Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome wide human data we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.
相關內容
Additive Noise Models (ANM) encode a popular functional assumption that enables learning causal structure from observational data. Due to a lack of real-world data meeting the assumptions, synthetic ANM data are often used to evaluate causal discovery algorithms. Reisach et al. (2021) show that, for common simulation parameters, a variable ordering by increasing variance is closely aligned with a causal order and introduce var-sortability to quantify the alignment. Here, we show that not only variance, but also the fraction of a variable's variance explained by all others, as captured by the coefficient of determination $R^2$, tends to increase along the causal order. Simple baseline algorithms can use $R^2$-sortability to match the performance of established methods. Since $R^2$-sortability is invariant under data rescaling, these algorithms perform equally well on standardized or rescaled data, addressing a key limitation of algorithms exploiting var-sortability. We characterize and empirically assess $R^2$-sortability for different simulation parameters. We show that all simulation parameters can affect $R^2$-sortability and must be chosen deliberately to control the difficulty of the causal discovery task and the real-world plausibility of the simulated data. We provide an implementation of the sortability measures and sortability-based algorithms in our library CausalDisco (//github.com/CausalDisco/CausalDisco).
In this paper, we investigate the optimal statistical performance and the impact of computational constraints for independent component analysis (ICA). Our goal is twofold. On the one hand, we characterize the precise role of dimensionality on sample complexity and statistical accuracy, and how computational consideration may affect them. In particular, we show that the optimal sample complexity is linear in dimensionality, and interestingly, the commonly used sample kurtosis-based approaches are necessarily suboptimal. However, the optimal sample complexity becomes quadratic, up to a logarithmic factor, in the dimension if we restrict ourselves to estimates that can be computed with low-degree polynomial algorithms. On the other hand, we develop computationally tractable estimates that attain both the optimal sample complexity and minimax optimal rates of convergence. We study the asymptotic properties of the proposed estimates and establish their asymptotic normality that can be readily used for statistical inferences. Our method is fairly easy to implement and numerical experiments are presented to further demonstrate its practical merits.
As a second-order method, the Natural Gradient Descent (NGD) has the ability to accelerate training of neural networks. However, due to the prohibitive computational and memory costs of computing and inverting the Fisher Information Matrix (FIM), efficient approximations are necessary to make NGD scalable to Deep Neural Networks (DNNs). Many such approximations have been attempted. The most sophisticated of these is KFAC, which approximates the FIM as a block-diagonal matrix, where each block corresponds to a layer of the neural network. By doing so, KFAC ignores the interactions between different layers. In this work, we investigate the interest of restoring some low-frequency interactions between the layers by means of two-level methods. Inspired from domain decomposition, several two-level corrections to KFAC using different coarse spaces are proposed and assessed. The obtained results show that incorporating the layer interactions in this fashion does not really improve the performance of KFAC. This suggests that it is safe to discard the off-diagonal blocks of the FIM, since the block-diagonal approach is sufficiently robust, accurate and economical in computation time.
Existing statistical methods can estimate a policy, or a mapping from covariates to decisions, which can then instruct decision makers (e.g., whether to administer hypotension treatment based on covariates blood pressure and heart rate). There is great interest in using such data-driven policies in healthcare. However, it is often important to explain to the healthcare provider, and to the patient, how a new policy differs from the current standard of care. This end is facilitated if one can pinpoint the aspects of the policy (i.e., the parameters for blood pressure and heart rate) that change when moving from the standard of care to the new, suggested policy. To this end, we adapt ideas from Trust Region Policy Optimization (TRPO). In our work, however, unlike in TRPO, the difference between the suggested policy and standard of care is required to be sparse, aiding with interpretability. This yields ``relative sparsity," where, as a function of a tuning parameter, $\lambda$, we can approximately control the number of parameters in our suggested policy that differ from their counterparts in the standard of care (e.g., heart rate only). We propose a criterion for selecting $\lambda$, perform simulations, and illustrate our method with a real, observational healthcare dataset, deriving a policy that is easy to explain in the context of the current standard of care. Our work promotes the adoption of data-driven decision aids, which have great potential to improve health outcomes.
The knowledge of the states of a vehicle is a necessity to perform proper planning and control. These quantities are usually accessible through measurements. Control theory brings extremely useful methods -- observers -- to deal with quantities that cannot be directly measured or with noisy measurements. Classical observers are mathematically derived from models. In spite of their success, such as the Kalman filter, they show their limits when systems display high non-linearities, modeling errors, high uncertainties or difficult interactions with the environment (e.g. road contact). In this work, we present a method to build a learning-based observer able to outperform classical observing methods. We compare several neural network architectures and define the data generation procedure used to train them. The method is evaluated on a kinematic bicycle model which allows to easily generate data for training and testing. This model is also used in an Extended Kalman Filter (EKF) for comparison of the learning-based observer with a state of the art model-based observer. The results prove the interest of our approach and pave the way for future improvements of the technique.
Satellite-based Synthetic Aperture Radar (SAR) images can be used as a source of remote sensed imagery regardless of cloud cover and day-night cycle. However, the speckle noise and varying image acquisition conditions pose a challenge for change detection classifiers. This paper proposes a new method of improving SAR image processing to produce higher quality difference images for the classification algorithms. The method is built on a neural network-based mapping transformation function that produces artificial SAR images from a location in the requested acquisition conditions. The inputs for the model are: previous SAR images from the location, imaging angle information from the SAR images, digital elevation model, and weather conditions. The method was tested with data from a location in North-East Finland by using Sentinel-1 SAR images from European Space Agency, weather data from Finnish Meteorological Institute, and a digital elevation model from National Land Survey of Finland. In order to verify the method, changes to the SAR images were simulated, and the performance of the proposed method was measured using experimentation where it gave substantial improvements to performance when compared to a more conventional method of creating difference images.
In large-scale systems there are fundamental challenges when centralised techniques are used for task allocation. The number of interactions is limited by resource constraints such as on computation, storage, and network communication. We can increase scalability by implementing the system as a distributed task-allocation system, sharing tasks across many agents. However, this also increases the resource cost of communications and synchronisation, and is difficult to scale. In this paper we present four algorithms to solve these problems. The combination of these algorithms enable each agent to improve their task allocation strategy through reinforcement learning, while changing how much they explore the system in response to how optimal they believe their current strategy is, given their past experience. We focus on distributed agent systems where the agents' behaviours are constrained by resource usage limits, limiting agents to local rather than system-wide knowledge. We evaluate these algorithms in a simulated environment where agents are given a task composed of multiple subtasks that must be allocated to other agents with differing capabilities, to then carry out those tasks. We also simulate real-life system effects such as networking instability. Our solution is shown to solve the task allocation problem to 6.7% of the theoretical optimal within the system configurations considered. It provides 5x better performance recovery over no-knowledge retention approaches when system connectivity is impacted, and is tested against systems up to 100 agents with less than a 9% impact on the algorithms' performance.
Causality can be described in terms of a structural causal model (SCM) that carries information on the variables of interest and their mechanistic relations. For most processes of interest the underlying SCM will only be partially observable, thus causal inference tries to leverage any exposed information. Graph neural networks (GNN) as universal approximators on structured input pose a viable candidate for causal learning, suggesting a tighter integration with SCM. To this effect we present a theoretical analysis from first principles that establishes a novel connection between GNN and SCM while providing an extended view on general neural-causal models. We then establish a new model class for GNN-based causal inference that is necessary and sufficient for causal effect identification. Our empirical illustration on simulations and standard benchmarks validate our theoretical proofs.
In structure learning, the output is generally a structure that is used as supervision information to achieve good performance. Considering the interpretation of deep learning models has raised extended attention these years, it will be beneficial if we can learn an interpretable structure from deep learning models. In this paper, we focus on Recurrent Neural Networks (RNNs) whose inner mechanism is still not clearly understood. We find that Finite State Automaton (FSA) that processes sequential data has more interpretable inner mechanism and can be learned from RNNs as the interpretable structure. We propose two methods to learn FSA from RNN based on two different clustering methods. We first give the graphical illustration of FSA for human beings to follow, which shows the interpretability. From the FSA's point of view, we then analyze how the performance of RNNs are affected by the number of gates, as well as the semantic meaning behind the transition of numerical hidden states. Our results suggest that RNNs with simple gated structure such as Minimal Gated Unit (MGU) is more desirable and the transitions in FSA leading to specific classification result are associated with corresponding words which are understandable by human beings.
We propose a novel approach to multimodal sentiment analysis using deep neural networks combining visual analysis and natural language processing. Our goal is different than the standard sentiment analysis goal of predicting whether a sentence expresses positive or negative sentiment; instead, we aim to infer the latent emotional state of the user. Thus, we focus on predicting the emotion word tags attached by users to their Tumblr posts, treating these as "self-reported emotions." We demonstrate that our multimodal model combining both text and image features outperforms separate models based solely on either images or text. Our model's results are interpretable, automatically yielding sensible word lists associated with emotions. We explore the structure of emotions implied by our model and compare it to what has been posited in the psychology literature, and validate our model on a set of images that have been used in psychology studies. Finally, our work also provides a useful tool for the growing academic study of images - both photographs and memes - on social networks.
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191