Chain of Ideas: Revolutionizing Research Via Novel Idea Development with LLM Agents

Effective research ideation is a critical step for scientific research. However, the exponential increase in scientific literature makes it challenging for researchers to stay current with recent advances and identify meaningful research directions. Recent developments in large language models~(LLMs) suggest a promising avenue for automating the generation of novel research ideas. However, existing methods for idea generation either trivially prompt LLMs or directly expose LLMs to extensive literature without indicating useful information. Inspired by the research process of human researchers, we propose a Chain-of-Ideas~(CoI) agent, an LLM-based agent that organizes relevant literature in a chain structure to effectively mirror the progressive development in a research domain. This organization facilitates LLMs to capture the current advancements in research, thereby enhancing their ideation capabilities. Furthermore, we propose Idea Arena, an evaluation protocol that can comprehensively evaluate idea generation methods from different perspectives, aligning closely with the preferences of human researchers. Experimental results indicate that the CoI agent consistently outperforms other methods and shows comparable quality as humans in research idea generation. Moreover, our CoI agent is budget-friendly, with a minimum cost of \$0.50 to generate a candidate idea and its corresponding experimental design.

Graph Pre-Training Models Are Strong Anomaly Detectors

Graph Anomaly Detection (GAD) is a challenging and practical research topic where Graph Neural Networks (GNNs) have recently shown promising results. The effectiveness of existing GNNs in GAD has been mainly attributed to the simultaneous learning of node representations and the classifier in an end-to-end manner. Meanwhile, graph pre-training, the two-stage learning paradigm such as DGI and GraphMAE, has shown potential in leveraging unlabeled graph data to enhance downstream tasks, yet its impact on GAD remains under-explored. In this work, we show that graph pre-training models are strong graph anomaly detectors. Specifically, we demonstrate that pre-training is highly competitive, markedly outperforming the state-of-the-art end-to-end training models when faced with limited supervision. To understand this phenomenon, we further uncover pre-training enhances the detection of distant, under-represented, unlabeled anomalies that go beyond 2-hop neighborhoods of known anomalies, shedding light on its superior performance against end-to-end models. Moreover, we extend our examination to the potential of pre-training in graph-level anomaly detection. We envision this work to stimulate a re-evaluation of pre-training's role in GAD and offer valuable insights for future research.

Chain of Ideas: Revolutionizing Research in Novel Idea Development with LLM Agents

Effective research ideation is a critical step for scientific research. However, the exponential increase in scientific literature makes it challenging for researchers to stay current with recent advances and identify meaningful research directions. Recent developments in large language models~(LLMs) suggest a promising avenue for automating the generation of novel research ideas. However, existing methods for idea generation either trivially prompt LLMs or directly expose LLMs to extensive literature without indicating useful information. Inspired by the research process of human researchers, we propose a Chain-of-Ideas~(CoI) agent, an LLM-based agent that organizes relevant literature in a chain structure to effectively mirror the progressive development in a research domain. This organization facilitates LLMs to capture the current advancements in research, thereby enhancing their ideation capabilities. Furthermore, we propose Idea Arena, an evaluation protocol that can comprehensively evaluate idea generation methods from different perspectives, aligning closely with the preferences of human researchers. Experimental results indicate that the CoI agent consistently outperforms other methods and shows comparable quality as humans in research idea generation. Moreover, our CoI agent is budget-friendly, with a minimum cost of \$0.50 to generate a candidate idea and its corresponding experimental design.

Adaptive Coordinators and Prompts on Heterogeneous Graphs for Cross-Domain Recommendations

In the online digital world, users frequently engage with diverse items across multiple domains (e.g., e-commerce platforms, streaming services, and social media networks), forming complex heterogeneous interaction graphs. Leveraging this multi-domain information can undoubtedly enhance the performance of recommendation systems by providing more comprehensive user insights and alleviating data sparsity in individual domains. However, integrating multi-domain knowledge for the cross-domain recommendation is very hard due to inherent disparities in user behavior and item characteristics and the risk of negative transfer, where irrelevant or conflicting information from the source domains adversely impacts the target domain's performance. To address these challenges, we offer HAGO, a novel framework with $\textbf{H}$eterogeneous $\textbf{A}$daptive $\textbf{G}$raph co$\textbf{O}$rdinators, which dynamically integrate multi-domain graphs into a cohesive structure by adaptively adjusting the connections between coordinators and multi-domain graph nodes, thereby enhancing beneficial inter-domain interactions while mitigating negative transfer effects. Additionally, we develop a universal multi-domain graph pre-training strategy alongside HAGO to collaboratively learn high-quality node representations across domains. To effectively transfer the learned multi-domain knowledge to the target domain, we design an effective graph prompting method, which incorporates pre-trained embeddings with learnable prompts for the recommendation task. Our framework is compatible with various graph-based models and pre-training techniques, demonstrating broad applicability and effectiveness. Further experimental results show that our solutions outperform state-of-the-art methods in multi-domain recommendation scenarios and highlight their potential for real-world applications.

GenCA: A Text-conditioned Generative Model for Realistic and Drivable Codec Avatars

Photo-realistic and controllable 3D avatars are crucial for various applications such as virtual and mixed reality (VR/MR), telepresence, gaming, and film production. Traditional methods for avatar creation often involve time-consuming scanning and reconstruction processes for each avatar, which limits their scalability. Furthermore, these methods do not offer the flexibility to sample new identities or modify existing ones. On the other hand, by learning a strong prior from data, generative models provide a promising alternative to traditional reconstruction methods, easing the time constraints for both data capture and processing. Additionally, generative methods enable downstream applications beyond reconstruction, such as editing and stylization. Nonetheless, the research on generative 3D avatars is still in its infancy, and therefore current methods still have limitations such as creating static avatars, lacking photo-realism, having incomplete facial details, or having limited drivability. To address this, we propose a text-conditioned generative model that can generate photo-realistic facial avatars of diverse identities, with more complete details like hair, eyes and mouth interior, and which can be driven through a powerful non-parametric latent expression space. Specifically, we integrate the generative and editing capabilities of latent diffusion models with a strong prior model for avatar expression driving. Our model can generate and control high-fidelity avatars, even those out-of-distribution. We also highlight its potential for downstream applications, including avatar editing and single-shot avatar reconstruction.

Relaxing Continuous Constraints of Equivariant Graph Neural Networks for Physical Dynamics Learning

Incorporating Euclidean symmetries (e.g. rotation equivariance) as inductive biases into graph neural networks has improved their generalization ability and data efficiency in unbounded physical dynamics modeling. However, in various scientific and engineering applications, the symmetries of dynamics are frequently discrete due to the boundary conditions. Thus, existing GNNs either overlook necessary symmetry, resulting in suboptimal representation ability, or impose excessive equivariance, which fails to generalize to unobserved symmetric dynamics. In this work, we propose a general Discrete Equivariant Graph Neural Network (DEGNN) that guarantees equivariance to a given discrete point group. Specifically, we show that such discrete equivariant message passing could be constructed by transforming geometric features into permutation-invariant embeddings. Through relaxing continuous equivariant constraints, DEGNN can employ more geometric feature combinations to approximate unobserved physical object interaction functions. Two implementation approaches of DEGNN are proposed based on ranking or pooling permutation-invariant functions. We apply DEGNN to various physical dynamics, ranging from particle, molecular, crowd to vehicle dynamics. In twenty scenarios, DEGNN significantly outperforms existing state-of-the-art approaches. Moreover, we show that DEGNN is data efficient, learning with less data, and can generalize across scenarios such as unobserved orientation.

MGCP: A Multi-Grained Correlation based Prediction Network for Multivariate Time Series

Multivariate time series prediction is widely used in daily life, which poses significant challenges due to the complex correlations that exist at multi-grained levels. Unfortunately, the majority of current time series prediction models fail to simultaneously learn the correlations of multivariate time series at multi-grained levels, resulting in suboptimal performance. To address this, we propose a Multi-Grained Correlations-based Prediction (MGCP) Network, which simultaneously considers the correlations at three granularity levels to enhance prediction performance. Specifically, MGCP utilizes Adaptive Fourier Neural Operators and Graph Convolutional Networks to learn the global spatiotemporal correlations and inter-series correlations, enabling the extraction of potential features from multivariate time series at fine-grained and medium-grained levels. Additionally, MGCP employs adversarial training with an attention mechanism-based predictor and conditional discriminator to optimize prediction results at coarse-grained level, ensuring high fidelity between the generated forecast results and the actual data distribution. Finally, we compare MGCP with several state-of-the-art time series prediction algorithms on real-world benchmark datasets, and our results demonstrate the generality and effectiveness of the proposed model.

Equivariant Spatio-Temporal Attentive Graph Networks to Simulate Physical Dynamics

Learning to represent and simulate the dynamics of physical systems is a crucial yet challenging task. Existing equivariant Graph Neural Network (GNN) based methods have encapsulated the symmetry of physics, \emph{e.g.}, translations, rotations, etc, leading to better generalization ability. Nevertheless, their frame-to-frame formulation of the task overlooks the non-Markov property mainly incurred by unobserved dynamics in the environment. In this paper, we reformulate dynamics simulation as a spatio-temporal prediction task, by employing the trajectory in the past period to recover the Non-Markovian interactions. We propose Equivariant Spatio-Temporal Attentive Graph Networks (ESTAG), an equivariant version of spatio-temporal GNNs, to fulfill our purpose. At its core, we design a novel Equivariant Discrete Fourier Transform (EDFT) to extract periodic patterns from the history frames, and then construct an Equivariant Spatial Module (ESM) to accomplish spatial message passing, and an Equivariant Temporal Module (ETM) with the forward attention and equivariant pooling mechanisms to aggregate temporal message. We evaluate our model on three real datasets corresponding to the molecular-, protein- and macro-level. Experimental results verify the effectiveness of ESTAG compared to typical spatio-temporal GNNs and equivariant GNNs.

Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields, including drug discovery and materials science. Existing studies adopt a global alignment approach to learn the knowledge from different modalities. These global alignment approaches fail to capture fine-grained information, such as molecular fragments and their corresponding textual description, which is crucial for downstream tasks. Furthermore, it is incapable to model such information using a similar global alignment strategy due to data scarcity of paired local part annotated data from existing datasets. In this paper, we propose Atomas, a multi-modal molecular representation learning framework to jointly learn representations from SMILES string and text. We design a Hierarchical Adaptive Alignment model to concurrently learn the fine-grained fragment correspondence between two modalities and align these representations of fragments in three levels. Additionally, Atomas's end-to-end training framework incorporates the tasks of understanding and generating molecule, thereby supporting a wider range of downstream tasks. In the retrieval task, Atomas exhibits robust generalization ability and outperforms the baseline by 30.8% of recall@1 on average. In the generation task, Atomas achieves state-of-the-art results in both molecule captioning task and molecule generation task. Moreover, the visualization of the Hierarchical Adaptive Alignment model further confirms the chemical significance of our approach. Our codes can be found at https://anonymous.4open.science/r/Atomas-03C3.

Functional Protein Design with Local Domain Alignment

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation (PAAG), a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a nearly sixfold increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 8.7% in the immunoglobulin domain) in comparison to the existing model.