Investigating ADR mechanisms with knowledge graph mining and explainable AI
Université de Lorraine（洛林大学）；CNRS（法国国家科学研究中心）；Inria（法国国家信息与自动化研究所）；LORIA（洛林计算机科学及其应用实验室）；Orange Labs（奥兰治实验室）；LIMICS（LIMICS实验室）；Inserm（法国国家健康与医学研究院）；Université Sorbonne Paris Nord（索邦巴黎北大学）；Sorbonne Université（索邦大学）；CHU de St Etienne（圣艾蒂安大学附属医院）；NGERE（NGERE实验室）；Centre Régional de Pharmacovigilance（区域药物警戒中心）；CHRU de Nancy（南锡大学区域医院中心）；Inria Paris（法国国家信息与自动化研究所巴黎中心）；Université de Paris（巴黎大学）
Adverse Drug Reactions (ADRs) are characterized within randomized clinical trials and postmarketing pharmacovigilance, but their molecular mechanism remains unknown in most cases. Aside from clinical trials, many elements of knowledge about drug ingredients are available in open-access knowledge graphs. In addition, drug classifications that label drugs as either causative or not for several ADRs, have been established. We propose to mine knowledge graphs for identifying biomolecular features that may enable reproducing automatically expert classifications that distinguish drug causative or not for a given type of ADR. In an explainable AI perspective, we explore simple classification techniques such as Decision Trees and Classification Rules because they provide human-readable models, which explain the classification itself, but may also provide elements of explanation for molecular mechanisms behind ADRs. In summary, we mine a knowledge graph for features; we train classifiers at distinguishing, drugs associated or not with ADRs; we isolate features that are both efficient in reproducing expert classifications and interpretable by experts (i.e., Gene Ontology terms, drug targets, or pathway names); and we manually evaluate how they may be explanatory. Extracted features reproduce with a good fidelity classifications of drugs causative or not for DILI and SCAR. Experts fully agreed that 73% and 38% of the most discriminative features are possibly explanatory for DILI and SCAR, respectively; and partially agreed (2/3) for 90% and 77% of them. Knowledge graphs provide diverse features to enable simple and explainable models to distinguish between drugs that are causative or not for ADRs. In addition to explaining classifications, most discriminative features appear to be good candidates for investigating ADR mechanisms further.
Social media has grown to be a crucial information source for pharmacovigilance studies where an increasing number of people post adverse reactions to medical drugs that are previously unreported. Aiming to effectively monitor various aspects of Adverse Drug Reactions (ADRs) from diversely expressed social medical posts, we propose a multi-task neural network framework that learns several tasks associated with ADR monitoring with different levels of supervisions collectively. Besides being able to correctly classify ADR posts and accurately extract ADR mentions from online posts, the proposed …
Navigating Healthcare Insights: A Birds Eye View of Explainability with Knowledge Graphs
Hajim School of Engineering and Applied Sciences, University of Rochester（罗切斯特大学哈吉米工程与应用科学学院）；College of Engineering and Applied Sciences, University at Albany, State University of New York（纽约州立大学奥尔巴尼分校工程与应用科学学院）；Deloitte LLC（德勤有限责任公司）
The Graduate University for Advanced Studies, SOKENDAI（综合研究大学院大学）；National Institute of Informatics（国立信息学研究所）
We propose a method for generating explainable rule sets from tree-ensemble learners using Answer Set Programming (ASP). To this end, we adopt a decompositional approach where the split structures of the base decision trees are exploited in the construction of rules, which in turn are assessed using pattern mining methods encoded in ASP to extract interesting rules. We show how user-defined constraints and preferences can be represented declaratively in ASP to allow for transparent and flexible rule set generation, and how rules can be used as explanations to help the user better understand th…
Recent machine learning approaches have been effective in Artificial Intelligence (AI) applications. They produce robust results with a high level of accuracy. However, most of these techniques do not provide human-understandable explanations for supporting their results and decisions. They usually act as black boxes, and it is not easy to understand how decisions have been made. Explainable Artificial Intelligence (XAI), which has received much interest recently, tries to provide human-understandable explanations for decision-making and trained AI models. For instance, in digital agriculture,…
Adverse drug reactions / events (ADR/ADE) have a major impact on patient health and health care costs. Detecting ADR's as early as possible and sharing them with regulators, pharma companies, and healthcare providers can prevent morbidity and save many lives. While most ADR's are not reported via formal channels, they are often documented in a variety of unstructured conversations such as social media posts by patients, customer support call transcripts, or CRM notes of meetings between healthcare providers and pharma sales reps. In this paper, we propose a natural language processing (NLP) so…
Since most machine learning models provide no explanations for the predictions, their predictions are obscure for the human. The ability to explain a model's prediction has become a necessity in many applications including Twitter mining. In this work, we propose a method called Explainable Twitter Mining (Ex-Twit) combining Topic Modeling and Local Interpretable Model-agnostic Explanation (LIME) to predict the topic and explain the model predictions. We demonstrate the effectiveness of Ex-Twit on Twitter health-related data.
EURECOM（EURECOM通信系统研究所）；Arizona State University（亚利桑那州立大学）
One challenge in fact checking is the ability to improve the transparency of the decision. We present a fact checking method that uses reference information in knowledge graphs (KGs) to assess claims and explain its decisions. KGs contain a formal representation of knowledge with semantic descriptions of entities and their relationships. We exploit such rich semantics to produce interpretable explanations for the fact checking output. As information in a KG is inevitably incomplete, we rely on logical rule discovery and on Web text mining to gather the evidence to assess a given claim. Uncerta…
Several decision points exist in business processes (e.g., whether a purchase order needs a manager's approval or not), and different decisions are made for different process instances based on their characteristics (e.g., a purchase order higher than $500 needs a manager approval). Decision mining in process mining aims to describe/predict the routing of a process instance at a decision point of the process. By predicting the decision, one can take proactive actions to improve the process. For instance, when a bottleneck is developing in one of the possible decisions, one can predict the deci…
German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心）；Saarland University（萨尔大学）
The contemporary process-aware information systems possess the capabilities to record the activities generated during the process execution. To leverage these process specific fine-granular data, process mining has recently emerged as a promising research discipline. As an important branch of process mining, predictive business process management, pursues the objective to generate forward-looking, predictive insights to shape business processes. In this study, we propose a conceptual framework sought to establish and promote understanding of decision-making environment, underlying business pro…
We present a fast and scalable algorithm to induce non-monotonic logic programs from statistical learning models. We reduce the problem of search for best clauses to instances of the High-Utility Itemset Mining (HUIM) problem. In the HUIM problem, feature values and their importance are treated as transactions and utilities respectively. We make use of TreeExplainer, a fast and scalable implementation of the Explainable AI tool SHAP, to extract locally important features and their weights from ensemble tree models. Our experiments with UCI standard benchmarks suggest a significant improvement …
Keen Eye（基恩眼科）；Laboratoire Traitement et Communication de l'Information（信息处理与通信实验室）；Telecom ParisTech（巴黎高等电信学院）；Universite Paris-Saclay（巴黎萨克雷大学）
This article adresses the problem of automatic squamous cells classification for cervical cancer screening using Deep Learning methods. We study different architectures on a public dataset called Herlev dataset, which consists in classifying cells, obtained by cervical pap smear, regarding the severity of the abnormalities they represent. Furthermore, we use an attribution method to understand which cytomorphological features are actually learned as discriminative to classify severity of the abnormalities. Through this paper, we show how we trained a performant classifier: 74.5\% accuracy on s…
Numerous metamorphic and polymorphic malicious variants are generated automatically on a daily basis by mutation engines that transform the code of a malicious program while retaining its functionality, in order to evade signature-based detection. These automatic processes have greatly increased the number of malware variants, deeming their fully-manual analysis impossible. Malware classification is the task of determining to which family a new malicious variant belongs. Variants of the same malware family show similar behavioral patterns. Thus, classifying newly discovered malicious programs …
The connectivity structure of graphs is typically related to the attributes of the nodes. In social networks for example, the probability of a friendship between two people depends on their attributes, such as their age, address, and hobbies. The connectivity of a graph can thus possibly be understood in terms of patterns of the form 'the subgroup of individuals with properties X are often (or rarely) friends with individuals in another subgroup with properties Y'. Such rules present potentially actionable and generalizable insights into the graph. We present a method that finds pairs of node …
Texas A&M University（德克萨斯农工大学）；University of Florida（佛罗里达大学）
In this paper, we study the problem of learning probabilistic logical rules for inductive and interpretable link prediction. Despite the importance of inductive link prediction, most previous works focused on transductive link prediction and cannot manage previously unseen entities. Moreover, they are black-box models that are not easily explainable for humans. We propose DRUM, a scalable and differentiable approach for mining first-order logical rules from knowledge graphs which resolves these problems. We motivate our method by making a connection between learning confidence scores for each …
We present a fast and scalable algorithm to induce non-monotonic logic programs from statistical learning models. We reduce the problem of search for best clauses to instances of the High-Utility Itemset Mining (HUIM) problem. In the HUIM problem, feature values and their importance are treated as transactions and utilities respectively. We make use of TreeExplainer, a fast and scalable implementation of the Explainable AI tool SHAP, to extract locally important features and their weights from ensemble tree models. Our experiments with UCI standard benchmarks suggest a significant improvement …
Jožef Stefan International Postgraduate School（约热夫·斯特凡国际研究生院）；Jožef Stefan Institute（约热夫·斯特凡研究所）；CNRS（法国国家科学研究中心）；Sorbonne Université（索邦大学）
Multi-label classification (MLC) is an ML task of predictive modeling in which a data instance can simultaneously belong to multiple classes. MLC is increasingly gaining interest in different application domains such as text mining, computer vision, and bioinformatics. Several MLC algorithms have been proposed in the literature, resulting in a meta-optimization problem that the user needs to address: which MLC approach to select for a given dataset? To address this algorithm selection problem, we investigate in this work the quality of an automated approach that uses characteristics of the dat…
Central University of Finance and Economics（中央财经大学）；Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）；University of Chinese Academy of Sciences（中国科学院大学）
Due to the powerful learning ability on high-rank and non-linear features, deep neural networks (DNNs) are being applied to data mining and machine learning in various fields, and exhibit higher discrimination performance than conventional methods. However, the applications based on DNNs are rare in enterprise credit rating tasks because most of DNNs employ the "end-to-end" learning paradigm, which outputs the high-rank representations of objects and predictive results without any explanations. Thus, users in the financial industry cannot understand how these high-rank representations are gene…
Conformalized Exceptional Model Mining: Telling Where Your Model Performs (Not) Well
School of Computing and Information Technology（计算与信息科技学院）；Great Bay University（大湾大学）；Great Bay Institute for Advanced Study（大湾先进研究院）；Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems（广东省数学与神经动力系统重点实验室）；Dongguan Key Laboratory for Intelligence and Information Technology（东莞智能与信息技术重点实验室）；Data and Artificial Intelligence Cluster, Department of Mathematics and Computer Science（数据与人工智能集群，数学与计算机科学系）；Eindhoven University of Technology（埃因霍温理工大学）
Multimodal Model with Text and Drug Embeddings for Adverse Drug Reaction Classification
Kazan Federal University（喀山联邦大学）；Lomonosov Moscow State University（莫斯科罗蒙诺索夫国立大学）；Sber AI；National Research University Higher School of Economics（国立研究型大学高等经济学院）
