Clinically driven semi-supervised class discovery in gene expression data

Abstract Motivation: Unsupervised class discovery in gene expression data relies on the statistical signals in the data to exclusively drive the results. It is often the case, however, that one is interested in constraining the search space to respect certain biological prior knowledge while still allowing a flexible search within these boundaries. Results: We develop an approach to semi-supervised class discovery. One component of our approach uses clinical sample information to constrain the search space and guide the class discovery process to yield biologically relevant partitions. A second component consists of using known biological annotation of genes to drive the search, seeking partitions that manifest strong differential expression in specific sets of genes. We develop efficient algorithmics for these tasks, implementing both approaches and combinations thereof. We show that our method is robust enough to detect known clinical parameters in accordance with expected clinical values. We also use our method to elucidate cardiovascular disease (CVD) putative risk factors. Availability: MonoClaD (Monotone Class Discovery). See http://bioinfo.cs.technion.ac.il/people/zohar/MonoClad/ Supplementary information: Supplementary data is available at http://bioinfo.cs.technion.ac.il/people/zohar/MonoClad/software.html Contact: [email protected]

An Efficient Learning of Constraints For Semi-Supervised Clustering using Neighbour Clustering Algorithm

Data mining is the process of finding the previously unknown and potentially interesting patterns and relation in database. Data mining is the step in the knowledge discovery in database process (KDD) .The structures that are the outcome of the data mining process must meet certain condition so that these can be considered as knowledge. These conditions are validity, understandability, utility, novelty, interestingness. Researcher identifies two fundamental goals of data mining: prediction and description. The proposed research work suggests the semi-supervised clustering problem where to know (with varying degree of certainty) that some sample pairs are (or are not) in the same class. A probabilistic model for semi-supervised clustering based on Shared Semi-supervised Neighbor clustering (SSNC) that provides a principled framework for incorporating supervision into prototype-based clustering. Semi-supervised clustering that combines the constraint-based and fitness-based approaches in a unified model. The proposed method first divides the Constraint-sensitive assignment of instances to clusters, where points are assigned to clusters so that the overall distortion of the points from the cluster centroids is minimized, while a minimum number of must-link and cannot-link constraints are violated. Experimental results across UCL Machine learning semi-supervised dataset results show that the proposed method has higher F-Measures than many existing Semi-Supervised Clustering methods

Semi-Supervised Discovery of DNN-Based Outcome Predictors from Scarcely-Labeled Process Logs

Predicting the final outcome of an ongoing process instance is a key problem in many real-life contexts. This problem has been addressed mainly by discovering a prediction model by using traditional machine learning methods and, more recently, deep learning methods, exploiting the supervision coming from outcome-class labels associated with historical log traces. However, a supervised learning strategy is unsuitable for important application scenarios where the outcome labels are known only for a small fraction of log traces. In order to address these challenging scenarios, a semi-supervised learning approach is proposed here, which leverages a multi-target DNN model supporting both outcome prediction and the additional auxiliary task of next-activity prediction. The latter task helps the DNN model avoid spurious trace embeddings and overfitting behaviors. In extensive experimentation, this approach is shown to outperform both fully-supervised and semi-supervised discovery methods using similar DNN architectures across different real-life datasets and label-scarce settings

Adapting to Change: Robust Counterfactual Explanations in Dynamic Data Landscapes

We introduce a novel semi-supervised Graph Counterfactual Explainer (GCE) methodology, Dynamic GRAph Counterfactual Explainer (DyGRACE). It leverages initial knowledge about the data distribution to search for valid counterfactuals while avoiding using information from potentially outdated decision functions in subsequent time steps. Employing two graph autoencoders (GAEs), DyGRACE learns the representation of each class in a binary classification scenario. The GAEs minimise the reconstruction error between the original graph and its learned representation during training. The method involves (i) optimising a parametric density function (implemented as a logistic regression function) to identify counterfactuals by maximising the factual autoencoder's reconstruction error, (ii) minimising the counterfactual autoencoder's error, and (iii) maximising the similarity between the factual and counterfactual graphs. This semi-supervised approach is independent of an underlying black-box oracle. A logistic regression model is trained on a set of graph pairs to learn weights that aid in finding counterfactuals. At inference, for each unseen graph, the logistic regressor identifies the best counterfactual candidate using these learned weights, while the GAEs can be iteratively updated to represent the continual adaptation of the learned graph representation over iterations. DyGRACE is quite effective and can act as a drift detector, identifying distributional drift based on differences in reconstruction errors between iterations. It avoids reliance on the oracle's predictions in successive iterations, thereby increasing the efficiency of counterfactual discovery. DyGRACE, with its capacity for contrastive learning and drift detection, will offer new avenues for semi-supervised learning and explanation generation