Machine learning models can greatly improve the search for strong gravitational lenses in imaging surveys by reducing the amount of human inspection required. In this work, we test the performance of supervised, semi-supervised, and unsupervised learning algorithms trained with the ResNetV2 neural network architecture on their ability to efficiently find strong gravitational lenses in the Deep Lens Survey (DLS). We use galaxy images from the survey, combined with simulated lensed sources, as labeled data in our training data sets. We find that models using semi-supervised learning along with data augmentations (transformations applied to an image during training, e.g. rotation) and Generative Adversarial Network (GAN) generated images yield the best performance. They offer 5 – 10 times better precision across all recall values compared to supervised algorithms. Applying the best performing models to the full 20 deg2 DLS survey, we find 3 Grade-A lens candidates within the top 17 image predictions from the model. This increases to 9 Grade-A and 13 Grade-B candidates when 1 per cent (∼2500 images) of the model predictions are visually inspected. This is ≳ 10 × the sky density of lens candidates compared to current shallower wide-area surveys (such as the Dark Energy Survey), indicating a trove of lenses awaiting discovery in upcoming deeper all-sky surveys. These results suggest that pipelines tasked with finding strong lens systems can be highly efficient, minimizing human effort. We additionally report spectroscopic confirmation of the lensing nature of two Grade-A candidates identified by our model, further validating our methods.
FRUGAL: Unlocking Semi-Supervised Learning for Software Analytics
Standard software analytics often involves having a large amount of data with labels in order to commission models with acceptable performance. However, prior work has shown that such require- ments can be expensive, taking several weeks to label thousands of commits, and not always available when traversing new research problems and domains. Unsupervised Learning is a promising di- rection to learn hidden patterns within unlabelled data, which has only been extensively studied in defect prediction. Nevertheless, unsupervised learning can be ineffective by itself and has not been explored in other domains (e.g., static analysis and issue close time).
Motivated by this literature gap and technical limitations, we present FRUGAL, a tuned semi-supervised method that builds on a simple optimization scheme that does not require sophisticated (e.g., deep learners) and expensive (e.g., 100% manually labelled data) methods. FRUGAL optimizes the unsupervised learner’s con- figurations (via a simple grid search) while validating our design decision of labelling just 2.5% of the data before prediction.
As shown by the experiments of this paper FRUGAL outperforms the state-of-the-art adoptable static code warning recognizer and issue closed time predictor, while reducing the cost of labelling by a factor of 40 (from 100% to 2.5%). Hence we assert that FRUGAL can save considerable effort in data labelling especially in validating prior work or researching new problems.
Based on this work, we suggest that proponents of complex and expensive methods should always baseline such methods against simpler and cheaper alternatives. For instance, a semi-supervised learner like FRUGAL can serve as a baseline to the state-of-the-art software analytics.
more »
« less
- Award ID(s):
- 1931425
- NSF-PAR ID:
- 10359071
- Date Published:
- Journal Name:
- Automated Software Engineering
- Volume:
- 2021
- Page Range / eLocation ID:
- 394 to 406
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
ABSTRACT -
Accurate pose estimation is often a requirement for robust robotic grasping and manipulation of objects placed in cluttered, tight environments, such as a shelf with multiple objects. When deep learning approaches are employed to perform this task, they typically require a large amount of training data. However, obtaining precise 6 degrees of freedom for ground-truth can be prohibitively expensive. This work therefore proposes an architecture and a training process to solve this issue. More precisely, we present a weak object detector that enables localizing objects and estimating their 6D poses in cluttered and occluded scenes. To minimize the human labor required for annotations, the proposed detector is trained with a combination of synthetic and a few weakly annotated real images (as little as 10 images per object), for which a human provides only a list of objects present in each image (no time-consuming annotations, such as bounding boxes, segmentation masks and object poses). To close the gap between real and synthetic images, we use multiple domain classifiers trained adversarially. During the inference phase, the resulting class-specific heatmaps of the weak detector are used to guide the search of 6D poses of objects. Our proposed approach is evaluated on several publicly available datasets for pose estimation. We also evaluated our model on classification and localization in unsupervised and semi-supervised settings. The results clearly indicate that this approach could provide an efficient way toward fully automating the training process of computer vision models used in robotics.more » « less
-
In recent years, deep learning has achieved tremendous success in image segmentation for computer vision applications. The performance of these models heavily relies on the availability of large-scale high-quality training labels (e.g., PASCAL VOC 2012). Unfortunately, such large-scale high-quality training data are often unavailable in many real-world spatial or spatiotemporal problems in earth science and remote sensing (e.g., mapping the nationwide river streams for water resource management). Although extensive efforts have been made to reduce the reliance on labeled data (e.g., semi-supervised or unsupervised learning, few-shot learning), the complex nature of geographic data such as spatial heterogeneity still requires sufficient training labels when transferring a pre-trained model from one region to another. On the other hand, it is often much easier to collect lower-quality training labels with imperfect alignment with earth imagery pixels (e.g., through interpreting coarse imagery by non-expert volunteers). However, directly training a deep neural network on imperfect labels with geometric annotation errors could significantly impact model performance. Existing research that overcomes imperfect training labels either focuses on errors in label class semantics or characterizes label location errors at the pixel level. These methods do not fully incorporate the geometric properties of label location errors in the vector representation. To fill the gap, this article proposes a weakly supervised learning framework to simultaneously update deep learning model parameters and infer hidden true vector label locations. Specifically, we model label location errors in the vector representation to partially reserve geometric properties (e.g., spatial contiguity within line segments). Evaluations on real-world datasets in the National Hydrography Dataset (NHD) refinement application illustrate that the proposed framework outperforms baseline methods in classification accuracy.more » « less
-
null (Ed.)The DeepLearningEpilepsyDetectionChallenge: design, implementation, andtestofanewcrowd-sourced AIchallengeecosystem Isabell Kiral*, Subhrajit Roy*, Todd Mummert*, Alan Braz*, Jason Tsay, Jianbin Tang, Umar Asif, Thomas Schaffter, Eren Mehmet, The IBM Epilepsy Consortium◊ , Joseph Picone, Iyad Obeid, Bruno De Assis Marques, Stefan Maetschke, Rania Khalaf†, Michal Rosen-Zvi† , Gustavo Stolovitzky† , Mahtab Mirmomeni† , Stefan Harrer† * These authors contributed equally to this work † Corresponding authors: rkhalaf@us.ibm.com, rosen@il.ibm.com, gustavo@us.ibm.com, mahtabm@au1.ibm.com, sharrer@au.ibm.com ◊ Members of the IBM Epilepsy Consortium are listed in the Acknowledgements section J. Picone and I. Obeid are with Temple University, USA. T. Schaffter is with Sage Bionetworks, USA. E. Mehmet is with the University of Illinois at Urbana-Champaign, USA. All other authors are with IBM Research in USA, Israel and Australia. Introduction This decade has seen an ever-growing number of scientific fields benefitting from the advances in machine learning technology and tooling. More recently, this trend reached the medical domain, with applications reaching from cancer diagnosis [1] to the development of brain-machine-interfaces [2]. While Kaggle has pioneered the crowd-sourcing of machine learning challenges to incentivise data scientists from around the world to advance algorithm and model design, the increasing complexity of problem statements demands of participants to be expert data scientists, deeply knowledgeable in at least one other scientific domain, and competent software engineers with access to large compute resources. People who match this description are few and far between, unfortunately leading to a shrinking pool of possible participants and a loss of experts dedicating their time to solving important problems. Participation is even further restricted in the context of any challenge run on confidential use cases or with sensitive data. Recently, we designed and ran a deep learning challenge to crowd-source the development of an automated labelling system for brain recordings, aiming to advance epilepsy research. A focus of this challenge, run internally in IBM, was the development of a platform that lowers the barrier of entry and therefore mitigates the risk of excluding interested parties from participating. The challenge: enabling wide participation With the goal to run a challenge that mobilises the largest possible pool of participants from IBM (global), we designed a use case around previous work in epileptic seizure prediction [3]. In this “Deep Learning Epilepsy Detection Challenge”, participants were asked to develop an automatic labelling system to reduce the time a clinician would need to diagnose patients with epilepsy. Labelled training and blind validation data for the challenge were generously provided by Temple University Hospital (TUH) [4]. TUH also devised a novel scoring metric for the detection of seizures that was used as basis for algorithm evaluation [5]. In order to provide an experience with a low barrier of entry, we designed a generalisable challenge platform under the following principles: 1. No participant should need to have in-depth knowledge of the specific domain. (i.e. no participant should need to be a neuroscientist or epileptologist.) 2. No participant should need to be an expert data scientist. 3. No participant should need more than basic programming knowledge. (i.e. no participant should need to learn how to process fringe data formats and stream data efficiently.) 4. No participant should need to provide their own computing resources. In addition to the above, our platform should further • guide participants through the entire process from sign-up to model submission, • facilitate collaboration, and • provide instant feedback to the participants through data visualisation and intermediate online leaderboards. The platform The architecture of the platform that was designed and developed is shown in Figure 1. The entire system consists of a number of interacting components. (1) A web portal serves as the entry point to challenge participation, providing challenge information, such as timelines and challenge rules, and scientific background. The portal also facilitated the formation of teams and provided participants with an intermediate leaderboard of submitted results and a final leaderboard at the end of the challenge. (2) IBM Watson Studio [6] is the umbrella term for a number of services offered by IBM. Upon creation of a user account through the web portal, an IBM Watson Studio account was automatically created for each participant that allowed users access to IBM's Data Science Experience (DSX), the analytics engine Watson Machine Learning (WML), and IBM's Cloud Object Storage (COS) [7], all of which will be described in more detail in further sections. (3) The user interface and starter kit were hosted on IBM's Data Science Experience platform (DSX) and formed the main component for designing and testing models during the challenge. DSX allows for real-time collaboration on shared notebooks between team members. A starter kit in the form of a Python notebook, supporting the popular deep learning libraries TensorFLow [8] and PyTorch [9], was provided to all teams to guide them through the challenge process. Upon instantiation, the starter kit loaded necessary python libraries and custom functions for the invisible integration with COS and WML. In dedicated spots in the notebook, participants could write custom pre-processing code, machine learning models, and post-processing algorithms. The starter kit provided instant feedback about participants' custom routines through data visualisations. Using the notebook only, teams were able to run the code on WML, making use of a compute cluster of IBM's resources. The starter kit also enabled submission of the final code to a data storage to which only the challenge team had access. (4) Watson Machine Learning provided access to shared compute resources (GPUs). Code was bundled up automatically in the starter kit and deployed to and run on WML. WML in turn had access to shared storage from which it requested recorded data and to which it stored the participant's code and trained models. (5) IBM's Cloud Object Storage held the data for this challenge. Using the starter kit, participants could investigate their results as well as data samples in order to better design custom algorithms. (6) Utility Functions were loaded into the starter kit at instantiation. This set of functions included code to pre-process data into a more common format, to optimise streaming through the use of the NutsFlow and NutsML libraries [10], and to provide seamless access to the all IBM services used. Not captured in the diagram is the final code evaluation, which was conducted in an automated way as soon as code was submitted though the starter kit, minimising the burden on the challenge organising team. Figure 1: High-level architecture of the challenge platform Measuring success The competitive phase of the "Deep Learning Epilepsy Detection Challenge" ran for 6 months. Twenty-five teams, with a total number of 87 scientists and software engineers from 14 global locations participated. All participants made use of the starter kit we provided and ran algorithms on IBM's infrastructure WML. Seven teams persisted until the end of the challenge and submitted final solutions. The best performing solutions reached seizure detection performances which allow to reduce hundred-fold the time eliptologists need to annotate continuous EEG recordings. Thus, we expect the developed algorithms to aid in the diagnosis of epilepsy by significantly shortening manual labelling time. Detailed results are currently in preparation for publication. Equally important to solving the scientific challenge, however, was to understand whether we managed to encourage participation from non-expert data scientists. Figure 2: Primary occupation as reported by challenge participants Out of the 40 participants for whom we have occupational information, 23 reported Data Science or AI as their main job description, 11 reported being a Software Engineer, and 2 people had expertise in Neuroscience. Figure 2 shows that participants had a variety of specialisations, including some that are in no way related to data science, software engineering, or neuroscience. No participant had deep knowledge and experience in data science, software engineering and neuroscience. Conclusion Given the growing complexity of data science problems and increasing dataset sizes, in order to solve these problems, it is imperative to enable collaboration between people with differences in expertise with a focus on inclusiveness and having a low barrier of entry. We designed, implemented, and tested a challenge platform to address exactly this. Using our platform, we ran a deep-learning challenge for epileptic seizure detection. 87 IBM employees from several business units including but not limited to IBM Research with a variety of skills, including sales and design, participated in this highly technical challenge.more » « less
-
Segata, Nicola (Ed.)The ability to predict human phenotypes and identify biomarkers of disease from metagenomic data is crucial for the development of therapeutics for microbiome-associated diseases. However, metagenomic data is commonly affected by technical variables unrelated to the phenotype of interest, such as sequencing protocol, which can make it difficult to predict phenotype and find biomarkers of disease. Supervised methods to correct for background noise, originally designed for gene expression and RNA-seq data, are commonly applied to microbiome data but may be limited because they cannot account for unmeasured sources of variation. Unsupervised approaches address this issue, but current methods are limited because they are ill-equipped to deal with the unique aspects of microbiome data, which is compositional, highly skewed, and sparse. We perform a comparative analysis of the ability of different denoising transformations in combination with supervised correction methods as well as an unsupervised principal component correction approach that is presently used in other domains but has not been applied to microbiome data to date. We find that the unsupervised principal component correction approach has comparable ability in reducing false discovery of biomarkers as the supervised approaches, with the added benefit of not needing to know the sources of variation apriori. However, in prediction tasks, it appears to only improve prediction when technical variables contribute to the majority of variance in the data. As new and larger metagenomic datasets become increasingly available, background noise correction will become essential for generating reproducible microbiome analyses.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/ASE51524.2021.9678617
