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Register a new userWiseR: An end-to-end structure learning and deployment framework for causal graphical models
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Added by
Shubham Maheshwari
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Structure learning offers an expressive, versatile and explainable approach to causal and mechanistic modeling of complex biological data. We present wiseR, an open source application for learning, evaluating and deploying robust causal graphical models using graph neural networks and Bayesian networks. We demonstrate the utility of this application through application on for biomarker discovery in a COVID-19 clinical dataset.
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We propose a novel end-to-end neural network architecture that, once trained, directly outputs a probabilistic clustering of a batch of input examples in one pass. It estimates a distribution over the number of clusters $k$, and for each $1 leq k leq k_mathrm{max}$, a distribution over the individual cluster assignment for each data point. The network is trained in advance in a supervised fashion on separate data to learn grouping by any perceptual similarity criterion based on pairwise labels (same/different group). It can then be applied to different data containing different groups. We demonstrate promising performance on high-dimensional data like images (COIL-100) and speech (TIMIT). We call this ``learning to cluster and show its conceptual difference to deep metric learning, semi-supervise clustering and other related approaches while having the advantage of performing learnable clustering fully end-to-end.
The annotation of domain experts is important for some medical applications where the objective groundtruth is ambiguous to define, e.g., the rehabilitation for some chronic diseases, and the prescreening of some musculoskeletal abnormalities without further medical examinations. However, improper uses of the annotations may hinder developing reliable models. On one hand, forcing the use of a single groundtruth generated from multiple annotations is less informative for the modeling. On the other hand, feeding the model with all the annotations without proper regularization is noisy given existing disagreements. For such issues, we propose a novel agreement learning framework to tackle the challenge of learning from multiple annotators without objective groundtruth. The framework has two streams, with one stream fitting with the multiple annotators and the other stream learning agreement information between the annotators. In particular, the agreement learning stream produces regularization information to the classifier stream, tuning its decision to be better in line with the agreement between the annotators. The proposed method can be easily plugged to existing backbones developed with majority-voted groundtruth or multiple annotations. Thereon, experiments on two medical datasets demonstrate improved agreement levels with annotators.
Learning continually from non-stationary data streams is a long-standing goal and a challenging problem in machine learning. Recently, we have witnessed a renewed and fast-growing interest in continual learning, especially within the deep learning community. However, algorithmic solutions are often difficult to re-implement, evaluate and port across different settings, where even results on standard benchmarks are hard to reproduce. In this work, we propose Avalanche, an open-source end-to-end library for continual learning research based on PyTorch. Avalanche is designed to provide a shared and collaborative codebase for fast prototyping, training, and reproducible evaluation of continual learning algorithms.
Point of interest (POI) data serves as a valuable source of semantic information for places of interest and has many geospatial applications in real estate, transportation, and urban planning. With the availability of different data sources, POI conflation serves as a valuable technique for enriching data quality and coverage by merging the POI data from multiple sources. This study proposes a novel end-to-end POI conflation framework consisting of six steps, starting with data procurement, schema standardisation, taxonomy mapping, POI matching, POI unification, and data verification. The feasibility of the proposed framework was demonstrated in a case study conducted in the eastern region of Singapore, where the POI data from five data sources was conflated to form a unified POI dataset. Based on the evaluation conducted, the resulting unified dataset was found to be more comprehensive and complete than any of the five POI data sources alone. Furthermore, the proposed approach for identifying POI matches between different data sources outperformed all baseline approaches with a matching accuracy of 97.6% with an average run time below 3 minutes when matching over 12,000 POIs to result in 8,699 unique POIs, thereby demonstrating the frameworks scalability for large scale implementation in dense urban contexts.
We propose a novel deep learning method for local self-supervised representation learning that does not require labels nor end-to-end backpropagation but exploits the natural order in data instead. Inspired by the observation that biological neural networks appear to learn without backpropagating a global error signal, we split a deep neural network into a stack of gradient-isolated modules. Each module is trained to maximally preserve the information of its inputs using the InfoNCE bound from Oord et al. [2018]. Despite this greedy training, we demonstrate that each module improves upon the output of its predecessor, and that the representations created by the top module yield highly competitive results on downstream classification tasks in the audio and visual domain. The proposal enables optimizing modules asynchronously, allowing large-scale distributed training of very deep neural networks on unlabelled datasets.
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