines, e.g. animation, composition, and simulation etc., greatly promoting its potential in wide applications. Demos are available at https://taoranyi.com/gaussiandreamerpro/.
Robust Surgical Phase Recognition From Annotation Efficient Supervision
Venue: arXiv cs.CV 2024
Year: 2024

Surgical phase recognition is a key task in computer-assisted surgery, aiming to automatically identify and categorize the different phases within a surgical procedure. Despite substantial advancements, most current approaches rely on fully supervised training, requiring expensive and time-consuming frame-level annotations. Timestamp supervision has recently emerged as a promising alternative, significantly reducing annotation costs while maintaining competitive performance. However, models trained on timestamp annotations can be negatively impacted by missing phase annotations, leading to a potential drawback in real-world scenarios. In this work, we address this issue by proposing a robust method for surgical phase recognition that can handle missing phase annotations effectively. Furthermore, we introduce the SkipTag@K annotation approach to the surgical domain, enabling a flexible balance between annotation effort and model performance. Our method achieves competitive results on two challenging datasets, demonstrating its efficacy in handling missing phase annotations and its potential for reducing annotation costs. Specifically, we achieve an accuracy of 85.1\% on the MultiBypass140 dataset using only 3 annotated frames per video, showcasing the effectiveness of our method and the potential of the SkipTag@K setup. We perform extensive experiments to validate the robustness of our method and provide valuable insights to guide future research in surgical phase recognition. Our work contributes to the advancement of surgical workflow recognition and paves the way for more efficient and reliable surgical phase recognition systems.
TexPainter: Generative Mesh Texturing with Multi-view Consistency
Venue: arXiv cs.CV 2024
Year: 2024

The recent success of pre-trained diffusion models unlocks the possibility of the automatic generation of textures for arbitrary 3D meshes in the wild. However, these models are trained in the screen space, while converting them to a multi-view consistent texture image poses a major obstacle to the output quality. In this paper, we propose a novel method to enforce multi-view consistency. Our method is based on the observation that latent space in a pre-trained diffusion model is noised separately for each camera view, making it difficult to achieve multi-view consistency by directly manipulating the latent codes. Based on the celebrated Denoising Diffusion Implicit Models (DDIM) scheme, we propose to use an optimization-based color-fusion to enforce consistency and indirectly modify the latent codes by gradient back-propagation. Our method further relaxes the sequential dependency assumption among the camera views. By evaluating on a series of general 3D models, we find our simple approach improves consistency and overall quality of the generated textures as compared to competing state-of-the-arts. Our implementation is available at: https://github.com/Quantuman134/TexPainter
Refining 3D Point Cloud Normal Estimation via Sample Selection
Venue: arXiv cs.CV 2024
Year: 2024

In recent years, point cloud normal estimation, as a classical and foundational algorithm, has garnered extensive attention in the field of 3D geometric processing. Despite the remarkable performance achieved by current Neural Network-based methods, their robustness is still influenced by the quality of training data and the models' performance. In this study, we designed a fundamental framework for normal estimation, enhancing existing model through the incorporation of global information and various constraint mechanisms. Additionally, we employed a confidence-based strategy to select the reasonable samples for fair and robust network training. The introduced sample confidence can be integrated into the loss function to balance the influence of different samples on model training. Finally, we utilized existing orientation methods to correct estimated non-oriented normals, achieving state-of-the-art performance in both oriented and non-oriented tasks. Extensive experimental results demonstrate that our method works well on the widely used benchmarks.
Generative AI Empowered LiDAR Point Cloud Generation with Multimodal Transformer
Venue: arXiv cs.CV 2024
Year: 2024

Integrated sensing and communications is a key enabler for the 6G wireless communication systems. The multiple sensing modalities will allow the base station to have a more accurate representation of the environment, leading to context-aware communications. Some widely equipped sensors such as cameras and RADAR sensors can provide some environmental perceptions. However, they are not enough to generate precise environmental representations, especially in adverse weather conditions. On the other hand, the LiDAR sensors provide more accurate representations, however, their widespread adoption is hindered by their high cost. This paper proposes a novel approach to enhance the wireless communication systems by synthesizing LiDAR point clouds from images and RADAR data. Specifically, it uses a multimodal transformer architecture and pre-trained encoding models to enable an accurate LiDAR generation. The proposed framework is evaluated on the DeepSense 6G dataset, which is a real-world dataset curated for context-aware wireless applications. Our results demonstrate the efficacy of the proposed approach in accurately generating LiDAR point clouds. We achieve a modified mean squared error of 10.3931. Visual examination of the images indicates that our model can successfully capture the majority of structures present in the LiDAR point cloud for diverse environments. This will enable the base stations to achieve more precise environmental sensing. By integrating LiDAR synthesis with existing sensing modalities, our method can enhance the performance of various wireless applications, including beam and blockage prediction.
A Set-based Approach for Feature Extraction of 3D CAD Models
Venue: arXiv cs.CV 2024
Year: 2024

Feature extraction is a critical technology to realize the automatic transmission of feature information throughout product life cycles. As CAD models primarily capture the 3D geometry of products, feature extraction heavily relies on geometric information. However, existing feature extraction methods often yield inaccurate outcomes due to the diverse interpretations of geometric information. This report presents a set-based feature extraction approach to address this uncertainty issue. Unlike existing methods that seek accurate feature results, our approach aims to transform the uncertainty of geometric information into a set of feature subgraphs. First, we define the convexity of basic geometric entities and introduce the concept of two-level attributed adjacency graphs. Second, a feature extraction workflow is designed to determine feature boundaries and identify feature subgraphs from CAD models. This set of feature subgraphs can be used for further feature recognition. A feature extraction system is programmed using C++ and UG/Open to demonstrate the feasibility of our proposed approach.
A PST Algorithm for FPs Suppression in Two-stage CNN Detection Methods
Venue: arXiv cs.CV 2024
Year: 2024

Pedestrian detection has been a hot spot in computer vision over the past decades due to the wide spectrum of promising applications, the major challenge of which is False Positives (FPs) that occur during pedestrian detection. The emergence various Convolutional Neural Network-based detection strategies substantially enhance the pedestrian detection accuracy but still not well solve this problem. This paper deeply analysis the detection framework of the two-stage CNN detection methods and find out false positives in detection results is due to its training strategy miss classify some false proposals, thus weakens the classification capability of following subnetwork and hardly to suppress false ones. To solve this problem, This paper proposes a pedestrian-sensitive training algorithm to effectively help two-stage CNN detection methods learn to distinguish the pedestrian and non-pedestrian samples and suppress the false positives in final detection results. The core of the proposed training algorithm is to redesign the training proposal generating pipeline of the two-stage CNN detection methods, which can avoid a certain number of false ones that mislead its training process. With the help of the proposed algorithm, the detection accuracy of the MetroNext, an smaller and accurate metro passenger detector, is further improved, which further decreases false ones in its metro passengers detection results. Based on various challenging benchmark datasets, experiment results have demonstrated that feasibility of the proposed algorithm to improve pedestrian detection accuracy by removing the false positives. Compared with the competitors, MetroNext-PST demonstrates better overall prediction performance in accuracy, total number of parameters, and inference time, thus it can become a practical solution for hunting pedestrian tailored for mobile and edge devices.
Interdisciplinary Expertise to Advance Equitable Explainable AI
Venue: arXiv cs.CY 2024
Year: 2024

The field of artificial intelligence (AI) is rapidly influencing health and healthcare, but bias and poor performance persists for populations who face widespread structural oppression. Previous work has clearly outlined the need for more rigorous attention to data representativeness and model performance to advance equity and reduce bias. However, there is an opportunity to also improve the explainability of AI by leveraging best practices of social epidemiology and health equity to help us develop hypotheses for associations found. In this paper, we focus on explainable AI (XAI) and describe a framework for interdisciplinary expert panel review to discuss and critically assess AI model explanations from multiple perspectives and identify areas of bias and directions for future research. We emphasize the importance of the interdisciplinary expert panel to produce more accurate, equitable interpretations which are historically and contextually informed. Interdisciplinary panel discussions can help reduce bias, identify potential confounders, and identify opportunities for additional research where there are gaps in the literature. In turn, these insights can suggest opportunities for AI model improvement.
Unsupervised Few-Shot Continual Learning for Remote Sensing Image Scene Classification
Venue: arXiv cs.CV 2024
Year: 2024

A continual learning (CL) model is desired for remote sensing image analysis because of varying camera parameters, spectral ranges, resolutions, etc. There exist some recent initiatives to develop CL techniques in this domain but they still depend on massive labelled samples which do not fully fit remote sensing applications because ground truths are often obtained via field-based surveys. This paper addresses this problem with a proposal of unsupervised flat-wide learning approach (UNISA) for unsupervised few-shot continual learning approaches of remote sensing image scene classifications which do not depend on any labelled samples for its model updates. UNISA is developed from the idea of prototype scattering and positive sampling for learning representations while the catastrophic forgetting problem is tackled with the flat-wide learning approach combined with a ball generator to address the data scarcity problem. Our numerical study with remote sensing image scene datasets and a hyperspectral dataset confirms the advantages of our solution. Source codes of UNISA are shared publicly in \url{https://github.com/anwarmaxsum/UNISA} to allow convenient future studies and reproductions of our numerical results.
Nomic Embed Vision: Expanding the Latent Space
Venue: arXiv cs.CV 2024
Year: 2024

This technical report describes the training of nomic-embed-vision, a highly performant, open-code, open-weights image embedding model that shares the same latent space as nomic-embed-text. Together, nomic-embed-vision and nomic-embed-text form the first unified latent space to achieve high performance across vision, language, and multimodal tasks.
Varying Manifolds in Diffusion: From Time-varying Geometries to Visual Saliency
Venue: arXiv cs.CV 2024
Year: 2024

Deep generative models learn the data distribution, which is concentrated on a low-dimensional manifold. The geometric analysis of distribution transformation provides a better understanding of data structure and enables a variety of applications. In this paper, we study the geometric properties of the diffusion model, whose forward diffusion process and reverse generation process construct a series of distributions on manifolds which vary over time. Our key contribution is the introduction of generation rate, which corresponds to the local deformation of manifold over time around an image component. We show that the generation rate is highly correlated with intuitive visual properties, such as visual saliency, of the image component. Further, we propose an efficient and differentiable scheme to estimate the generation rate for a given image component over time, giving rise to a generation curve. The differentiable nature of our scheme allows us to control the shape of the generation curve via optimization. Using different loss functions, our generation curve matching algorithm provides a unified framework for a range of image manipulation tasks, including semantic transfer, object removal, saliency manipulation, image blending, etc. We conduct comprehensive analytical evaluations to support our findings and evaluate our framework on various manipulation tasks. The results show that our method consistently leads to better manipulation results, compared to recent baselines.
Composition Vision-Language Understanding via Segment and Depth Anything Model
Venue: arXiv cs.CV 2024
Year: 2024

We introduce a pioneering unified library that leverages depth anything, segment anything models to augment neural comprehension in language-vision model zero-shot understanding. This library synergizes the capabilities of the Depth Anything Model (DAM), Segment Anything Model (SAM), and GPT-4V, enhancing multimodal tasks such as vision-question-answering (VQA) and composition reasoning. Through the fusion of segmentation and depth analysis at the symbolic instance level, our library provides nuanced inputs for language models, significantly advancing image interpretation. Validated across a spectrum of in-the-wild real-world images, our findings showcase progress in vision-language models through neural-symbolic integration. This novel approach melds visual and language analysis in an unprecedented manner. Overall, our library opens new directions for future research aimed at decoding the complexities of the real world through advanced multimodal technologies and our code is available at \url{https://github.com/AnthonyHuo/SAM-DAM-for-Compositional-Reasoning}.