pwc-archive/papers-with-abstracts huggingface dataset:
A Riemannian Approach for Spatiotemporal Analysis and Generation of 4D Tree-shaped Structures
Authors: Tahmina Khanam, Hamid Laga, Mohammed Bennamoun, Guanjin Wang, Ferdous Sohel, Farid Boussaid, Guan Wang, Anuj Srivastava
Date: 2024-08-22 00:00:00

We propose the first comprehensive approach for modeling and analyzing the spatiotemporal shape variability in tree-like 4D objects, i.e., 3D objects whose shapes bend, stretch, and change in their branching structure over time as they deform, grow, and interact with their environment. Our key contribution is the representation of tree-like 3D shapes using Square Root Velocity Function Trees (SRVFT). By solving the spatial registration in the SRVFT space, which is equipped with an L2 metric, 4D tree-shaped structures become time-parameterized trajectories in this space. This reduces the problem of modeling and analyzing 4D tree-like shapes to that of modeling and analyzing elastic trajectories in the SRVFT space, where elasticity refers to time warping. In this paper, we propose a novel mathematical representation of the shape space of such trajectories, a Riemannian metric on that space, and computational tools for fast and accurate spatiotemporal registration and geodesics computation between 4D tree-shaped structures. Leveraging these building blocks, we develop a full framework for modelling the spatiotemporal variability using statistical models and generating novel 4D tree-like structures from a set of exemplars. We demonstrate and validate the proposed framework using real 4D plant data.
Enhanced Infield Agriculture with Interpretable Machine Learning Approaches for Crop Classification
Authors: Sudi Murindanyi, Joyce Nakatumba-Nabende, Rahman Sanya, Rose Nakibuule, Andrew Katumba
Date: 2024-08-22 00:00:00
Tasks: Crop Classification, image-classification, Image Classification, Interpretable Machine Learning, Transfer Learning

The increasing popularity of Artificial Intelligence in recent years has led to a surge in interest in image classification, especially in the agricultural sector. With the help of Computer Vision, Machine Learning, and Deep Learning, the sector has undergone a significant transformation, leading to the development of new techniques for crop classification in the field. Despite the extensive research on various image classification techniques, most have limitations such as low accuracy, limited use of data, and a lack of reporting model size and prediction. The most significant limitation of all is the need for model explainability. This research evaluates four different approaches for crop classification, namely traditional ML with handcrafted feature extraction methods like SIFT, ORB, and Color Histogram; Custom Designed CNN and established DL architecture like AlexNet; transfer learning on five models pre-trained using ImageNet such as EfficientNetV2, ResNet152V2, Xception, Inception-ResNetV2, MobileNetV3; and cutting-edge foundation models like YOLOv8 and DINOv2, a self-supervised Vision Transformer Model. All models performed well, but Xception outperformed all of them in terms of generalization, achieving 98% accuracy on the test data, with a model size of 80.03 MB and a prediction time of 0.0633 seconds. A key aspect of this research was the application of Explainable AI to provide the explainability of all the models. This journal presents the explainability of Xception model with LIME, SHAP, and GradCAM, ensuring transparency and trustworthiness in the models' predictions. This study highlights the importance of selecting the right model according to task-specific needs. It also underscores the important role of explainability in deploying AI in agriculture, providing insightful information to help enhance AI-driven crop management strategies.
Multi-Knowledge Fusion Network for Time Series Representation Learning
Authors: Sagar Srinivas Sakhinana, Shivam Gupta, Krishna Sai Sudhir Aripirala, Venkataramana Runkana
Date: 2024-08-22 00:00:00
Tasks: Representation Learning, Time Series

Forecasting the behaviour of complex dynamical systems such as interconnected sensor networks characterized by high-dimensional multivariate time series(MTS) is of paramount importance for making informed decisions and planning for the future in a broad spectrum of applications. Graph forecasting networks(GFNs) are well-suited for forecasting MTS data that exhibit spatio-temporal dependencies. However, most prior works of GFN-based methods on MTS forecasting rely on domain-expertise to model the nonlinear dynamics of the system, but neglect the potential to leverage the inherent relational-structural dependencies among time series variables underlying MTS data. On the other hand, contemporary works attempt to infer the relational structure of the complex dependencies between the variables and simultaneously learn the nonlinear dynamics of the interconnected system but neglect the possibility of incorporating domain-specific prior knowledge to improve forecast accuracy. To this end, we propose a hybrid architecture that combines explicit prior knowledge with implicit knowledge of the relational structure within the MTS data. It jointly learns intra-series temporal dependencies and inter-series spatial dependencies by encoding time-conditioned structural spatio-temporal inductive biases to provide more accurate and reliable forecasts. It also models the time-varying uncertainty of the multi-horizon forecasts to support decision-making by providing estimates of prediction uncertainty. The proposed architecture has shown promising results on multiple benchmark datasets and outperforms state-of-the-art forecasting methods by a significant margin. We report and discuss the ablation studies to validate our forecasting architecture.
Dataset | Mindset = Explainable AI | Interpretable AI
Authors: Caesar Wu, Rajkumar Buyya, Yuan Fang Li, Pascal Bouvry
Date: 2024-08-22 00:00:00
Tasks: Explainable artificial intelligence, Explainable Artificial Intelligence (XAI), Fairness

We often use "explainable" Artificial Intelligence (XAI)" and "interpretable AI (IAI)" interchangeably when we apply various XAI tools for a given dataset to explain the reasons that underpin machine learning (ML) outputs. However, these notions can sometimes be confusing because interpretation often has a subjective connotation, while explanations lean towards objective facts. We argue that XAI is a subset of IAI. The concept of IAI is beyond the sphere of a dataset. It includes the domain of a mindset. At the core of this ambiguity is the duality of reasons, in which we can reason either outwards or inwards. When directed outwards, we want the reasons to make sense through the laws of nature. When turned inwards, we want the reasons to be happy, guided by the laws of the heart. While XAI and IAI share reason as the common notion for the goal of transparency, clarity, fairness, reliability, and accountability in the context of ethical AI and trustworthy AI (TAI), their differences lie in that XAI emphasizes the post-hoc analysis of a dataset, and IAI requires a priori mindset of abstraction. This hypothesis can be proved by empirical experiments based on an open dataset and harnessed by High-Performance Computing (HPC). The demarcation of XAI and IAI is indispensable because it would be impossible to determine regulatory policies for many AI applications, especially in healthcare, human resources, banking, and finance. We aim to clarify these notions and lay the foundation of XAI, IAI, EAI, and TAI for many practitioners and policymakers in future AI applications and research.
AlphaFolding: 4D Diffusion for Dynamic Protein Structure Prediction with Reference and Motion Guidance
Authors: Kaihui Cheng, Ce Liu, Qingkun Su, Jun Wang, Liwei Zhang, Yining Tang, Yao Yao, Siyu Zhu, Yuan Qi
Date: 2024-08-22 00:00:00
Tasks: Experimental Design, Protein Structure Prediction

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes. URL: https://fudan-generative-vision.github.io/AlphaFolding/#/
CODE: Confident Ordinary Differential Editing
Authors: Bastien Van Delft, Tommaso Martorella, Alexandre Alahi
Date: 2024-08-22 00:00:00
Tasks: Conditional Image Generation, Image Generation, Image Restoration

Conditioning image generation facilitates seamless editing and the creation of photorealistic images. However, conditioning on noisy or Out-of-Distribution (OoD) images poses significant challenges, particularly in balancing fidelity to the input and realism of the output. We introduce Confident Ordinary Differential Editing (CODE), a novel approach for image synthesis that effectively handles OoD guidance images. Utilizing a diffusion model as a generative prior, CODE enhances images through score-based updates along the probability-flow Ordinary Differential Equation (ODE) trajectory. This method requires no task-specific training, no handcrafted modules, and no assumptions regarding the corruptions affecting the conditioning image. Our method is compatible with any diffusion model. Positioned at the intersection of conditional image generation and blind image restoration, CODE operates in a fully blind manner, relying solely on a pre-trained generative model. Our method introduces an alternative approach to blind restoration: instead of targeting a specific ground truth image based on assumptions about the underlying corruption, CODE aims to increase the likelihood of the input image while maintaining fidelity. This results in the most probable in-distribution image around the input. Our contributions are twofold. First, CODE introduces a novel editing method based on ODE, providing enhanced control, realism, and fidelity compared to its SDE-based counterpart. Second, we introduce a confidence interval-based clipping method, which improves CODE's effectiveness by allowing it to disregard certain pixels or information, thus enhancing the restoration process in a blind manner. Experimental results demonstrate CODE's effectiveness over existing methods, particularly in scenarios involving severe degradation or OoD inputs.
Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures
Authors: Ce Liu, Jun Wang, Zhiqiang Cai, Yingxu Wang, Huizhen Kuang, Kaihui Cheng, Liwei Zhang, Qingkun Su, Yining Tang, Fenglei Cao, Limei Han, Siyu Zhu, Yuan Qi
Date: 2024-08-22 00:00:00
Tasks: Benchmarking, Trajectory Prediction

Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed to the limited availability, diversity, and heterogeneity of dynamic protein datasets. To address this gap, we propose to enhance existing prestigious static 3D protein structural databases, such as the Protein Data Bank (PDB), by integrating dynamic data and additional physical properties. Specifically, we introduce a large-scale dataset, Dynamic PDB, encompassing approximately 12.6K proteins, each subjected to all-atom molecular dynamics (MD) simulations lasting 1 microsecond to capture conformational changes. Furthermore, we provide a comprehensive suite of physical properties, including atomic velocities and forces, potential and kinetic energies of proteins, and the temperature of the simulation environment, recorded at 1 picosecond intervals throughout the simulations. For benchmarking purposes, we evaluate state-of-the-art methods on the proposed dataset for the task of trajectory prediction. To demonstrate the value of integrating richer physical properties in the study of protein dynamics and related model design, we base our approach on the SE(3) diffusion model and incorporate these physical properties into the trajectory prediction process. Preliminary results indicate that this straightforward extension of the SE(3) model yields improved accuracy, as measured by MAE and RMSD, when the proposed physical properties are taken into consideration. https://fudan-generative-vision.github.io/dynamicPDB/ .
Multi-Source Knowledge-Based Hybrid Neural Framework for Time Series Representation Learning
Authors: Sagar Srinivas Sakhinana, Krishna Sai Sudhir Aripirala, Shivam Gupta, Venkataramana Runkana
Date: 2024-08-22 00:00:00
Tasks: Decision Making, Representation Learning, Time Series

Accurately predicting the behavior of complex dynamical systems, characterized by high-dimensional multivariate time series(MTS) in interconnected sensor networks, is crucial for informed decision-making in various applications to minimize risk. While graph forecasting networks(GFNs) are ideal for forecasting MTS data that exhibit spatio-temporal dependencies, prior works rely solely on the domain-specific knowledge of time-series variables inter-relationships to model the nonlinear dynamics, neglecting inherent relational structural dependencies among the variables within the MTS data. In contrast, contemporary works infer relational structures from MTS data but neglect domain-specific knowledge. The proposed hybrid architecture addresses these limitations by combining both domain-specific knowledge and implicit knowledge of the relational structure underlying the MTS data using Knowledge-Based Compositional Generalization. The hybrid architecture shows promising results on multiple benchmark datasets, outperforming state-of-the-art forecasting methods. Additionally, the architecture models the time varying uncertainty of multi-horizon forecasts.
Multi-Style Facial Sketch Synthesis through Masked Generative Modeling
Authors: Bowen Sun, Guo Lu, Shibao Zheng
Date: 2024-08-22 00:00:00
Tasks: 3D geometry, Face Recognition

The facial sketch synthesis (FSS) model, capable of generating sketch portraits from given facial photographs, holds profound implications across multiple domains, encompassing cross-modal face recognition, entertainment, art, media, among others. However, the production of high-quality sketches remains a formidable task, primarily due to the challenges and flaws associated with three key factors: (1) the scarcity of artist-drawn data, (2) the constraints imposed by limited style types, and (3) the deficiencies of processing input information in existing models. To address these difficulties, we propose a lightweight end-to-end synthesis model that efficiently converts images to corresponding multi-stylized sketches, obviating the necessity for any supplementary inputs (\eg, 3D geometry). In this study, we overcome the issue of data insufficiency by incorporating semi-supervised learning into the training process. Additionally, we employ a feature extraction module and style embeddings to proficiently steer the generative transformer during the iterative prediction of masked image tokens, thus achieving a continuous stylized output that retains facial features accurately in sketches. The extensive experiments demonstrate that our method consistently outperforms previous algorithms across multiple benchmarks, exhibiting a discernible disparity.
Cell-ontology guided transcriptome foundation model
Authors: Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang
Date: 2024-08-22 00:00:00
Tasks: model, Self-Supervised Learning

Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present \textbf{s}ingle \textbf{c}ell, \textbf{Cell}-\textbf{o}ntology guided TFM scCello. We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training. The novel loss component guide scCello to learn the cell-type-specific representation and the structural relation between cell types from the cell ontology graph, respectively. We pre-trained scCello on 22 million cells from CellxGene database leveraging their cell-type labels mapped to the cell ontology graph from Open Biological and Biomedical Ontology Foundry. Our TFM demonstrates competitive generalization and transferability performance over the existing TFMs on biologically important tasks including identifying novel cell types of unseen cells, prediction of cell-type-specific marker genes, and cancer drug responses.
RoundTable: Leveraging Dynamic Schema and Contextual Autocomplete for Enhanced Query Precision in Tabular Question Answering
Authors: Pratyush Kumar, Kuber Vijaykumar Bellad, Bharat Vadlamudi, Aman Chadha
Date: 2024-08-22 00:00:00
Tasks: Natural Language Queries, Question Answering

With advancements in Large Language Models (LLMs), a major use case that has emerged is querying databases in plain English, translating user questions into executable database queries, which has improved significantly. However, real-world datasets often feature a vast array of attributes and complex values, complicating the LLMs task of accurately identifying relevant columns or values from natural language queries. Traditional methods cannot fully relay the datasets size and complexity to the LLM. To address these challenges, we propose a novel framework that leverages Full-Text Search (FTS) on the input table. This approach not only enables precise detection of specific values and columns but also narrows the search space for language models, thereby enhancing query accuracy. Additionally, it supports a custom auto-complete feature that suggests queries based on the data in the table. This integration significantly refines the interaction between the user and complex datasets, offering a sophisticated solution to the limitations faced by current table querying capabilities. This work is accompanied by an application for both Mac and Windows platforms, which readers can try out themselves on their own data.
SAM-SP: Self-Prompting Makes SAM Great Again
Authors: Chunpeng Zhou, Kangjie Ning, Qianqian Shen, Sheng Zhou, Zhi Yu, Haishuai Wang
Date: 2024-08-22 00:00:00
Tasks: Segmentation, Zero Shot Segmentation

The recently introduced Segment Anything Model (SAM), a Visual Foundation Model (VFM), has demonstrated impressive capabilities in zero-shot segmentation tasks across diverse natural image datasets. Despite its success, SAM encounters noticeably performance degradation when applied to specific domains, such as medical images. Current efforts to address this issue have involved fine-tuning strategies, intended to bolster the generalizability of the vanilla SAM. However, these approaches still predominantly necessitate the utilization of domain specific expert-level prompts during the evaluation phase, which severely constrains the model's practicality. To overcome this limitation, we introduce a novel self-prompting based fine-tuning approach, called SAM-SP, tailored for extending the vanilla SAM model. Specifically, SAM-SP leverages the output from the previous iteration of the model itself as prompts to guide subsequent iteration of the model. This self-prompting module endeavors to learn how to generate useful prompts autonomously and alleviates the dependence on expert prompts during the evaluation phase, significantly broadening SAM's applicability. Additionally, we integrate a self-distillation module to enhance the self-prompting process further. Extensive experiments across various domain specific datasets validate the effectiveness of the proposed SAM-SP. Our SAM-SP not only alleviates the reliance on expert prompts but also exhibits superior segmentation performance comparing to the state-of-the-art task-specific segmentation approaches, the vanilla SAM, and SAM-based approaches.
Class-balanced Open-set Semi-supervised Object Detection for Medical Images
Authors: Zhanyun Lu, Renshu Gu, Huimin Cheng, Siyu Pang, Mingyu Xu, Peifang Xu, Yaqi Wang, Yuichiro Kinoshita, Juan Ye, Gangyong Jia, Qing Wu
Date: 2024-08-22 00:00:00
Tasks: Object, object-detection, Object Detection, Out-of-Distribution Detection, Semi-Supervised Object Detection

Medical image datasets in the real world are often unlabeled and imbalanced, and Semi-Supervised Object Detection (SSOD) can utilize unlabeled data to improve an object detector. However, existing approaches predominantly assumed that the unlabeled data and test data do not contain out-of-distribution (OOD) classes. The few open-set semi-supervised object detection methods have two weaknesses: first, the class imbalance is not considered; second, the OOD instances are distinguished and simply discarded during pseudo-labeling. In this paper, we consider the open-set semi-supervised object detection problem which leverages unlabeled data that contain OOD classes to improve object detection for medical images. Our study incorporates two key innovations: Category Control Embed (CCE) and out-of-distribution Detection Fusion Classifier (OODFC). CCE is designed to tackle dataset imbalance by constructing a Foreground information Library, while OODFC tackles open-set challenges by integrating the ``unknown'' information into basic pseudo-labels. Our method outperforms the state-of-the-art SSOD performance, achieving a 4.25 mAP improvement on the public Parasite dataset.