Low-stage lung cancer is known to recur unpredictably, and patients receiving various treatment methods like radiation, chemotherapy, and immunotherapies have been seen to respond very differently. Identifying a priori if a patient is going to relapse or not could make a difference in terms of saving lives and personalized care offered. In this work, we provide an answer to the following research question: Is it possible to enhance the machine learning (ML) of the estimated probability of relapse in early-stage non-small-cell lung cancer (NSCLC) patients with aneuploidy imputation scores? To predict recurrence in 1,348 early-stage (I-II) NSCLC patients, we train graph ML models utilizing the Spanish pulmonary cancer group knowledge graph enriched with triples from pathway imputation. ML models trained on Knowledge graph data enriched with triples from pathway score imputation present an 82% Precision and 91% Specificity in predicting relapse over 200 patients from a held-out test set. ML models trained using graphs data could prove useful supplemental tool in the TNM classification systems and improve a lung cancer patient’s prognosis.

Lung cancer is one of the leading health complications causing high mortality worldwide. The relapsing behavior of medically treated early-stage lung cancer makes this disease even more complicated. Thus predicting such relapse using a data-centric approach provides a complementary perspective for clinicians to understand the disease. In this preliminary work, we explored off-the-shelf survival models to predict the relapse of early-stage lung cancer patients. We analyzed the survival models on a cohort of 1348 early-stage non-small cell lung cancer (NSCLC) patients in different timestamps. Using the prediction explanation model SHAP (SHapley Additive exPlanations), we further explained the best-performing survival model's predictions. Our explainable predictive model is a potential tool for oncologists that address an unmet clinical need for post-treatment patient stratification based on the relapse hazard.

OBJECTIVE: Lung cancer exhibits unpredictable recurrence in low-stage tumors and variable responses to different therapeutic interventions. Predicting relapse in early-stage lung cancer can facilitate precision medicine and improve patient survivability. While existing machine learning models rely on clinical data, incorporating genomic information could enhance their efficiency. This study aims to impute and integrate specific types of genomic data with clinical data to improve the accuracy of machine learning models for predicting relapse in early-stage, non-small cell lung cancer patients. METHODS: The study utilized a publicly available TCGA lung cancer cohort and imputed genetic pathway scores into the Spanish Lung Cancer Group (SLCG) data, specifically in 1348 early-stage patients. Initially, tumor recurrence was predicted without imputed pathway scores. Subsequently, the SLCG data were augmented with pathway scores imputed from TCGA. The integrative approach aimed to enhance relapse risk prediction performance. RESULTS: The integrative approach achieved improved relapse risk prediction with the following evaluation metrics: an area under the precision-recall curve (PR-AUC) score of 0.75, an area under the ROC (ROC-AUC) score of 0.80, an F1 score of 0.61, and a Precision of 0.80. The prediction explanation model SHAP (SHapley Additive exPlanations) was employed to explain the machine learning model's predictions. CONCLUSION: We conclude that our explainable predictive model is a promising tool for oncologists that addresses an unmet clinical need of post-treatment patient stratification based on the relapse risk while also improving the predictive power by incorporating proxy genomic data not available for specific patients.

Peru Bhardwaj, John Kelleher, Luca Costabello, Declan O’Sullivan. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2021.

Counterfactual explanations (CEs) are a practical tool for demonstrating why machine learning classifiers make particular decisions. For CEs to be useful, it is important that they are easy for users to interpret. Existing methods for generating interpretable CEs rely on auxiliary generative models, which may not be suitable for complex datasets, and incur engineering overhead. We introduce a simple and fast method for generating interpretable CEs in a white-box setting without an auxiliary model, by using the predictive uncertainty of the classifier. Our experiments show that our proposed algorithm generates more interpretable CEs, according to IM1 scores (Van Looveren et al., 2019), than existing methods. Additionally, our approach allows us to estimate the uncertainty of a CE, which may be important in safety-critical applications, such as those in the medical domain.

Despite the widespread use of Knowledge Graph Embeddings (KGE), little is known about the security vulnerabilities that might disrupt their intended behaviour.We study data poisoning attacks against KGE models for link prediction.These attacks craft adversarial additions or deletions at training time to cause model failure at test time.To select adversarial deletions, we propose to use the model-agnostic instance attribution methods from Interpretable Machine Learning, which identify the training instances that are most influential to a neural model's predictions on test instances.We use these influential triples as adversarial deletions.We further propose a heuristic method to replace one of the two entities in each influential triple to generate adversarial additions.Our experiments show that the proposed strategies outperform the state-ofart data poisoning attacks on KGE models and improve the MRR degradation due to the attacks by up to 62% over the baselines.

Numeric values associated to edges of a knowledge graph have been used to represent uncertainty, edge importance, and even out-of-band knowledge in a growing number of scenarios, ranging from genetic data to social networks. Nevertheless, traditional knowledge graph embedding models are not designed to capture such information, to the detriment of predictive power. We propose a novel method that injects numeric edge attributes into the scoring layer of a traditional knowledge graph embedding architecture. Experiments with publicly available numeric-enriched knowledge graphs show that our method outperforms traditional numeric-unaware baselines as well as the recent UKGE model.

Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering specific kinase-substrate relationships is time-consuming and often rather serendipitous. Computational predictions alleviate these challenges, but the current approaches suffer from limitations like restricted kinome coverage and inaccuracy. They also typically utilise only local features without reflecting broader interaction context. To address these limitations, we have developed an alternative predictive model. It uses statistical relational learning on top of phosphorylation networks interpreted as knowledge graphs, a simple yet robust model for representing networked knowledge. Compared to a representative selection of six existing systems, our model has the highest kinome coverage and produces biologically valid high-confidence predictions not possible with the other tools. Specifically, we have experimentally validated predictions of previously unknown phosphorylations by the LATS1, AKT1, PKA and MST2 kinases in human. Thus, our tool is useful for focusing phosphoproteomic experiments, and facilitates the discovery of new phosphorylation reactions. Our model can be accessed publicly via an easy-to-use web interface (LinkPhinder).

In this paper the authors focus on context-aware adaptation for linked data on mobile. They split up the problem in two sub-questions: how to declaratively describe context at RDF presentation level, and how to overcome context imprecisions and incompleteness when selecting the proper context description at runtime. The authors answer their two-fold research question with PRISSMA, a context-aware presentation layer for Linked Data. PRISSMA extends the Fresnel vocabulary with the notion of mobile context. Besides, it includes an algorithm that determines whether the sensed context is compatible with some context declarations. The algorithm finds optimal error-tolerant subgraph isomorphisms between RDF graphs using the notion of graph edit distance and is sublinear in the number of context declarations in the system.

We describe two mashups based on context data and multimedia content retrieved from a client application running on mobile devices. This information is processed by our Context Aware Platform that provides specific APIs to deliver context data to our mashups. First of all, these APIs enable context