scholarly journals CounterFactual Regression with Importance Sampling Weights

Author(s):  
Negar Hassanpour ◽  
Russell Greiner

Perhaps the most pressing concern of a patient diagnosed with cancer is her life expectancy under various treatment options. For a binary-treatment case, this translates into estimating the difference between the outcomes (e.g., survival time) of the two available treatment options – i.e., her Individual Treatment Effect (ITE). This is especially challenging to estimate from observational data, as that data has selection bias: the treatment assigned to a patient depends on that patient's attributes. In this work, we borrow ideas from domain adaptation to address the distributional shift between the source (outcome of the administered treatment, appearing in the observed training data) and target (outcome of the alternative treatment) that exists due to selection bias. We propose a context-aware importance sampling re-weighing scheme, built on top of a representation learning module, for estimating ITEs. Empirical results on two publicly available benchmarks demonstrate that the proposed method significantly outperforms state-of-the-art.

Author(s):  
A. Paul ◽  
F. Rottensteiner ◽  
C. Heipke

Domain adaptation techniques in transfer learning try to reduce the amount of training data required for classification by adapting a classifier trained on samples from a source domain to a new data set (target domain) where the features may have different distributions. In this paper, we propose a new technique for domain adaptation based on logistic regression. Starting with a classifier trained on training data from the source domain, we iteratively include target domain samples for which class labels have been obtained from the current state of the classifier, while at the same time removing source domain samples. In each iteration the classifier is re-trained, so that the decision boundaries are slowly transferred to the distribution of the target features. To make the transfer procedure more robust we introduce weights as a function of distance from the decision boundary and a new way of regularisation. Our methodology is evaluated using a benchmark data set consisting of aerial images and digital surface models. The experimental results show that in the majority of cases our domain adaptation approach can lead to an improvement of the classification accuracy without additional training data, but also indicate remaining problems if the difference in the feature distributions becomes too large.


2021 ◽  
Author(s):  
◽  
Muhammad Ghifary

<p>Machine learning has achieved great successes in the area of computer vision, especially in object recognition or classification. One of the core factors of the successes is the availability of massive labeled image or video data for training, collected manually by human. Labeling source training data, however, can be expensive and time consuming. Furthermore, a large amount of labeled source data may not always guarantee traditional machine learning techniques to generalize well; there is a potential bias or mismatch in the data, i.e., the training data do not represent the target environment.  To mitigate the above dataset bias/mismatch, one can consider domain adaptation: utilizing labeled training data and unlabeled target data to develop a well-performing classifier on the target environment. In some cases, however, the unlabeled target data are nonexistent, but multiple labeled sources of data exist. Such situations can be addressed by domain generalization: using multiple source training sets to produce a classifier that generalizes on the unseen target domain. Although several domain adaptation and generalization approaches have been proposed, the domain mismatch in object recognition remains a challenging, open problem – the model performance has yet reached to a satisfactory level in real world applications.  The overall goal of this thesis is to progress towards solving dataset bias in visual object recognition through representation learning in the context of domain adaptation and domain generalization. Representation learning is concerned with finding proper data representations or features via learning rather than via engineering by human experts. This thesis proposes several representation learning solutions based on deep learning and kernel methods.  This thesis introduces a robust-to-noise deep neural network for handwritten digit classification trained on “clean” images only, which we name Deep Hybrid Network (DHN). DHNs are based on a particular combination of sparse autoencoders and restricted Boltzmann machines. The results show that DHN performs better than the standard deep neural network in recognizing digits with Gaussian and impulse noise, block and border occlusions.  This thesis proposes the Domain Adaptive Neural Network (DaNN), a neural network based domain adaptation algorithm that minimizes the classification error and the domain discrepancy between the source and target data representations. The experiments show the competitiveness of DaNN against several state-of-the-art methods on a benchmark object dataset.  This thesis develops the Multi-task Autoencoder (MTAE), a domain generalization algorithm based on autoencoders trained via multi-task learning. MTAE learns to transform the original image into its analogs in multiple related domains simultaneously. The results show that the MTAE’s representations provide better classification performance than some alternative autoencoder-based models as well as the current state-of-the-art domain generalization algorithms.  This thesis proposes a fast kernel-based representation learning algorithm for both domain adaptation and domain generalization, Scatter Component Analysis (SCA). SCA finds a data representation that trades between maximizing the separability of classes, minimizing the mismatch between domains, and maximizing the separability of the whole data points. The results show that SCA performs much faster than some competitive algorithms, while providing state-of-the-art accuracy in both domain adaptation and domain generalization.  Finally, this thesis presents the Deep Reconstruction-Classification Network (DRCN), a deep convolutional network for domain adaptation. DRCN learns to classify labeled source data and also to reconstruct unlabeled target data via a shared encoding representation. The results show that DRCN provides competitive or better performance than the prior state-of-the-art model on several cross-domain object datasets.</p>


Author(s):  
A. Paul ◽  
F. Rottensteiner ◽  
C. Heipke

Domain adaptation techniques in transfer learning try to reduce the amount of training data required for classification by adapting a classifier trained on samples from a source domain to a new data set (target domain) where the features may have different distributions. In this paper, we propose a new technique for domain adaptation based on logistic regression. Starting with a classifier trained on training data from the source domain, we iteratively include target domain samples for which class labels have been obtained from the current state of the classifier, while at the same time removing source domain samples. In each iteration the classifier is re-trained, so that the decision boundaries are slowly transferred to the distribution of the target features. To make the transfer procedure more robust we introduce weights as a function of distance from the decision boundary and a new way of regularisation. Our methodology is evaluated using a benchmark data set consisting of aerial images and digital surface models. The experimental results show that in the majority of cases our domain adaptation approach can lead to an improvement of the classification accuracy without additional training data, but also indicate remaining problems if the difference in the feature distributions becomes too large.


2021 ◽  
Author(s):  
◽  
Muhammad Ghifary

<p>Machine learning has achieved great successes in the area of computer vision, especially in object recognition or classification. One of the core factors of the successes is the availability of massive labeled image or video data for training, collected manually by human. Labeling source training data, however, can be expensive and time consuming. Furthermore, a large amount of labeled source data may not always guarantee traditional machine learning techniques to generalize well; there is a potential bias or mismatch in the data, i.e., the training data do not represent the target environment.  To mitigate the above dataset bias/mismatch, one can consider domain adaptation: utilizing labeled training data and unlabeled target data to develop a well-performing classifier on the target environment. In some cases, however, the unlabeled target data are nonexistent, but multiple labeled sources of data exist. Such situations can be addressed by domain generalization: using multiple source training sets to produce a classifier that generalizes on the unseen target domain. Although several domain adaptation and generalization approaches have been proposed, the domain mismatch in object recognition remains a challenging, open problem – the model performance has yet reached to a satisfactory level in real world applications.  The overall goal of this thesis is to progress towards solving dataset bias in visual object recognition through representation learning in the context of domain adaptation and domain generalization. Representation learning is concerned with finding proper data representations or features via learning rather than via engineering by human experts. This thesis proposes several representation learning solutions based on deep learning and kernel methods.  This thesis introduces a robust-to-noise deep neural network for handwritten digit classification trained on “clean” images only, which we name Deep Hybrid Network (DHN). DHNs are based on a particular combination of sparse autoencoders and restricted Boltzmann machines. The results show that DHN performs better than the standard deep neural network in recognizing digits with Gaussian and impulse noise, block and border occlusions.  This thesis proposes the Domain Adaptive Neural Network (DaNN), a neural network based domain adaptation algorithm that minimizes the classification error and the domain discrepancy between the source and target data representations. The experiments show the competitiveness of DaNN against several state-of-the-art methods on a benchmark object dataset.  This thesis develops the Multi-task Autoencoder (MTAE), a domain generalization algorithm based on autoencoders trained via multi-task learning. MTAE learns to transform the original image into its analogs in multiple related domains simultaneously. The results show that the MTAE’s representations provide better classification performance than some alternative autoencoder-based models as well as the current state-of-the-art domain generalization algorithms.  This thesis proposes a fast kernel-based representation learning algorithm for both domain adaptation and domain generalization, Scatter Component Analysis (SCA). SCA finds a data representation that trades between maximizing the separability of classes, minimizing the mismatch between domains, and maximizing the separability of the whole data points. The results show that SCA performs much faster than some competitive algorithms, while providing state-of-the-art accuracy in both domain adaptation and domain generalization.  Finally, this thesis presents the Deep Reconstruction-Classification Network (DRCN), a deep convolutional network for domain adaptation. DRCN learns to classify labeled source data and also to reconstruct unlabeled target data via a shared encoding representation. The results show that DRCN provides competitive or better performance than the prior state-of-the-art model on several cross-domain object datasets.</p>


2020 ◽  
Vol 36 (9) ◽  
pp. 2690-2696
Author(s):  
Jarkko Toivonen ◽  
Pratyush K Das ◽  
Jussi Taipale ◽  
Esko Ukkonen

Abstract Motivation Position-specific probability matrices (PPMs, also called position-specific weight matrices) have been the dominating model for transcription factor (TF)-binding motifs in DNA. There is, however, increasing recent evidence of better performance of higher order models such as Markov models of order one, also called adjacent dinucleotide matrices (ADMs). ADMs can model dependencies between adjacent nucleotides, unlike PPMs. A modeling technique and software tool that would estimate such models simultaneously both for monomers and their dimers have been missing. Results We present an ADM-based mixture model for monomeric and dimeric TF-binding motifs and an expectation maximization algorithm MODER2 for learning such models from training data and seeds. The model is a mixture that includes monomers and dimers, built from the monomers, with a description of the dimeric structure (spacing, orientation). The technique is modular, meaning that the co-operative effect of dimerization is made explicit by evaluating the difference between expected and observed models. The model is validated using HT-SELEX and generated datasets, and by comparing to some earlier PPM and ADM techniques. The ADM models explain data slightly better than PPM models for 314 tested TFs (or their DNA-binding domains) from four families (bHLH, bZIP, ETS and Homeodomain), the ADM mixture models by MODER2 being the best on average. Availability and implementation Software implementation is available from https://github.com/jttoivon/moder2. Supplementary information Supplementary data are available at Bioinformatics online.


Author(s):  
Natasha Ansari ◽  
Eric Johnson ◽  
Jennifer A. Sinnott ◽  
Sikandar Ansari

Background: Oncology provider discussions of treatment options, outcomes of treatment, and end of life planning are essential to care for patients with advanced malignancies. Studies have shown that despite this, many patients do not have adequate care planning, including end of life planning. It is thought that the accessibility of information outside of clinical encounters and individual factors and/or beliefs may influence the patient’s perception of disease. Aims: The objective of this study was to evaluate if patient understanding of treatment goals matched the provider and if there were areas of discrepancy. If a discrepancy was found, the survey inquired further into more specific aspects. Methods: A questionnaire-based survey was performed at a cancer hospital outpatient clinic. 100 consecutive and consenting patients who had stage IV non-curable lung, gastrointestinal (GI), or other cancer were included in the study. Patients must have had at least 2 visits with their oncologist. Results: 40 patients reported their disease might be curable and 60 reported their disease was not curable. Patients who reported their disease was not curable were more likely to be 65 years or older (P-value: 0.055). They were more likely to report that their doctor discussed the possibility of their cancer getting worse (78.3% VS 55%; P-value 0.024), that their doctor discussed end of life plans (58.3% VS 30%; P- value: 0.01), and that they had appointed a health care decision-maker (86.7% VS 62.5%; P-value: 0.01). 65% of patients who thought their disease might be curable reported that their doctor said it might be curable, compared with only 6.7% of patients who thought their disease was not curable (p < 0.001). Or, equivalently, 35% of patients who thought their disease might be curable reported that their doctor’s opinion was that it was not curable, compared with 93% of patients who thought their disease was not curable (p < 0.001). Patients who had lung cancer were more likely to believe their cancer was not curable than patients with gastrointestinal or other cancer, though the difference was not statistically significant (p = 0.165). Patients who said their disease might be curable selected as possible reasons that a miracle (50%) or alternative medicine (66.7%) would get rid of the cancer, or said their family wanted them to believe the cancer would go away (16.7%) or that another doctor said it would (4.2%). Patients who said their disease might be curable said they did so due to alternative medications, another doctor, or their family. Restricting to the 70 patients who reported their doctors telling them their disease was not curable, 20% of them still said that they personally felt their disease might be curable. Patients below 65 years of age were more likely to disagree with the doctor in this case (P-value: 0.047). Conclusion: This survey of patients diagnosed with stage IV cancer shows that a significant number of patients had misunderstandings of the treatment and curability of their disease. Findings suggest that a notable proportion kept these beliefs even after being told by treating physicians that their disease is not curable.


Author(s):  
Margaret C. Fang ◽  
Alan S. Go ◽  
Priya A. Prasad ◽  
Jin-Wen Hsu ◽  
Dongjie Fan ◽  
...  

AbstractTreatment options for patients with venous thromboembolism (VTE) include warfarin and direct oral anticoagulants (DOACs). Although DOACs are easier to administer than warfarin and do not require routine laboratory monitoring, few studies have directly assessed whether patients are more satisfied with DOACs. We surveyed adults from two large integrated health systems taking DOACs or warfarin for incident VTE occurring between January 1, 2015 and June 30, 2018. Treatment satisfaction was assessed using the validated Anti-Clot Treatment Scale (ACTS), divided into the ACTS Burdens and ACTS Benefits scores; higher scores indicate greater satisfaction. Mean treatment satisfaction was compared using multivariable linear regression, adjusting for patient demographic and clinical characteristics. The effect size of the difference in means was calculated using a Cohen’s d (0.20 is considered a small effect and ≥ 0.80 is considered large). We surveyed 2217 patients, 969 taking DOACs and 1248 taking warfarin at the time of survey. Thirty-one point five percent of the cohort was aged ≥ 75 years and 43.1% were women. DOAC users were on average more satisfied with anticoagulant treatment, with higher adjusted mean ACTS Burdens (50.18 v. 48.01, p < 0.0001) and ACTS Benefits scores (10.21 v. 9.84, p = 0.046) for DOACs vs. warfarin, respectively. The magnitude of the difference was small (Cohen’s d of 0.29 for ACTS Burdens and 0.12 for ACTS Benefits). Patients taking DOACs for venous thromboembolism were on average more satisfied with anticoagulant treatment than were warfarin users, although the magnitude of the difference was small.


2020 ◽  
Vol 13 (1) ◽  
pp. 23
Author(s):  
Wei Zhao ◽  
William Yamada ◽  
Tianxin Li ◽  
Matthew Digman ◽  
Troy Runge

In recent years, precision agriculture has been researched to increase crop production with less inputs, as a promising means to meet the growing demand of agriculture products. Computer vision-based crop detection with unmanned aerial vehicle (UAV)-acquired images is a critical tool for precision agriculture. However, object detection using deep learning algorithms rely on a significant amount of manually prelabeled training datasets as ground truths. Field object detection, such as bales, is especially difficult because of (1) long-period image acquisitions under different illumination conditions and seasons; (2) limited existing prelabeled data; and (3) few pretrained models and research as references. This work increases the bale detection accuracy based on limited data collection and labeling, by building an innovative algorithms pipeline. First, an object detection model is trained using 243 images captured with good illimitation conditions in fall from the crop lands. In addition, domain adaptation (DA), a kind of transfer learning, is applied for synthesizing the training data under diverse environmental conditions with automatic labels. Finally, the object detection model is optimized with the synthesized datasets. The case study shows the proposed method improves the bale detecting performance, including the recall, mean average precision (mAP), and F measure (F1 score), from averages of 0.59, 0.7, and 0.7 (the object detection) to averages of 0.93, 0.94, and 0.89 (the object detection + DA), respectively. This approach could be easily scaled to many other crop field objects and will significantly contribute to precision agriculture.


2021 ◽  
Vol 15 (6) ◽  
pp. 1-21
Author(s):  
Huandong Wang ◽  
Yong Li ◽  
Mu Du ◽  
Zhenhui Li ◽  
Depeng Jin

Both app developers and service providers have strong motivations to understand when and where certain apps are used by users. However, it has been a challenging problem due to the highly skewed and noisy app usage data. Moreover, apps are regarded as independent items in existing studies, which fail to capture the hidden semantics in app usage traces. In this article, we propose App2Vec, a powerful representation learning model to learn the semantic embedding of apps with the consideration of spatio-temporal context. Based on the obtained semantic embeddings, we develop a probabilistic model based on the Bayesian mixture model and Dirichlet process to capture when , where , and what semantics of apps are used to predict the future usage. We evaluate our model using two different app usage datasets, which involve over 1.7 million users and 2,000+ apps. Evaluation results show that our proposed App2Vec algorithm outperforms the state-of-the-art algorithms in app usage prediction with a performance gap of over 17.0%.


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