Accuracy
The application of adaptive minimum match k-nearest neighbors to identify at-risk students in health professions education
Kumar, Anshul, DiJohnson, Taylor, Edwards, Roger, Walker, Lisa
Purpose: When a learner fails to reach a milestone, educators often wonder if there had been any warning signs that could have allowed them to intervene sooner. Machine learning can predict which students are at risk of failing a high-stakes certification exam. If predictions can be made well in advance of the exam, then educators can meaningfully intervene before students take the exam to reduce the chances of a failing score. Methods: Using already-collected, first-year student assessment data from five cohorts in a Master of Physician Assistant Studies program, the authors implement an "adaptive minimum match" version of the k-nearest neighbors algorithm (AMMKNN), using changing numbers of neighbors to predict each student's future exam scores on the Physician Assistant National Certifying Examination (PANCE). Validation occurred in two ways: Leave-one-out cross-validation (LOOCV) and evaluating the predictions in a new cohort. Results: AMMKNN achieved an accuracy of 93% in LOOCV. AMMKNN generates a predicted PANCE score for each student, one year before they are scheduled to take the exam. Students can then be classified into extra support, optional extra support, or no extra support groups. The educator then has one year to provide the appropriate customized support to each category of student. Conclusions: Predictive analytics can identify at-risk students, so they can receive additional support or remediation when preparing for high-stakes certification exams. Educators can use the included methods and code to generate predicted test outcomes for students. The authors recommend that educators use this or similar predictive methods responsibly and transparently, as one of many tools used to support students.
Adversarial Machine Learning-Based Anticipation of Threats Against Vehicle-to-Microgrid Services
In this paper, we study the expanding attack surface of Adversarial Machine Learning (AML) and the potential attacks against Vehicle-to-Microgrid (V2M) services. We present an anticipatory study of a multi-stage gray-box attack that can achieve a comparable result to a white-box attack. Adversaries aim to deceive the targeted Machine Learning (ML) classifier at the network edge to misclassify the incoming energy requests from microgrids. With an inference attack, an adversary can collect real-time data from the communication between smart microgrids and a 5G gNodeB to train a surrogate (i.e., shadow) model of the targeted classifier at the edge. To anticipate the associated impact of an adversary's capability to collect real-time data instances, we study five different cases, each representing different amounts of real-time data instances collected by an adversary. Out of six ML models trained on the complete dataset, K-Nearest Neighbour (K-NN) is selected as the surrogate model, and through simulations, we demonstrate that the multi-stage gray-box attack is able to mislead the ML classifier and cause an Evasion Increase Rate (EIR) up to 73.2% using 40% less data than what a white-box attack needs to achieve a similar EIR.
Counterfactual Phenotyping with Censored Time-to-Events
Nagpal, Chirag, Goswami, Mononito, Dufendach, Keith, Dubrawski, Artur
Estimation of treatment efficacy of real-world clinical interventions involves working with continuous outcomes such as time-to-death, re-hospitalization, or a composite event that may be subject to censoring. Counterfactual reasoning in such scenarios requires decoupling the effects of confounding physiological characteristics that affect baseline survival rates from the effects of the interventions being assessed. In this paper, we present a latent variable approach to model heterogeneous treatment effects by proposing that an individual can belong to one of latent clusters with distinct response characteristics. We show that this latent structure can mediate the base survival rates and helps determine the effects of an intervention. We demonstrate the ability of our approach to discover actionable phenotypes of individuals based on their treatment response on multiple large randomized clinical trials originally conducted to assess appropriate treatments to reduce cardiovascular risk.
D-BIAS: A Causality-Based Human-in-the-Loop System for Tackling Algorithmic Bias
With the rise of AI, algorithms have become better at learning underlying patterns from the training data including ingrained social biases based on gender, race, etc. Deployment of such algorithms to domains such as hiring, healthcare, law enforcement, etc. has raised serious concerns about fairness, accountability, trust and interpretability in machine learning algorithms. To alleviate this problem, we propose D-BIAS, a visual interactive tool that embodies human-in-the-loop AI approach for auditing and mitigating social biases from tabular datasets. It uses a graphical causal model to represent causal relationships among different features in the dataset and as a medium to inject domain knowledge. A user can detect the presence of bias against a group, say females, or a subgroup, say black females, by identifying unfair causal relationships in the causal network and using an array of fairness metrics. Thereafter, the user can mitigate bias by acting on the unfair causal edges. For each interaction, say weakening/deleting a biased causal edge, the system uses a novel method to simulate a new (debiased) dataset based on the current causal model. Users can visually assess the impact of their interactions on different fairness metrics, utility metrics, data distortion, and the underlying data distribution. Once satisfied, they can download the debiased dataset and use it for any downstream application for fairer predictions. We evaluate D-BIAS by conducting experiments on 3 datasets and also a formal user study. We found that D-BIAS helps reduce bias significantly compared to the baseline debiasing approach across different fairness metrics while incurring little data distortion and a small loss in utility. Moreover, our human-in-the-loop based approach significantly outperforms an automated approach on trust, interpretability and accountability.
A Novel Ontology-guided Attribute Partitioning Ensemble Learning Model for Early Prediction of Cognitive Deficits using Quantitative Structural MRI in Very Preterm Infants
Li, Zhiyuan, Li, Hailong, Braimah, Adebayo, Dillman, Jonathan R., Parikh, Nehal A., He, Lili
Structural magnetic resonance imaging studies have shown that brain anatomical abnormalities are associated with cognitive deficits in preterm infants. Brain maturation and geometric features can be used with machine learning models for predicting later neurodevelopmental deficits. However, traditional machine learning models would suffer from a large feature-to-instance ratio (i.e., a large number of features but a small number of instances/samples). Ensemble learning is a paradigm that strategically generates and integrates a library of machine learning classifiers and has been successfully used on a wide variety of predictive modeling problems to boost model performance. Attribute (i.e., feature) bagging method is the most commonly used feature partitioning scheme, which randomly and repeatedly draws feature subsets from the entire feature set. Although attribute bagging method can effectively reduce feature dimensionality to handle the large feature-to-instance ratio, it lacks consideration of domain knowledge and latent relationship among features. In this study, we proposed a novel Ontology-guided Attribute Partitioning (OAP) method to better draw feature subsets by considering the domain-specific relationship among features. With the better partitioned feature subsets, we developed an ensemble learning framework, which is referred to as OAP-Ensemble Learning (OAP-EL). We applied the OAP-EL to predict cognitive deficits at 2 years of age using quantitative brain maturation and geometric features obtained at term equivalent age in very preterm infants. We demonstrated that the proposed OAP-EL approach significantly outperformed the peer ensemble learning and traditional machine learning approaches.
Discover the Mysteries of the Maya: Selected Contributions from the Machine Learning Challenge & The Discovery Challenge Workshop at ECML PKDD 2021
Kocev, Dragi, Simidjievski, Nikola, Kostovska, Ana, Dimitrovski, Ivica, Kokalj, ลฝiga
The volume contains selected contributions from the Machine Learning Challenge "Discover the Mysteries of the Maya", presented at the Discovery Challenge Track of The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2021). Remote sensing has greatly accelerated traditional archaeological landscape surveys in the forested regions of the ancient Maya. Typical exploration and discovery attempts, beside focusing on whole ancient cities, focus also on individual buildings and structures. Recently, there have been several successful attempts of utilizing machine learning for identifying ancient Maya settlements. These attempts, while relevant, focus on narrow areas and rely on high-quality aerial laser scanning (ALS) data which covers only a fraction of the region where ancient Maya were once settled. Satellite image data, on the other hand, produced by the European Space Agency's (ESA) Sentinel missions, is abundant and, more importantly, publicly available. The "Discover the Mysteries of the Maya" challenge aimed at locating and identifying ancient Maya architectures (buildings, aguadas, and platforms) by performing integrated image segmentation of different types of satellite imagery (from Sentinel-1 and Sentinel-2) data and ALS (lidar) data.
A guide to Predictive Lead Scoring using Machine Learning
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Causality, Causal Discovery, and Causal Inference in Structural Engineering
Much of our experiments are designed to uncover the cause(s) and effect(s) behind a data generating mechanism (i.e., phenomenon) we happen to be interested in. Uncovering such relationships allows us to identify the true working of a phenomenon and, most importantly, articulate a model that may enable us to further explore the phenomenon on hand and/or allow us to predict it accurately. Fundamentally, such models are likely to be derived via a causal approach (as opposed to an observational or empirical mean). In this approach, causal discovery is required to create a causal model, which can then be applied to infer the influence of interventions, and answer any hypothetical questions (i.e., in the form of What ifs? Etc.) that we might have. This paper builds a case for causal discovery and causal inference and contrasts that against traditional machine learning approaches; all from a civil and structural engineering perspective. More specifically, this paper outlines the key principles of causality and the most commonly used algorithms and packages for causal discovery and causal inference. Finally, this paper also presents a series of examples and case studies of how causal concepts can be adopted for our domain.
Multiple Similarity Drug-Target Interaction Prediction with Random Walks and Matrix Factorization
Liu, Bin, Papadopoulos, Dimitrios, Malliaros, Fragkiskos D., Tsoumakas, Grigorios, Papadopoulos, Apostolos N.
The discovery of drug-target interactions (DTIs) is a very promising area of research with great potential. The accurate identification of reliable interactions among drugs and proteins via computational methods, which typically leverage heterogeneous information retrieved from diverse data sources, can boost the development of effective pharmaceuticals. Although random walk and matrix factorization techniques are widely used in DTI prediction, they have several limitations. Random walk-based embedding generation is usually conducted in an unsupervised manner, while the linear similarity combination in matrix factorization distorts individual insights offered by different views. To tackle these issues, we take a multi-layered network approach to handle diverse drug and target similarities, and propose a novel optimization framework, called Multiple similarity DeepWalk-based Matrix Factorization (MDMF), for DTI prediction. The framework unifies embedding generation and interaction prediction, learning vector representations of drugs and targets that not only retain higher-order proximity across all hyper-layers and layer-specific local invariance, but also approximate the interactions with their inner product. Furthermore, we develop an ensemble method (MDMF2A) that integrates two instantiations of the MDMF model, optimizing the area under the precision-recall curve (AUPR) and the area under the receiver operating characteristic curve (AUC) respectively. The empirical study on real-world DTI datasets shows that our method achieves statistically significant improvement over current state-of-the-art approaches in four different settings. Moreover, the validation of highly ranked non-interacting pairs also demonstrates the potential of MDMF2A to discover novel DTIs.
Bridging the gap between target-based and cell-based drug discovery with a graph generative multi-task model
Hu, Fan, Wang, Dongqi, Huang, Huazhen, Hu, Yishen, Yin, Peng
Drug discovery is vitally important for protecting human against disease. Target-based screening is one of the most popular methods to develop new drugs in the past several decades. This method efficiently screens candidate drugs inhibiting target protein in vitro, but it often fails due to inadequate activity of the selected drugs in vivo. Accurate computational methods are needed to bridge this gap. Here, we propose a novel graph multi task deep learning model to identify compounds carrying both target inhibitory and cell active (MATIC) properties. On a carefully curated SARS-CoV-2 dataset, the proposed MATIC model shows advantages comparing with traditional method in screening effective compounds in vivo. Next, we explored the model interpretability and found that the learned features for target inhibition (in vitro) or cell active (in vivo) tasks are different with molecular property correlations and atom functional attentions. Based on these findings, we utilized a monte carlo based reinforcement learning generative model to generate novel multi-property compounds with both in vitro and in vivo efficacy, thus bridging the gap between target-based and cell-based drug discovery.