Roshni G. Iyer

Zhichun Guo, Kehan Guo, Bozhao Nan et al.

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recently, MRL has achieved considerable progress, especially in methods based on deep molecular graph learning. In this survey, we systematically review these graph-based molecular representation techniques, especially the methods incorporating chemical domain knowledge. Specifically, we first introduce the features of 2D and 3D molecular graphs. Then we summarize and categorize MRL methods into three groups based on their input. Furthermore, we discuss some typical chemical applications supported by MRL. To facilitate studies in this fast-developing area, we also list the benchmarks and commonly used datasets in the paper. Finally, we share our thoughts on future research directions.

Roshni G. Iyer, Wei Wang, Yizhou Sun

Recent graph neural networks (GNNs) with the attention mechanism have historically been limited to small-scale homogeneous graphs (HoGs). However, GNNs handling heterogeneous graphs (HeGs), which contain several entity and relation types, all have shortcomings in handling attention. Most GNNs that learn graph attention for HeGs learn either node-level or relation-level attention, but not both, limiting their ability to predict both important entities and relations in the HeG. Even the best existing method that learns both levels of attention has the limitation of assuming graph relations are independent and that its learned attention disregards this dependency association. To effectively model both multi-relational and multi-entity large-scale HeGs, we present Bi-Level Attention Graph Neural Networks (BA-GNN), scalable neural networks (NNs) that use a novel bi-level graph attention mechanism. BA-GNN models both node-node and relation-relation interactions in a personalized way, by hierarchically attending to both types of information from local neighborhood contexts instead of the global graph context. Rigorous experiments on seven real-world HeGs show BA-GNN consistently outperforms all baselines, and demonstrate quality and transferability of its learned relation-level attention to improve performance of other GNNs.

Roshni G. Iyer, Yunsheng Bai, Wei Wang et al.

Two-view knowledge graphs (KGs) jointly represent two components: an ontology view for abstract and commonsense concepts, and an instance view for specific entities that are instantiated from ontological concepts. As such, these KGs contain heterogeneous structures that are hierarchical, from the ontology-view, and cyclical, from the instance-view. Despite these various structures in KGs, most recent works on embedding KGs assume that the entire KG belongs to only one of the two views but not both simultaneously. For works that seek to put both views of the KG together, the instance and ontology views are assumed to belong to the same geometric space, such as all nodes embedded in the same Euclidean space or non-Euclidean product space, an assumption no longer reasonable for two-view KGs where different portions of the graph exhibit different structures. To address this issue, we define and construct a dual-geometric space embedding model (DGS) that models two-view KGs using a complex non-Euclidean geometric space, by embedding different portions of the KG in different geometric spaces. DGS utilizes the spherical space, hyperbolic space, and their intersecting space in a unified framework for learning embeddings. Furthermore, for the spherical space, we propose novel closed spherical space operators that directly operate in the spherical space without the need for mapping to an approximate tangent space. Experiments on public datasets show that DGS significantly outperforms previous state-of-the-art baseline models on KG completion tasks, demonstrating its ability to better model heterogeneous structures in KGs.

Roshni G. Iyer, Yewen Wang, Wei Wang et al.

It is largely agreed that social network links are formed due to either homophily or social influence. Inspired by this, we aim at understanding the generation of links via providing a novel embedding-based graph formation model. Different from existing graph representation learning, where link generation probabilities are defined as a simple function of the corresponding node embeddings, we model the link generation as a mixture model of the two factors. In addition, we model the homophily factor in spherical space and the influence factor in hyperbolic space to accommodate the fact that (1) homophily results in cycles and (2) influence results in hierarchies in networks. We also design a special projection to align these two spaces. We call this model Non-Euclidean Mixture Model, i.e., NMM. We further integrate NMM with our non-Euclidean graph variational autoencoder (VAE) framework, NMM-GNN. NMM-GNN learns embeddings through a unified framework which uses non-Euclidean GNN encoders, non-Euclidean Gaussian priors, a non-Euclidean decoder, and a novel space unification loss component to unify distinct non-Euclidean geometric spaces. Experiments on public datasets show NMM-GNN significantly outperforms state-of-the-art baselines on social network generation and classification tasks, demonstrating its ability to better explain how the social network is formed.

Roshni G. Iyer, Wei Wang, Yizhou Sun

We present Bi-Level Attention-Based Relational Graph Convolutional Networks (BR-GCN), unique neural network architectures that utilize masked self-attentional layers with relational graph convolutions, to effectively operate on highly multi-relational data. BR-GCN models use bi-level attention to learn node embeddings through (1) node-level attention, and (2) relation-level attention. The node-level self-attentional layers use intra-relational graph interactions to learn relation-specific node embeddings using a weighted aggregation of neighborhood features in a sparse subgraph region. The relation-level self-attentional layers use inter-relational graph interactions to learn the final node embeddings using a weighted aggregation of relation-specific node embeddings. The BR-GCN bi-level attention mechanism extends Transformer-based multiplicative attention from the natural language processing (NLP) domain, and Graph Attention Networks (GAT)-based attention, to large-scale heterogeneous graphs (HGs). On node classification, BR-GCN outperforms baselines from 0.29% to 14.95% as a stand-alone model, and on link prediction, BR-GCN outperforms baselines from 0.02% to 7.40% as an auto-encoder model. We also conduct ablation studies to evaluate the quality of BR-GCN's relation-level attention and discuss how its learning of graph structure may be transferred to enrich other graph neural networks (GNNs). Through various experiments, we show that BR-GCN's attention mechanism is both scalable and more effective in learning compared to state-of-the-art GNNs.

Shashank Kirtania, Param Biyani, Priyanshu Gupta et al.

Large Language Model (LLM)-based agents are increasingly applied to tasks requiring structured reasoning, tool use, and environmental adaptation, such as data manipulation, multistep planning, and computer-use automation. However, despite their versatility, current training paradigms for model weight optimization methods, like PPO and GRPO, remain relatively impractical with their high computational overhead for rollout convergence. In addition, the resulting agent policies are difficult to interpret, adapt, or incrementally improve. To address this, we investigate creating and refining structured memory of experiential learning of an agent from its environment as an alternative route to agent optimization. We introduce BREW (Bootstrapping expeRientially-learned Environmental knoWledge), a framework for agent optimization for downstream tasks via KB construction and refinement. In our formulation, we introduce an effective method for partitioning agent memory for more efficient retrieval and refinement. BREW uses task graders and behavior rubrics to learn insights while leveraging state-space search for ensuring robustness from the noise and non-specificity in natural language. Empirical results on real world, domain-grounded benchmarks -- OSWorld, $τ^2$Bench, and SpreadsheetBench -- show BREW achieves $10-20\%$ improvement in task precision, $10-15\%$ reduction in API/tool calls leading to faster execution time, all while maintaining computational efficiency on par with base models. Unlike prior work where memory is treated as static context, we establish the KB as a modular and controllable substrate for agent optimization -- an explicit lever for shaping behavior in a transparent, interpretable, and extensible manner.

Khiem Le, Zhichun Guo, Kaiwen Dong et al.

Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain remains restricted, especially in solving molecule-related tasks. This challenge is attributed to their inherent limitations in comprehending molecules using only common textual representations, i.e. SMILES strings. In this study, we seek to enhance the ability of LLMs to comprehend molecules by equipping them with a multi-modal external module, termed MolX. Instead of directly using SMILES strings to represent a molecule, we utilize specific encoders to extract fine-grained features from both SMILES string and 2D molecular graph representations for feeding into an LLM. A hand-crafted molecular fingerprint is incorporated to leverage its embedded domain knowledge. To establish an alignment between MolX and the LLM's textual input space, the model in which the LLM is frozen, is pre-trained with a strategy including a diverse set of tasks. Experimental evaluations show that our proposed method outperforms baselines across downstream molecule-related tasks ranging from molecule-to-text translation to molecular property prediction, with and without fine-tuning the LLM, while only introducing a small number of trainable parameters-0.53% and 0.82%, respectively.

Roshni G. Iyer, Thuy Vu, Alessandro Moschitti et al.

This research studies graph-based approaches for Answer Sentence Selection (AS2), an essential component for retrieval-based Question Answering (QA) systems. During offline learning, our model constructs a small-scale relevant training graph per question in an unsupervised manner, and integrates with Graph Neural Networks. Graph nodes are question sentence to answer sentence pairs. We train and integrate state-of-the-art (SOTA) models for computing scores between question-question, question-answer, and answer-answer pairs, and use thresholding on relevance scores for creating graph edges. Online inference is then performed to solve the AS2 task on unseen queries. Experiments on two well-known academic benchmarks and a real-world dataset show that our approach consistently outperforms SOTA QA baseline models.

Roshni G. Iyer, Yizhou Sun, Wei Wang et al.

Traditional code transformation structures, such as abstract syntax trees (ASTs), conteXtual flow graphs (XFGs), and more generally, compiler intermediate representations (IRs), may have limitations in extracting higher-order semantics from code. While work has already begun on higher-order semantics lifting (e.g., Aroma's simplified parse tree (SPT), verified lifting's lambda calculi, and Halide's intentional domain specific language (DSL)), research in this area is still immature. To continue to advance this research, we present the program-derived semantics graph, a new graphical structure to capture semantics of code. The PSG is designed to provide a single structure for capturing program semantics at multiple levels of abstraction. The PSG may be in a class of emerging structural representations that cannot be built from a traditional set of predefined rules and instead must be learned. In this paper, we describe the PSG and its fundamental structural differences compared to state-of-the-art structures. Although our exploration into the PSG is in its infancy, our early results and architectural analysis indicate it is a promising new research direction to automatically extract program semantics.