Caihua Shan

Ruoxi Shi, Xinyang Jiang, Caihua Shan et al.

Vector graphics (VG) have been ubiquitous in our daily life with vast applications in engineering, architecture, designs, etc. The VG recognition process of most existing methods is to first render the VG into raster graphics (RG) and then conduct recognition based on RG formats. However, this procedure discards the structure of geometries and loses the high resolution of VG. Recently, another category of algorithms is proposed to recognize directly from the original VG format. But it is affected by the topological errors that can be filtered out by RG rendering. Instead of looking at one format, it is a good solution to utilize the formats of VG and RG together to avoid these shortcomings. Besides, we argue that the VG-to-RG rendering process is essential to effectively combine VG and RG information. By specifying the rules on how to transfer VG primitives to RG pixels, the rendering process depicts the interaction and correlation between VG and RG. As a result, we propose RendNet, a unified architecture for recognition on both 2D and 3D scenarios, which considers both VG/RG representations and exploits their interaction by incorporating the VG-to-RG rasterization process. Experiments show that RendNet can achieve state-of-the-art performance on 2D and 3D object recognition tasks on various VG datasets.

Xixi Wu, Yifei Shen, Fangzhou Ge et al.

Node classification is a fundamental task in graph analysis, with broad applications across various fields. Recent breakthroughs in Large Language Models (LLMs) have enabled LLM-based approaches for this task. Although many studies demonstrate the impressive performance of LLM-based methods, the lack of clear design guidelines may hinder their practical application. In this work, we aim to establish such guidelines through a fair and systematic comparison of these algorithms. As a first step, we developed LLMNodeBed, a comprehensive codebase and testbed for node classification using LLMs. It includes 10 homophilic datasets, 4 heterophilic datasets, 8 LLM-based algorithms, 8 classic baselines, and 3 learning paradigms. Subsequently, we conducted extensive experiments, training and evaluating over 2,700 models, to determine the key settings (e.g., learning paradigms and homophily) and components (e.g., model size and prompt) that affect performance. Our findings uncover 8 insights, e.g., (1) LLM-based methods can significantly outperform traditional methods in a semi-supervised setting, while the advantage is marginal in a supervised setting; (2) Graph Foundation Models can beat open-source LLMs but still fall short of strong LLMs like GPT-4o in a zero-shot setting. We hope that the release of LLMNodeBed, along with our insights, will facilitate reproducible research and inspire future studies in this field. Codes and datasets are released at \href{https://llmnodebed.github.io/}{\texttt{https://llmnodebed.github.io/}}.

Zehui Li, Vallijah Subasri, Yifei Shen et al.

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

Xinyang Jiang, Lu Liu, Caihua Shan et al.

In this paper, we consider a different data format for images: vector graphics. In contrast to raster graphics which are widely used in image recognition, vector graphics can be scaled up or down into any resolution without aliasing or information loss, due to the analytic representation of the primitives in the document. Furthermore, vector graphics are able to give extra structural information on how low-level elements group together to form high level shapes or structures. These merits of graphic vectors have not been fully leveraged in existing methods. To explore this data format, we target on the fundamental recognition tasks: object localization and classification. We propose an efficient CNN-free pipeline that does not render the graphic into pixels (i.e. rasterization), and takes textual document of the vector graphics as input, called YOLaT (You Only Look at Text). YOLaT builds multi-graphs to model the structural and spatial information in vector graphics, and a dual-stream graph neural network is proposed to detect objects from the graph. Our experiments show that by directly operating on vector graphics, YOLaT out-performs raster-graphic based object detection baselines in terms of both average precision and efficiency.

Xiang Li, Ben Kao, Caihua Shan et al.

We study the problem of applying spectral clustering to cluster multi-scale data, which is data whose clusters are of various sizes and densities. Traditional spectral clustering techniques discover clusters by processing a similarity matrix that reflects the proximity of objects. For multi-scale data, distance-based similarity is not effective because objects of a sparse cluster could be far apart while those of a dense cluster have to be sufficiently close. Following [16], we solve the problem of spectral clustering on multi-scale data by integrating the concept of objects' "reachability similarity" with a given distance-based similarity to derive an objects' coefficient matrix. We propose the algorithm CAST that applies trace Lasso to regularize the coefficient matrix. We prove that the resulting coefficient matrix has the "grouping effect" and that it exhibits "sparsity". We show that these two characteristics imply very effective spectral clustering. We evaluate CAST and 10 other clustering methods on a wide range of datasets w.r.t. various measures. Experimental results show that CAST provides excellent performance and is highly robust across test cases of multi-scale data.

Caihua Shan, Leong Hou U, Nikos Mamoulis et al.

Crowdsourcing can be used to determine a total order for an object set (e.g., the top-10 NBA players) based on crowd opinions. This ranking problem is often decomposed into a set of microtasks (e.g., pairwise comparisons). These microtasks are passed to a large number of workers and their answers are aggregated to infer the ranking. The number of microtasks depends on the budget allocated for the problem. Intuitively, the higher the number of microtask answers, the more accurate the ranking becomes. However, it is often hard to decide the budget required for an accurate ranking. We study how a ranking process can be terminated early, and yet achieve a high-quality ranking and great savings in the budget. We use statistical tools to estimate the quality of the ranking result at any stage of the crowdsourcing process and terminate the process as soon as the desired quality is achieved. Our proposed early-stopping module can be seamlessly integrated with most existing inference algorithms and task assignment methods. We conduct extensive experiments and show that our early-stopping module is better than other existing general stopping criteria. We also implement a prototype system to demonstrate the usability and effectiveness of our approach in practice.

Caihua Shan, Nikos Mamoulis, Reynold Cheng et al.

In this paper, we propose a Deep Reinforcement Learning (RL) framework for task arrangement, which is a critical problem for the success of crowdsourcing platforms. Previous works conduct the personalized recommendation of tasks to workers via supervised learning methods. However, the majority of them only consider the benefit of either workers or requesters independently. In addition, they cannot handle the dynamic environment and may produce sub-optimal results. To address these issues, we utilize Deep Q-Network (DQN), an RL-based method combined with a neural network to estimate the expected long-term return of recommending a task. DQN inherently considers the immediate and future reward simultaneously and can be updated in real-time to deal with evolving data and dynamic changes. Furthermore, we design two DQNs that capture the benefit of both workers and requesters and maximize the profit of the platform. To learn value functions in DQN effectively, we also propose novel state representations, carefully design the computation of Q values, and predict transition probabilities and future states. Experiments on synthetic and real datasets demonstrate the superior performance of our framework.