Relationship Discovery for Drug Recommendation

Medication recommendation systems are designed to deliver personalized drug suggestions that are closely aligned with individual patient needs. Previous studies have primarily concentrated on developing medication embeddings, achieving significant progress. Nonetheless, these approaches often fall short in accurately reflecting individual patient profiles, mainly due to challenges in distinguishing between various patient conditions and the inability to establish precise correlations between specific conditions and appropriate medications. In response to these issues, we introduce DisMed, a model that focuses on patient conditions to enhance personalization. DisMed employs causal inference to discern clear, quantifiable causal links. It then examines patient conditions in depth, recognizing and adapting to the evolving nuances of these conditions, and mapping them directly to corresponding medications. Additionally, DisMed leverages data from multiple patient visits to propose combinations of medications. Comprehensive testing on real-world datasets demonstrates that DisMed not only improves the customization of patient profiles but also surpasses leading models in both precision and safety.

KGExplainer: Towards Exploring Connected Subgraph Explanations for Knowledge Graph Completion

Knowledge graph completion (KGC) aims to alleviate the inherent incompleteness of knowledge graphs (KGs), which is a critical task for various applications, such as recommendations on the web. Although knowledge graph embedding (KGE) models have demonstrated superior predictive performance on KGC tasks, these models infer missing links in a black-box manner that lacks transparency and accountability, preventing researchers from developing accountable models. Existing KGE-based explanation methods focus on exploring key paths or isolated edges as explanations, which is information-less to reason target prediction. Additionally, the missing ground truth leads to these explanation methods being ineffective in quantitatively evaluating explored explanations. To overcome these limitations, we propose KGExplainer, a model-agnostic method that identifies connected subgraph explanations and distills an evaluator to assess them quantitatively. KGExplainer employs a perturbation-based greedy search algorithm to find key connected subgraphs as explanations within the local structure of target predictions. To evaluate the quality of the explored explanations, KGExplainer distills an evaluator from the target KGE model. By forwarding the explanations to the evaluator, our method can examine the fidelity of them. Extensive experiments on benchmark datasets demonstrate that KGExplainer yields promising improvement and achieves an optimal ratio of 83.3% in human evaluation.

Dual-Granularity Medication Recommendation Based on Causal Inference

As medical demands grow and machine learning technology advances, AI-based diagnostic and treatment systems are garnering increasing attention. Medication recommendation aims to integrate patients' long-term health records with medical knowledge, recommending accuracy and safe medication combinations for specific conditions. However, most existing researches treat medication recommendation systems merely as variants of traditional recommendation systems, overlooking the heterogeneity between medications and diseases. To address this challenge, we propose DGMed, a framework for medication recommendation. DGMed utilizes causal inference to uncover the connections among medical entities and presents an innovative feature alignment method to tackle heterogeneity issues. Specifically, this study first applies causal inference to analyze the quantified therapeutic effects of medications on specific diseases from historical records, uncovering potential links between medical entities. Subsequently, we integrate molecular-level knowledge, aligning the embeddings of medications and diseases within the molecular space to effectively tackle their heterogeneity. Ultimately, based on relationships at the entity level, we adaptively adjust the recommendation probabilities of medication and recommend medication combinations according to the patient's current health condition. Experimental results on a real-world dataset show that our method surpasses existing state-of-the-art baselines in four evaluation metrics, demonstrating superior performance in both accuracy and safety aspects. Compared to the sub-optimal model, our approach improved accuracy by 4.40%, reduced the risk of side effects by 6.14%, and increased time efficiency by 47.15%.

Learning to Denoise Unreliable Interactions for Link Prediction on Biomedical Knowledge Graph

Link prediction in biomedical knowledge graphs (KGs) aims at predicting unknown interactions between entities, including drug-target interaction (DTI) and drug-drug interaction (DDI), which is critical for drug discovery and therapeutics. Previous methods prefer to utilize the rich semantic relations and topological structure of the KG to predict missing links, yielding promising outcomes. However, all these works only focus on improving the predictive performance without considering the inevitable noise and unreliable interactions existing in the KGs, which limits the development of KG-based computational methods. To address these limitations, we propose a Denoised Link Prediction framework, called DenoisedLP. DenoisedLP obtains reliable interactions based on the local subgraph by denoising noisy links in a learnable way, providing a universal module for mining underlying task-relevant relations. To collaborate with the smoothed semantic information, DenoisedLP introduces the semantic subgraph by blurring conflict relations around the predicted link. By maximizing the mutual information between the reliable structure and smoothed semantic relations, DenoisedLP emphasizes the informative interactions for predicting relation-specific links. Experimental results on real-world datasets demonstrate that DenoisedLP outperforms state-of-the-art methods on DTI and DDI prediction tasks, and verify the effectiveness and robustness of denoising unreliable interactions on the contaminated KGs.

Cycle Invariant Positional Encoding for Graph Representation Learning

Cycles are fundamental elements in graph-structured data and have demonstrated their effectiveness in enhancing graph learning models. To encode such information into a graph learning framework, prior works often extract a summary quantity, ranging from the number of cycles to the more sophisticated persistence diagram summaries. However, more detailed information, such as which edges are encoded in a cycle, has not yet been used in graph neural networks. In this paper, we make one step towards addressing this gap, and propose a structure encoding module, called CycleNet, that encodes cycle information via edge structure encoding in a permutation invariant manner. To efficiently encode the space of all cycles, we start with a cycle basis (i.e., a minimal set of cycles generating the cycle space) which we compute via the kernel of the 1-dimensional Hodge Laplacian of the input graph. To guarantee the encoding is invariant w.r.t. the choice of cycle basis, we encode the cycle information via the orthogonal projector of the cycle basis, which is inspired by BasisNet proposed by Lim et al. We also develop a more efficient variant which however requires that the input graph has a unique shortest cycle basis. To demonstrate the effectiveness of the proposed module, we provide some theoretical understandings of its expressive power. Moreover, we show via a range of experiments that networks enhanced by our CycleNet module perform better in various benchmarks compared to several existing SOTA models.

AdaCCD: Adaptive Semantic Contrasts Discovery based Cross Lingual Adaptation for Code Clone Detection

Code Clone Detection, which aims to retrieve functionally similar programs from large code bases, has been attracting increasing attention. Modern software often involves a diverse range of programming languages. However, current code clone detection methods are generally limited to only a few popular programming languages due to insufficient annotated data as well as their own model design constraints. To address these issues, we present AdaCCD, a novel cross-lingual adaptation method that can detect cloned codes in a new language without any annotations in that language. AdaCCD leverages language-agnostic code representations from pre-trained programming language models and propose an Adaptively Refined Contrastive Learning framework to transfer knowledge from resource-rich languages to resource-poor languages. We evaluate the cross-lingual adaptation results of AdaCCD by constructing a multilingual code clone detection benchmark consisting of 5 programming languages. AdaCCD achieves significant improvements over other baselines, and it is even comparable to supervised fine-tuning.

CP-BCS: Binary Code Summarization Guided by Control Flow Graph and Pseudo Code

Automatically generating function summaries for binaries is an extremely valuable but challenging task, since it involves translating the execution behavior and semantics of the low-level language (assembly code) into human-readable natural language. However, most current works on understanding assembly code are oriented towards generating function names, which involve numerous abbreviations that make them still confusing. To bridge this gap, we focus on generating complete summaries for binary functions, especially for stripped binary (no symbol table and debug information in reality). To fully exploit the semantics of assembly code, we present a control flow graph and pseudo code guided binary code summarization framework called CP-BCS. CP-BCS utilizes a bidirectional instruction-level control flow graph and pseudo code that incorporates expert knowledge to learn the comprehensive binary function execution behavior and logic semantics. We evaluate CP-BCS on 3 different binary optimization levels (O1, O2, and O3) for 3 different computer architectures (X86, X64, and ARM). The evaluation results demonstrate CP-BCS is superior and significantly improves the efficiency of reverse engineering.

StratMed: Relevance Stratification for Low-resource Medication Recommendation

With the growing imbalance between limited medical resources and escalating demands, AI-based clinical tasks have become paramount. Medication recommendation, as a sub-domain, aims to amalgamate longitudinal patient history with medical knowledge, assisting physicians in prescribing safer and more accurate medication combinations. Existing methods overlook the inherent long-tail distribution in medical data, lacking balanced representation between head and tail data, which leads to sub-optimal model performance. To address this challenge, we introduce StratMed, a model that incorporates an innovative relevance stratification mechanism. It harmonizes discrepancies in data long-tail distribution and strikes a balance between the safety and accuracy of medication combinations. Specifically, we first construct a pre-training method using deep learning networks to obtain entity representation. After that, we design a pyramid-like data stratification method to obtain more generalized entity relationships by reinforcing the features of unpopular entities. Based on this relationship, we designed two graph structures to express medication precision and safety at the same level to obtain visit representations. Finally, the patient's historical clinical information is fitted to generate medication combinations for the current health condition. Experiments on the MIMIC-III dataset demonstrate that our method has outperformed current state-of-the-art methods in four evaluation metrics (including safety and accuracy).

Federated Learning of Models Pre-Trained on Different Features with Consensus Graphs

Learning an effective global model on private and decentralized datasets has become an increasingly important challenge of machine learning when applied in practice. Existing distributed learning paradigms, such as Federated Learning, enable this via model aggregation which enforces a strong form of modeling homogeneity and synchronicity across clients. This is however not suitable to many practical scenarios. For example, in distributed sensing, heterogeneous sensors reading data from different views of the same phenomenon would need to use different models for different data modalities. Local learning therefore happens in isolation but inference requires merging the local models to achieve consensus. To enable consensus among local models, we propose a feature fusion approach that extracts local representations from local models and incorporates them into a global representation that improves the prediction performance. Achieving this requires addressing two non-trivial problems. First, we need to learn an alignment between similar feature components which are arbitrarily arranged across clients to enable representation aggregation. Second, we need to learn a consensus graph that captures the high-order interactions between local feature spaces and how to combine them to achieve a better prediction. This paper presents solutions to these problems and demonstrates them in real-world applications on time series data such as power grids and traffic networks.

Tram: A Token-level Retrieval-augmented Mechanism for Source Code Summarization

Automatically generating human-readable text describing the functionality of a program is the intent of source code summarization. Although Neural Language Models achieve significant performance in this field, an emerging trend is combining neural models with external knowledge. Most previous approaches rely on the sentence-level retrieval and combination paradigm (retrieval of similar code snippets and use of the corresponding code and summary pairs) on the encoder side. However, this paradigm is coarse-grained and cannot directly take advantage of the high-quality retrieved summary tokens on the decoder side. In this paper, we explore a fine-grained token-level retrieval-augmented mechanism on the decoder side to help the vanilla neural model generate a better code summary. Furthermore, to mitigate the limitation of token-level retrieval on capturing contextual code semantics, we propose to integrate code semantics into summary tokens. Extensive experiments and human evaluation reveal that our token-level retrieval-augmented approach significantly improves performance and is more interpretive.