arXiv subjects

Jing Yuan

Publications and source records attributed to Jing Yuan.

At least 37 records · Page 2Linked to original sources

arXiv2024

CryoFM: A Flow-based Foundation Model for Cryo-EM Densities

Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of over 38,626 protein density maps at various resolutions1. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning the distribution of high-quality density maps and generalizing effectively to downstream tasks. Built on flow matching, CryoFM is trained to accurately capture the prior distribution of biomolecular density maps. Furthermore, we introduce a flow posterior sampling method that leverages CRYOFM as a flexible prior for several downstream tasks in cryo-EM and cryo-electron tomography (cryo-ET) without the need for fine-tuning, achieving state-of-the-art performance on most tasks and demonstrating its potential as a foundational model for broader applications in these fields.

q-bio.BM↗

arXiv2024

TableGPT2: A Large Multimodal Model with Tabular Data Integration

The emergence of models like GPTs, Claude, LLaMA, and Qwen has reshaped AI applications, presenting vast new opportunities across industries. Yet, the integration of tabular data remains notably underdeveloped, despite its foundational role in numerous real-world domains. This gap is critical for three main reasons. First, database or data warehouse data integration is essential for advanced applications; second, the vast and largely untapped resource of tabular data offers immense potential for analysis; and third, the business intelligence domain specifically demands adaptable, precise solutions that many current LLMs may struggle to provide. In response, we introduce TableGPT2, a model rigorously pre-trained and fine-tuned with over 593.8K tables and 2.36M high-quality query-table-output tuples, a scale of table-related data unprecedented in prior research. This extensive training enables TableGPT2 to excel in table-centric tasks while maintaining strong general language and coding abilities. One of TableGPT2's key innovations is its novel table encoder, specifically designed to capture schema-level and cell-level information. This encoder strengthens the model's ability to handle ambiguous queries, missing column names, and irregular tables commonly encountered in real-world applications. Similar to visual language models, this pioneering approach integrates with the decoder to form a robust large multimodal model. We believe the results are compelling: over 23 benchmarking metrics, TableGPT2 achieves an average performance improvement of 35.20% in the 7B model and 49.32% in the 72B model over prior benchmark-neutral LLMs, with robust general-purpose capabilities intact.

cs.LG↗

arXiv2024

Natural fumigation as a mechanism for volatile transport between flower organs

Plants synthesize volatile organic compounds (VOCs) to attract pollinators and beneficial microorganisms, to defend themselves against herbivores and pathogens and for plant-plant communication. Generally, accumulation and emission of VOCs occur from the tissue of their biosynthesis. However, using biochemical and reverse genetic approaches, we demonstrate a new physiological phenomenon: inter-organ aerial transport of VOCs via natural fumigation. Before petunia flowers open, a tube-specific terpene synthase produces sesquiterpenes, which are released inside the buds and then accumulate in the stigma, potentially defending the developing stigma from pathogens. These VOCs also affect reproductive organ development and seed yield, which is a previously unknown function for terpenoid compounds. could serve as a mechanism to coordinate the timing of pistil development with petal development in order to insure that the stigma is receptive when the flowers are most likely to attract pollinators. Further studies are required to assess whether natural fumigation is conserved in flowering plants, to uncover the mechanisms involved, and to determine its evolutionary advantage in plant reproduction.

q-bio.BM↗

arXiv2024

Learning Submodular Sequencing from Samples

This paper addresses the problem of sequential submodular maximization: selecting and ranking items in a sequence to optimize some composite submodular function. In contrast to most of the previous works, which assume access to the utility function, we assume that we are given only a set of samples. Each sample includes a random sequence of items and its associated utility. We present an algorithm that, given polynomially many samples drawn from a two-stage uniform distribution, achieves an approximation ratio dependent on the curvature of individual submodular functions. Our results apply in a wide variety of real-world scenarios, such as ranking products in online retail platforms, where complete knowledge of the utility function is often impossible to obtain. Our algorithm gives an empirically useful solution in such contexts, thus proving that limited data can be of great use in sequencing tasks. From a technical perspective, our results extend prior work on ``optimization from samples'' by generalizing from optimizing a set function to a sequence-dependent function.

cs.LG↗

arXiv2024

The Power of Second Chance: Personalized Submodular Maximization with Two Candidates

Most of existing studies on submodular maximization focus on selecting a subset of items that maximizes a \emph{single} submodular function. However, in many real-world scenarios, we might have multiple user-specific functions, each of which models the utility of a particular type of user. In these settings, our goal would be to choose a set of items that performs well across all the user-specific functions. One way to tackle this problem is to select a single subset that maximizes the sum of all of the user-specific functions. Although this aggregate approach is efficient in the sense that it avoids computation of sets for individual functions, it really misses the power of personalization - for it does not allow to choose different sets for different functions. In this paper, we introduce the problem of personalized submodular maximization with two candidate solutions. For any two candidate solutions, the utility of each user-specific function is defined as the better of these two candidates. Our objective is, therefore, to select the best set of two candidates that maximize the sum of utilities of all the user-specific functions. We have designed effective algorithms for this problem. We also discuss how our approach generalizes to multiple candidate solutions, increasing flexibility and personalization in our solution.

cs.LG↗

arXiv2024

Size Aware Cross-shape Scribble Supervision for Medical Image Segmentation

Scribble supervision, a common form of weakly supervised learning, involves annotating pixels using hand-drawn curve lines, which helps reduce the cost of manual labelling. This technique has been widely used in medical image segmentation tasks to fasten network training. However, scribble supervision has limitations in terms of annotation consistency across samples and the availability of comprehensive groundtruth information. Additionally, it often grapples with the challenge of accommodating varying scale targets, particularly in the context of medical images. In this paper, we propose three novel methods to overcome these challenges, namely, 1) the cross-shape scribble annotation method; 2) the pseudo mask method based on cross shapes; and 3) the size-aware multi-branch method. The parameter and structure design are investigated in depth. Experimental results show that the proposed methods have achieved significant improvement in mDice scores across multiple polyp datasets. Notably, the combination of these methods outperforms the performance of state-of-the-art scribble supervision methods designed for medical image segmentation.

cs.CV↗

arXiv2024

Mean Height Aided Post-Processing for Pedestrian Detection

The design of pedestrian detectors seldom considers the unique characteristics of this task and usually follows the common strategies for general object detection. To explore the potential of these characteristics, we take the perspective effect in pedestrian datasets as an example and propose the mean height aided suppression for post-processing. This method rejects predictions that fall at levels with a low possibility of containing any pedestrians or that have an abnormal height compared to the average. To achieve this, the existence score and mean height generators are proposed. Comprehensive experiments on various datasets and detectors are performed; the choice of hyper-parameters is discussed in depth. The proposed method is easy to implement and is plug-and-play. Results show that the proposed methods significantly improve detection accuracy when applied to different existing pedestrian detectors and datasets. The combination of mean height aided suppression with particular detectors outperforms state-of-the-art pedestrian detectors on Caltech and Citypersons datasets.

cs.CV↗

arXiv2024

Submodular Participatory Budgeting

Participatory budgeting refers to the practice of allocating public resources by collecting and aggregating individual preferences. Most existing studies in this field often assume an additive utility function, where each individual holds a private utility for each candidate project, and the total utility of a set of funded projects is simply the sum of the utilities of all projects. We argue that this assumption does not always hold in reality. For example, building two playgrounds in the same neighborhood does not necessarily lead to twice the utility of building a single playground. To address this, we extend the existing study by proposing a submodular participatory budgeting problem, assuming that the utility function of each individual is a monotone and submodular function over funded projects. We propose and examine three preference elicitation methods, including \emph{ranking-by-marginal-values}, \emph{ranking-by-values} and \emph{threshold approval votes}, and analyze their performances in terms of distortion. Notably, if the utility function is addicative, our aggregation rule designed for threshold approval votes achieves a better distortion than the state-of-the-art approach.

cs.GT↗

arXiv2024

A Partition-insensitive Parallel Framework for Distributed Model Fitting

Distributed model fitting refers to the process of fitting a mathematical or statistical model to the data using distributed computing resources, such that computing tasks are divided among multiple interconnected computers or nodes, often organized in a cluster or network. Most of the existing methods for distributed model fitting are to formulate it in a consensus optimization problem, and then build up algorithms based on the alternating direction method of multipliers (ADMM). This paper introduces a novel parallel framework for achieving a distributed model fitting. In contrast to previous consensus frameworks, the introduced parallel framework offers two notable advantages. Firstly, it exhibits insensitivity to sample partitioning, meaning that the solution of the algorithm remains unaffected by variations in the number of slave nodes or/and the amount of data each node carries. Secondly, fewer variables are required to be updated at each iteration, so that the proposed parallel framework performs in a more succinct and efficient way, and adapts to high-dimensional data. In addition, we prove that the algorithms under the new parallel framework have a worst-case linear convergence rate in theory. Numerical experiments confirm the generality, robustness, and accuracy of our proposed parallel framework.

stat.CO↗

arXiv2024

Deep Convolutional Neural Networks Meet Variational Shape Compactness Priors for Image Segmentation

Shape compactness is a key geometrical property to describe interesting regions in many image segmentation tasks. In this paper, we propose two novel algorithms to solve the introduced image segmentation problem that incorporates a shape-compactness prior. Existing algorithms for such a problem often suffer from computational inefficiency, difficulty in reaching a local minimum, and the need to fine-tune the hyperparameters. To address these issues, we propose a novel optimization model along with its equivalent primal-dual model and introduce a new optimization algorithm based on primal-dual threshold dynamics (PD-TD). Additionally, we relax the solution constraint and propose another novel primal-dual soft threshold-dynamics algorithm (PD-STD) to achieve superior performance. Based on the variational explanation of the sigmoid layer, the proposed PD-STD algorithm can be integrated into Deep Neural Networks (DNNs) to enforce compact regions as image segmentation results. Compared to existing deep learning methods, extensive experiments demonstrated that the proposed algorithms outperformed state-of-the-art algorithms in numerical efficiency and effectiveness, especially while applying to the popular networks of DeepLabV3 and IrisParseNet with higher IoU, dice, and compactness metrics on noisy Iris datasets. In particular, the proposed algorithms significantly improve IoU by 20% training on a highly noisy image dataset.

cs.CV↗

arXiv2024

G$ \mathbf{^2} $VD Planner: Efficient Motion Planning With Grid-based Generalized Voronoi Diagrams

In this paper, an efficient motion planning approach with grid-based generalized Voronoi diagrams (G$ \mathbf{^2} $VD) is newly proposed for mobile robots. Different from existing approaches, the novelty of this work is twofold: 1) a new state lattice-based path searching approach is proposed, in which the search space is reduced to a novel Voronoi corridor to further improve the search efficiency; 2) an efficient quadratic programming-based path smoothing approach is presented, wherein the clearance to obstacles is considered to improve the path clearance of hard-constrained path smoothing approaches. We validate the efficiency and smoothness of our approach in various challenging simulation scenarios and outdoor environments. It is shown that the computational efficiency is improved by 17.1% in the path searching stage, and path smoothing with the proposed approach is 6.6 times faster than an advanced sparse-banded structure-based path smoothing approach and 53.3 times faster than the popular timed-elastic-band planner. A video showing outdoor navigation on our campus is available at https://youtu.be/iMXGthgvp58.

cs.RO↗

arXiv2023

Non-monotone Sequential Submodular Maximization

In this paper, we study a fundamental problem in submodular optimization, which is called sequential submodular maximization. Specifically, we aim to select and rank a group of $k$ items from a ground set $V$ such that the weighted summation of $k$ (possibly non-monotone) submodular functions $f_1, \cdots ,f_k: 2^V \rightarrow \mathbb{R}^+$ is maximized, here each function $f_j$ takes the first $j$ items from this sequence as input. The existing research on sequential submodular maximization has predominantly concentrated on the monotone setting, assuming that the submodular functions are non-decreasing. However, in various real-world scenarios, like diversity-aware recommendation systems, adding items to an existing set might negatively impact the overall utility. In response, this paper pioneers the examination of the aforementioned problem with non-monotone submodular functions and offers effective solutions for both flexible and fixed length constraints, as well as a special case with identical utility functions. The empirical evaluations further validate the effectiveness of our proposed algorithms in the domain of video recommendations. The results of this research have implications in various fields, including recommendation systems and assortment optimization, where the ordering of items significantly impacts the overall value obtained.

cs.LG↗

arXiv2023

Group Equality in Adaptive Submodular Maximization

In this paper, we study the classic submodular maximization problem subject to a group equality constraint under both non-adaptive and adaptive settings. It has been shown that the utility function of many machine learning applications, including data summarization, influence maximization in social networks, and personalized recommendation, satisfies the property of submodularity. Hence, maximizing a submodular function subject to various constraints can be found at the heart of many of those applications. On a high level, submodular maximization aims to select a group of most representative items (e.g., data points). However, the design of most existing algorithms does not incorporate the fairness constraint, leading to under- or over-representation of some particular groups. This motivates us to study the submodular maximization problem with group equality, where we aim to select a group of items to maximize a (possibly non-monotone) submodular utility function subject to a group equality constraint. To this end, we develop the first constant-factor approximation algorithm for this problem. The design of our algorithm is robust enough to be extended to solving the submodular maximization problem under a more complicated adaptive setting. Moreover, we further extend our study to incorporating a global cardinality constraint and other fairness notations.

cs.LG↗

arXiv2023

TableGPT: Towards Unifying Tables, Nature Language and Commands into One GPT

Tables are prevalent in real-world databases, requiring significant time and effort for humans to analyze and manipulate. The advancements in large language models (LLMs) have made it possible to interact with tables using natural language input, bringing this capability closer to reality. In this paper, we present TableGPT, a unified fine-tuned framework that enables LLMs to understand and operate on tables using external functional commands. It introduces the capability to seamlessly interact with tables, enabling a wide range of functionalities such as question answering, data manipulation (e.g., insert, delete, query, and modify operations), data visualization, analysis report generation, and automated prediction. TableGPT aims to provide convenience and accessibility to users by empowering them to effortlessly leverage tabular data. At the core of TableGPT lies the novel concept of global tabular representations, which empowers LLMs to gain a comprehensive understanding of the entire table beyond meta-information. By jointly training LLMs on both table and text modalities, TableGPT achieves a deep understanding of tabular data and the ability to perform complex operations on tables through chain-of-command instructions. Importantly, TableGPT offers the advantage of being a self-contained system rather than relying on external API interfaces. Moreover, it supports efficient data process flow, query rejection (when appropriate) and private deployment, enabling faster domain data fine-tuning and ensuring data privacy, which enhances the framework's adaptability to specific use cases.

cs.AI↗

arXiv2023

Beyond Submodularity: A Unified Framework of Randomized Set Selection with Group Fairness Constraints

Machine learning algorithms play an important role in a variety of important decision-making processes, including targeted advertisement displays, home loan approvals, and criminal behavior predictions. Given the far-reaching impact of these algorithms, it is crucial that they operate fairly, free from bias or prejudice towards certain groups in the population. Ensuring impartiality in these algorithms is essential for promoting equality and avoiding discrimination. To this end we introduce a unified framework for randomized subset selection that incorporates group fairness constraints. Our problem involves a global utility function and a set of group utility functions for each group, here a group refers to a group of individuals (e.g., people) sharing the same attributes (e.g., gender). Our aim is to generate a distribution across feasible subsets, specifying the selection probability of each feasible set, to maximize the global utility function while meeting a predetermined quota for each group utility function in expectation. Note that there may not necessarily be any direct connections between the global utility function and each group utility function. We demonstrate that this framework unifies and generalizes many significant applications in machine learning and operations research. Our algorithmic results either improves the best known result or provide the first approximation algorithms for new applications.

cs.LG↗

arXiv2023

Achieving Long-term Fairness in Submodular Maximization through Randomization

Submodular function optimization has numerous applications in machine learning and data analysis, including data summarization which aims to identify a concise and diverse set of data points from a large dataset. It is important to implement fairness-aware algorithms when dealing with data items that may contain sensitive attributes like race or gender, to prevent biases that could lead to unequal representation of different groups. With this in mind, we investigate the problem of maximizing a monotone submodular function while meeting group fairness constraints. Unlike previous studies in this area, we allow for randomized solutions, with the objective being to calculate a distribution over feasible sets such that the expected number of items selected from each group is subject to constraints in the form of upper and lower thresholds, ensuring that the representation of each group remains balanced in the long term. Here a set is considered feasible if its size does not exceed a constant value of $b$. Our research includes the development of a series of approximation algorithms for this problem.

cs.DS↗

arXiv2023

Group Fairness in Non-monotone Submodular Maximization

Maximizing a submodular function has a wide range of applications in machine learning and data mining. One such application is data summarization whose goal is to select a small set of representative and diverse data items from a large dataset. However, data items might have sensitive attributes such as race or gender, in this setting, it is important to design \emph{fairness-aware} algorithms to mitigate potential algorithmic bias that may cause over- or under- representation of particular groups. Motivated by that, we propose and study the classic non-monotone submodular maximization problem subject to novel group fairness constraints. Our goal is to select a set of items that maximizes a non-monotone submodular function, while ensuring that the number of selected items from each group is proportionate to its size, to the extent specified by the decision maker. We develop the first constant-factor approximation algorithms for this problem. We also extend the basic model to incorporate an additional global size constraint on the total number of selected items.

cs.LG↗

arXiv2023

Worst-Case Adaptive Submodular Cover

In this paper, we study the adaptive submodular cover problem under the worst-case setting. This problem generalizes many previously studied problems, namely, the pool-based active learning and the stochastic submodular set cover. The input of our problem is a set of items (e.g., medical tests) and each item has a random state (e.g., the outcome of a medical test), whose realization is initially unknown. One must select an item at a fixed cost in order to observe its realization. There is an utility function which maps a subset of items and their states to a non-negative real number. We aim to sequentially select a group of items to achieve a ``target value'' while minimizing the maximum cost across realizations (a.k.a. worst-case cost). To facilitate our study, we assume that the utility function is \emph{worst-case submodular}, a property that is commonly found in many machine learning applications. With this assumption, we develop a tight $(\log (Q/η)+1)$-approximation policy, where $Q$ is the ``target value'' and $η$ is the smallest difference between $Q$ and any achievable utility value $\hat{Q}<Q$. We also study a worst-case maximum-coverage problem, a dual problem of the minimum-cost-cover problem, whose goal is to select a group of items to maximize its worst-case utility subject to a budget constraint. To solve this problem, we develop a $(1-1/e)/2$-approximation solution.

cs.DS↗