Weighted Diversified Sampling for Efficient Data-Driven Single-Cell Gene-Gene Interaction Discovery

Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational tools, leveraging an advanced Transformer model, to unearth noteworthy gene-gene interactions. Despite the efficacy of Transformer models, their parameter intensity presents a bottleneck in data ingestion, hindering data efficiency. To mitigate this, we introduce a novel weighted diversified sampling algorithm. This algorithm computes the diversity score of each data sample in just two passes of the dataset, facilitating efficient subset generation for interaction discovery. Our extensive experimentation demonstrates that by sampling a mere 1\% of the single-cell dataset, we achieve performance comparable to that of utilizing the entire dataset.

GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data

By leveraging GPT-4 for ontology narration, we developed GPTON to infuse structured knowledge into LLMs through verbalized ontology terms, achieving accurate text and ontology annotations for over 68% of gene sets in the top five predictions. Manual evaluations confirm GPTON's robustness, highlighting its potential to harness LLMs and structured knowledge to significantly advance biomedical research beyond gene set annotation.

AIPatient: Simulating Patients with EHRs and LLM Powered Agentic Workflow

Simulated patient systems play a crucial role in modern medical education and research, providing safe, integrative learning environments and enabling clinical decision-making simulations. Large Language Models (LLM) could advance simulated patient systems by replicating medical conditions and patient-doctor interactions with high fidelity and low cost. However, ensuring the effectiveness and trustworthiness of these systems remains a challenge, as they require a large, diverse, and precise patient knowledgebase, along with a robust and stable knowledge diffusion to users. Here, we developed AIPatient, an advanced simulated patient system with AIPatient Knowledge Graph (AIPatient KG) as the input and the Reasoning Retrieval-Augmented Generation (Reasoning RAG) agentic workflow as the generation backbone. AIPatient KG samples data from Electronic Health Records (EHRs) in the Medical Information Mart for Intensive Care (MIMIC)-III database, producing a clinically diverse and relevant cohort of 1,495 patients with high knowledgebase validity (F1 0.89). Reasoning RAG leverages six LLM powered agents spanning tasks including retrieval, KG query generation, abstraction, checker, rewrite, and summarization. This agentic framework reaches an overall accuracy of 94.15% in EHR-based medical Question Answering (QA), outperforming benchmarks that use either no agent or only partial agent integration. Our system also presents high readability (median Flesch Reading Ease 77.23; median Flesch Kincaid Grade 5.6), robustness (ANOVA F-value 0.6126, p<0.1), and stability (ANOVA F-value 0.782, p<0.1). The promising performance of the AIPatient system highlights its potential to support a wide range of applications, including medical education, model evaluation, and system integration.

CL4KGE: A Curriculum Learning Method for Knowledge Graph Embedding

Knowledge graph embedding (KGE) constitutes a foundational task, directed towards learning representations for entities and relations within knowledge graphs (KGs), with the objective of crafting representations comprehensive enough to approximate the logical and symbolic interconnections among entities. In this paper, we define a metric Z-counts to measure the difficulty of training each triple ($<$head entity, relation, tail entity$>$) in KGs with theoretical analysis. Based on this metric, we propose \textbf{CL4KGE}, an efficient \textbf{C}urriculum \textbf{L}earning based training strategy for \textbf{KGE}. This method includes a difficulty measurer and a training scheduler that aids in the training of KGE models. Our approach possesses the flexibility to act as a plugin within a wide range of KGE models, with the added advantage of adaptability to the majority of KGs in existence. The proposed method has been evaluated on popular KGE models, and the results demonstrate that it enhances the state-of-the-art methods. The use of Z-counts as a metric has enabled the identification of challenging triples in KGs, which helps in devising effective training strategies.

SAM2-PATH: A better segment anything model for semantic segmentation in digital pathology

The semantic segmentation task in pathology plays an indispensable role in assisting physicians in determining the condition of tissue lesions. Foundation models, such as the SAM (Segment Anything Model) and SAM2, exhibit exceptional performance in instance segmentation within everyday natural scenes. SAM-PATH has also achieved impressive results in semantic segmentation within the field of pathology. However, in computational pathology, the models mentioned above still have the following limitations. The pre-trained encoder models suffer from a scarcity of pathology image data; SAM and SAM2 are not suitable for semantic segmentation. In this paper, we have designed a trainable Kolmogorov-Arnold Networks(KAN) classification module within the SAM2 workflow, and we have introduced the largest pretrained vision encoder for histopathology (UNI) to date. Our proposed framework, SAM2-PATH, augments SAM2's capability to perform semantic segmentation in digital pathology autonomously, eliminating the need for human provided input prompts. The experimental results demonstrate that, after fine-tuning the KAN classification module and decoder, Our dataset has achieved competitive results on publicly available pathology data. The code has been open-sourced and can be found at the following address: https://github.com/simzhangbest/SAM2PATH.

Large Language Model Enhanced Knowledge Representation Learning: A Survey

The integration of Large Language Models (LLMs) with Knowledge Representation Learning (KRL) signifies a pivotal advancement in the field of artificial intelligence, enhancing the ability to capture and utilize complex knowledge structures. This synergy leverages the advanced linguistic and contextual understanding capabilities of LLMs to improve the accuracy, adaptability, and efficacy of KRL, thereby expanding its applications and potential. Despite the increasing volume of research focused on embedding LLMs within the domain of knowledge representation, a thorough review that examines the fundamental components and processes of these enhanced models is conspicuously absent. Our survey addresses this by categorizing these models based on three distinct Transformer architectures, and by analyzing experimental data from various KRL downstream tasks to evaluate the strengths and weaknesses of each approach. Finally, we identify and explore potential future research directions in this emerging yet underexplored domain, proposing pathways for continued progress.

Decision-focused Graph Neural Networks for Combinatorial Optimization

In recent years, there has been notable interest in investigating combinatorial optimization (CO) problems by neural-based framework. An emerging strategy to tackle these challenging problems involves the adoption of graph neural networks (GNNs) as an alternative to traditional algorithms, a subject that has attracted considerable attention. Despite the growing popularity of GNNs and traditional algorithm solvers in the realm of CO, there is limited research on their integrated use and the correlation between them within an end-to-end framework. The primary focus of our work is to formulate a more efficient and precise framework for CO by employing decision-focused learning on graphs. Additionally, we introduce a decision-focused framework that utilizes GNNs to address CO problems with auxiliary support. To realize an end-to-end approach, we have designed two cascaded modules: (a) an unsupervised trained graph predictive model, and (b) a solver for quadratic binary unconstrained optimization. Empirical evaluations are conducted on various classical tasks, including maximum cut, maximum independent set, and minimum vertex cover. The experimental results on classical CO problems (i.e. MaxCut, MIS, and MVC) demonstrate the superiority of our method over both the standalone GNN approach and classical methods.

Combinatorial Optimization with Automated Graph Neural Networks

In recent years, graph neural networks (GNNs) have become increasingly popular for solving NP-hard combinatorial optimization (CO) problems, such as maximum cut and maximum independent set. The core idea behind these methods is to represent a CO problem as a graph and then use GNNs to learn the node/graph embedding with combinatorial information. Although these methods have achieved promising results, given a specific CO problem, the design of GNN architectures still requires heavy manual work with domain knowledge. Existing automated GNNs are mostly focused on traditional graph learning problems, which is inapplicable to solving NP-hard CO problems. To this end, we present a new class of \textbf{AUTO}mated \textbf{G}NNs for solving \textbf{NP}-hard problems, namely \textbf{AutoGNP}. We represent CO problems by GNNs and focus on two specific problems, i.e., mixed integer linear programming and quadratic unconstrained binary optimization. The idea of AutoGNP is to use graph neural architecture search algorithms to automatically find the best GNNs for a given NP-hard combinatorial optimization problem. Compared with existing graph neural architecture search algorithms, AutoGNP utilizes two-hop operators in the architecture search space. Moreover, AutoGNP utilizes simulated annealing and a strict early stopping policy to avoid local optimal solutions. Empirical results on benchmark combinatorial problems demonstrate the superiority of our proposed model.

Collaborate to Adapt: Source-Free Graph Domain Adaptation via Bi-directional Adaptation

Unsupervised Graph Domain Adaptation (UGDA) has emerged as a practical solution to transfer knowledge from a label-rich source graph to a completely unlabelled target graph. However, most methods require a labelled source graph to provide supervision signals, which might not be accessible in the real-world settings due to regulations and privacy concerns. In this paper, we explore the scenario of source-free unsupervised graph domain adaptation, which tries to address the domain adaptation problem without accessing the labelled source graph. Specifically, we present a novel paradigm called GraphCTA, which performs model adaptation and graph adaptation collaboratively through a series of procedures: (1) conduct model adaptation based on node's neighborhood predictions in target graph considering both local and global information; (2) perform graph adaptation by updating graph structure and node attributes via neighborhood contrastive learning; and (3) the updated graph serves as an input to facilitate the subsequent iteration of model adaptation, thereby establishing a collaborative loop between model adaptation and graph adaptation. Comprehensive experiments are conducted on various public datasets. The experimental results demonstrate that our proposed model outperforms recent source-free baselines by large margins.

HyCubE: Efficient Knowledge Hypergraph 3D Circular Convolutional Embedding

Existing knowledge hypergraph embedding methods mainly focused on improving model performance, but their model structures are becoming more complex and redundant. Furthermore, due to the inherent complex semantic knowledge, the computation of knowledge hypergraph embedding models is often very expensive, leading to low efficiency. In this paper, we propose a feature interaction and extraction-enhanced 3D circular convolutional embedding model, HyCubE, which designs a novel 3D circular convolutional neural network and introduces the alternate mask stack strategy to achieve efficient n-ary knowledge hypergraph embedding. By adaptively adjusting the 3D circular convolution kernel size and uniformly embedding the entity position information, HyCubE improves the model performance with fewer parameters and reaches a better trade-off between model performance and efficiency. In addition, we use 1-N multilinear scoring based on the entity mask mechanism to further accelerate the model training efficiency. Finally, extensive experimental results on all datasets demonstrate that HyCubE consistently outperforms state-of-the-art baselines, with an average improvement of 4.08%-10.77% and a maximum improvement of 21.16% across all metrics. Commendably, HyCubE speeds up by an average of 7.55x and reduces memory usage by an average of 77.02% compared to the latest state-of-the-art baselines.