Recent agent-based recommendation frameworks aim to simulate user behaviors by incorporating memory mechanisms and prompting strategies, but they struggle with hallucinating non-existent items and full-catalog ranking. Besides, a largely underexplored opportunity lies in leveraging LLMs' commonsense reasoning to capture user intent through substitute and complement relationships between items, which are usually implicit in datasets and difficult for traditional ID-based recommenders to capture. In this work, we propose a novel LLM-agent framework, AgentDR, which bridges LLM reasoning with scalable recommendation tools. Our approach delegates full-ranking tasks to traditional models while utilizing LLMs to (i) integrate multiple recommendation outputs based on personalized tool suitability and (ii) reason over substitute and complement relationships grounded in user history. This design mitigates hallucination, scales to large catalogs, and enhances recommendation relevance through relational reasoning. Through extensive experiments on three public grocery datasets, we show that our framework achieves superior full-ranking performance, yielding on average a twofold improvement over its underlying tools. We also introduce a new LLM-based evaluation metric that jointly measures semantic alignment and ranking correctness.

Distributed graph neural network (GNN) training facilitates learning on massive graphs that surpass the storage and computational capabilities of a single machine. Traditional distributed frameworks strive for performance parity with centralized training by maximally recovering cross-instance node dependencies, relying either on inter-instance communication or periodic fallback to centralized training. However, these processes create overhead and constrain the scalability of the framework. In this work, we propose a streamlined framework for distributed GNN training that eliminates these costly operations, yielding improved scalability, convergence speed, and performance over state-of-the-art approaches. Our framework (1) comprises independent trainers that asynchronously learn local models from locally available parts of the training graph and (2) synchronizes these local models only through periodic (time-based) model aggregation. Contrary to prevailing belief, our theoretical analysis shows that it is not essential to maximize the recovery of cross-instance node dependencies to achieve performance parity with centralized training. Instead, our framework leverages randomized assignment of nodes or super-nodes (i.e., collections of original nodes) to partition the training graph in order to enhance data uniformity and minimize discrepancies in gradient and loss function across instances. Experiments on social and e-commerce networks with up to 1.3 billion edges show that our proposed framework achieves state-of-the-art performance and 2.31 \(\times\) speedup compared to the fastest baseline despite using less training data.

Graphs are a fundamental data structure used to represent relationships in domains as diverse as the social sciences, bioinformatics, cybersecurity, the Internet, and more. One of the central observations in network science is that real-world graphs are globally sparse, yet contain numerous "pockets" of high edge density. A fundamental task in graph mining is to discover these dense subgraphs. Most common formulations of the problem involve finding a single (or a few) "optimally" dense subsets. But in most real applications, one does not care for the optimality. Instead, we want to find a large collection of dense subsets that covers a significant fraction of the input graph. We give a mathematical formulation of this problem, using a new definition of regularly triangle-rich (RTR) families. These families capture the notion of dense subgraphs that contain many triangles and have degrees comparable to the subgraph size. We design a provable algorithm, RTRExtractor, that can discover RTR families that approximately cover any RTR set. The algorithm is efficient and is inspired by recent results that use triangle counts for community testing and clustering. We show that RTRExtractor has excellent behavior on a large variety of real-world datasets. It is able to process graphs with hundreds of millions of edges within minutes. Across many datasets, RTRExtractor achieves high coverage using high edge density datasets. For example, the output covers a quarter of the vertices with subgraphs of edge density more than (say) 0.5, for datasets with 10M+ edges. We show an example of how the output of RTRExtractor correlates with meaningful sets of similar vertices in a citation network, demonstrating the utility of RTRExtractor for unsupervised graph discovery tasks.

Developing text mining approaches to mine aspects from customer reviews has been well-studied due to its importance in understanding customer needs and product attributes. In contrast, it remains unclear how to predict the future emerging aspects of a new product that currently has little review information. This task, which we named product aspect forecasting, is critical for recommending new products, but also challenging because of the missing reviews. Here, we propose ForeSeer, a novel textual mining and product embedding approach progressively trained on temporal product graphs for this novel product aspect forecasting task. ForeSeer transfers reviews from similar products on a large product graph and exploits these reviews to predict aspects that might emerge in future reviews. A key novelty of our method is to jointly provide review, product, and aspect embeddings that are both time-sensitive and less affected by extremely imbalanced aspect frequencies. We evaluated ForeSeer on a real-world product review system containing 11,536,382 reviews and 11,000 products over 3 years. We observe that ForeSeer substantially outperformed existing approaches with at least 49.1% AUPRC improvement under the real setting where aspect associations are not given. ForeSeer further improves future link prediction on the product graph and the review aspect association prediction. Collectively, Foreseer offers a novel framework for review forecasting by effectively integrating review text, product network, and temporal information, opening up new avenues for online shopping recommendation and e-commerce applications.

At E-Commerce stores such as Amazon, eBay, and Taobao, the shopping items and the query words that customers use to search for the items form a bipartite graph that captures search behavior. Such a query-item graph can be used to forecast search trends or improve search results. For example, generating query-item associations, which is equivalent to predicting links in the bipartite graph, can yield recommendations that can customize and improve the user search experience. Although the bipartite shopping graphs are straightforward to model search behavior, they suffer from two challenges: 1) The majority of items are sporadically searched and hence have noisy/sparse query associations, leading to a long-tail distribution. 2) Infrequent queries are more likely to link to popular items, leading to another hurdle known as disassortative mixing.

Graph Neural Networks (GNNs) have emerged as powerful tools to encode graph-structured data. Due to their broad applications, there is an increasing need to develop tools to explain how GNNs make decisions given graph-structured data. Existing learning-based GNN explanation approaches are task-specific in training and hence suffer from crucial drawbacks. Specifically, they are incapable of producing explanations for a multitask prediction model with a single explainer. They are also unable to provide explanations in cases where the GNN is trained in a self-supervised manner, and the resulting representations are used in future downstream tasks. To address these limitations, we propose a Task-Agnostic GNN Explainer (TAGE) that is independent of downstream models and trained under self-supervision with no knowledge of downstream tasks. TAGE enables the explanation of GNN embedding models with unseen downstream tasks and allows efficient explanation of multitask models. Our extensive experiments show that TAGE can significantly speed up the explanation efficiency by using the same model to explain predictions for multiple downstream tasks while achieving explanation quality as good as or even better than current state-of-the-art GNN explanation approaches.

Prediction of clinical drug response (CDR) of cancer patients, based on their clinical and molecular profiles obtained prior to administration of the drug, can play a significant role in individualized medicine. Machine learning models have the potential to address this issue but training them requires data from a large number of patients treated with each drug, limiting their feasibility. While large databases of drug response and molecular profiles of preclinical in-vitro cancer cell lines (CCLs) exist for many drugs, it is unclear whether preclinical samples can be used to predict CDR of real patients. We designed a systematic approach to evaluate how well different algorithms, trained on gene expression and drug response of CCLs, can predict CDR of patients. Using data from two large databases, we evaluated various linear and non-linear algorithms, some of which utilized information on gene interactions. Then, we developed a new algorithm called TG-LASSO that explicitly integrates information on samples' tissue of origin with gene expression profiles to improve prediction performance. Our results showed that regularized regression methods provide better prediction performance. However, including the network information or common methods of including information on the tissue of origin did not improve the results. On the other hand, TG-LASSO improved the predictions and distinguished resistant and sensitive patients for 7 out of 13 drugs. Additionally, TG-LASSO identified genes associated with the drug response, including known targets and pathways involved in the drugs' mechanism of action. Moreover, genes identified by TG-LASSO for multiple drugs in a tissue were associated with patient survival. In summary, our analysis suggests that preclinical samples can be used to predict CDR of patients and identify biomarkers of drug sensitivity and survival.

Basal gene expression levels have been shown to be predictive of cellular response to cytotoxic treatments. However, such analyses do not fully reveal complex genotype- phenotype relationships, which are partly encoded in highly interconnected molecular networks. Biological pathways provide a complementary way of understanding drug response variation among individuals. In this study, we integrate chemosensitivity data from a large-scale pharmacogenomics study with basal gene expression data from the CCLE project and prior knowledge of molecular networks to identify specific pathways mediating chemical response. We first develop a computational method called PACER, which ranks pathways for enrichment in a given set of genes using a novel network embedding method. It examines a molecular network that encodes known gene-gene as well as gene-pathway relationships, and determines a vector representation of each gene and pathway in the same low-dimensional vector space. The relevance of a pathway to the given gene set is then captured by the similarity between the pathway vector and gene vectors. To apply this approach to chemosensitivity data, we identify genes whose basal expression levels in a panel of cell lines are correlated with cytotoxic response to a compound, and then rank pathways for relevance to these response-correlated genes using PACER. Extensive evaluation of this approach on benchmarks constructed from databases of compound target genes and large collections of drug response signatures demonstrates its advantages in identifying compound-pathway associations compared to existing statistical methods of pathway enrichment analysis. The associations identified by PACER can serve as testable hypotheses on chemosensitivity pathways and help further study the mechanisms of action of specific cytotoxic drugs. More broadly, PACER represents a novel technique of identifying enriched properties of any gene set of interest while also taking into account networks of known gene-gene relationships and interactions.

Traditional Chinese medicine (TCM) can provide important complementary medical care to modern medicine, and is widely practiced in China and many other countries. Unfortunately, due to its empirical nature and history of trial and error, effective diagnosis and prescription methods are not well-defined. This setback results in a significant challenge in retaining, sharing, and inheriting knowledge among physicians. In this paper, we propose a new asymmetric probabilistic model for the joint analysis of symptoms, diseases, and herbs in patient records to discover and extract latent TCM knowledge. We base our model on the comprehensive evaluation of modern medicine and TCM-specific symptoms in addition to herb prescriptions for particular diseases. Experimental results on a large dataset demonstrate the effectiveness of the proposed model for discovering useful knowledge and its potential clinical applications.