Cell type deconvolution is a computational approach to infer proportions of individual cell types from bulk transcriptomics data. Though many new methods have been developed for cell type deconvolution, most of them only provide point estimation of the cell type proportions. On the other hand, estimates of the cell type proportions can be very noisy due to various sources of bias and randomness, and ignoring their uncertainty may greatly affect the validity of downstream analyses. In this paper, we propose a comprehensive statistical framework for cell type deconvolution and construct asymptotically valid confidence intervals both for each individual's cell type proportion and for quantifying how cell type proportions change across multiple bulk individuals in downstream regression analyses. Our analysis takes into account various factors including the biological randomness of gene expressions across cells and individuals, gene-gene dependence, and the cross-platform biases and sequencing errors, and avoids any parametric assumptions on the data distributions. We also provide identification conditions of the cell type proportions when there are arbitrary platforms-specific bias across sequencing technologies.
The mainstream of data-driven abstractive summarization models tends to explore the correlations rather than the causal relationships. Among such correlations, there can be spurious ones which suffer from the language prior learned from the training corpus and therefore undermine the overall effectiveness of the learned model. To tackle this issue, we introduce a Structural Causal Model (SCM) to induce the underlying causal structure of the summarization data. We assume several latent causal factors and non-causal factors, representing the content and style of the document and summary. Theoretically, we prove that the latent factors in our SCM can be identified by fitting the observed training data under certain conditions. On the basis of this, we propose a Causality Inspired Sequence-to-Sequence model (CI-Seq2Seq) to learn the causal representations that can mimic the causal factors, guiding us to pursue causal information for summary generation. The key idea is to reformulate the Variational Auto-encoder (VAE) to fit the joint distribution of the document and summary variables from the training corpus. Experimental results on two widely used text summarization datasets demonstrate the advantages of our approach.
The future of automated driving (AD) is rooted in the development of robust, fair and explainable artificial intelligence methods. Upon request, automated vehicles must be able to explain their decisions to the driver and the car passengers, to the pedestrians and other vulnerable road users and potentially to external auditors in case of accidents. However, nowadays, most explainable methods still rely on quantitative analysis of the AD scene representations captured by multiple sensors. This paper proposes a novel representation of AD scenes, called Qualitative eXplainable Graph (QXG), dedicated to qualitative spatiotemporal reasoning of long-term scenes. The construction of this graph exploits the recent Qualitative Constraint Acquisition paradigm. Our experimental results on NuScenes, an open real-world multi-modal dataset, show that the qualitative eXplainable graph of an AD scene composed of 40 frames can be computed in real-time and light in space storage which makes it a potentially interesting tool for improved and more trustworthy perception and control processes in AD.
Generating samples given a specific label requires estimating conditional distributions. We derive a tractable upper bound of the Wasserstein distance between conditional distributions to lay the theoretical groundwork to learn conditional distributions. Based on this result, we propose a novel conditional generation algorithm where conditional distributions are fully characterized by a metric space defined by a statistical distance. We employ optimal transport theory to propose the Wasserstein geodesic generator, a new conditional generator that learns the Wasserstein geodesic. The proposed method learns both conditional distributions for observed domains and optimal transport maps between them. The conditional distributions given unobserved intermediate domains are on the Wasserstein geodesic between conditional distributions given two observed domain labels. Experiments on face images with light conditions as domain labels demonstrate the efficacy of the proposed method.
We present an exact approach to analyze and quantify the sensitivity of higher moments of probabilistic loops with symbolic parameters, polynomial arithmetic and potentially uncountable state spaces. Our approach integrates methods from symbolic computation, probability theory, and static analysis in order to automatically capture sensitivity information about probabilistic loops. Sensitivity information allows us to formally establish how value distributions of probabilistic loop variables influence the functional behavior of loops, which can in particular be helpful when choosing values of loop variables in order to ensure efficient/expected computations. Our work uses algebraic techniques to model higher moments of loop variables via linear recurrence equations and introduce the notion of sensitivity recurrences. We show that sensitivity recurrences precisely model loop sensitivities, even in cases where the moments of loop variables do not satisfy a system of linear recurrences. As such, we enlarge the class of probabilistic loops for which sensitivity analysis was so far feasible. We demonstrate the success of our approach while analyzing the sensitivities of probabilistic loops.
Porous crystalline materials have the potential to play a key role in developing solutions for molecular storage, gas separation and carbon adsorption. For these solutions, we need to develop new materials with specific properties. Estimating the properties of such porous materials involves first principle simulation using classical molecular simulations. The computational complexity of these methods can be a barrier to high throughput screening of the potential materials as the space of possible materials is vast. Data-driven methods, specifically machine learning methods based on deep neural networks offer a significant opportunity to significantly scale the simulation of the behavior of these materials. However, to effectively achieve this the Deep Learning models need to utilize the symmetries present in the crystals. Crystals pose specific symmetries that are present in their space group. Existing methods for crystal property prediction either have symmetry constraints that are too restrictive or only incorporate symmetries between unit cells. In addition, these models do not explicitly model the porous structure of the crystal. In this paper, we develop a model which incorporates the symmetries of the unit cell of a crystal in its architecture and explicitly models the porous structure. We evaluate our model by predicting the heat of adsorption of CO$_2$ for different configurations of the Mordenite and ZSM-5 zeolites. Our results confirm that our method performs better than existing methods for crystal property prediction and that the inclusion of pores results in a more efficient model.
In object detection, the cost of labeling is much high because it needs not only to confirm the categories of multiple objects in an image but also to accurately determine the bounding boxes of each object. Thus, integrating active learning into object detection will raise pretty positive significance. In this paper, we propose a classification committee for active deep object detection method by introducing a discrepancy mechanism of multiple classifiers for samples' selection when training object detectors. The model contains a main detector and a classification committee. The main detector denotes the target object detector trained from a labeled pool composed of the selected informative images. The role of the classification committee is to select the most informative images according to their uncertainty values from the view of classification, which is expected to focus more on the discrepancy and representative of instances. Specifically, they compute the uncertainty for a specified instance within the image by measuring its discrepancy output by the committee pre-trained via the proposed Maximum Classifiers Discrepancy Group Loss (MCDGL). The most informative images are finally determined by selecting the ones with many high-uncertainty instances. Besides, to mitigate the impact of interference instances, we design a Focus on Positive Instances Loss (FPIL) to make the committee the ability to automatically focus on the representative instances as well as precisely encode their discrepancies for the same instance. Experiments are conducted on Pascal VOC and COCO datasets versus some popular object detectors. And results show that our method outperforms the state-of-the-art active learning methods, which verifies the effectiveness of the proposed method.
Benefit from the quick development of deep learning techniques, salient object detection has achieved remarkable progresses recently. However, there still exists following two major challenges that hinder its application in embedded devices, low resolution output and heavy model weight. To this end, this paper presents an accurate yet compact deep network for efficient salient object detection. More specifically, given a coarse saliency prediction in the deepest layer, we first employ residual learning to learn side-output residual features for saliency refinement, which can be achieved with very limited convolutional parameters while keep accuracy. Secondly, we further propose reverse attention to guide such side-output residual learning in a top-down manner. By erasing the current predicted salient regions from side-output features, the network can eventually explore the missing object parts and details which results in high resolution and accuracy. Experiments on six benchmark datasets demonstrate that the proposed approach compares favorably against state-of-the-art methods, and with advantages in terms of simplicity, efficiency (45 FPS) and model size (81 MB).
We advocate the use of implicit fields for learning generative models of shapes and introduce an implicit field decoder for shape generation, aimed at improving the visual quality of the generated shapes. An implicit field assigns a value to each point in 3D space, so that a shape can be extracted as an iso-surface. Our implicit field decoder is trained to perform this assignment by means of a binary classifier. Specifically, it takes a point coordinate, along with a feature vector encoding a shape, and outputs a value which indicates whether the point is outside the shape or not. By replacing conventional decoders by our decoder for representation learning and generative modeling of shapes, we demonstrate superior results for tasks such as shape autoencoding, generation, interpolation, and single-view 3D reconstruction, particularly in terms of visual quality.
Deep learning has yielded state-of-the-art performance on many natural language processing tasks including named entity recognition (NER). However, this typically requires large amounts of labeled data. In this work, we demonstrate that the amount of labeled training data can be drastically reduced when deep learning is combined with active learning. While active learning is sample-efficient, it can be computationally expensive since it requires iterative retraining. To speed this up, we introduce a lightweight architecture for NER, viz., the CNN-CNN-LSTM model consisting of convolutional character and word encoders and a long short term memory (LSTM) tag decoder. The model achieves nearly state-of-the-art performance on standard datasets for the task while being computationally much more efficient than best performing models. We carry out incremental active learning, during the training process, and are able to nearly match state-of-the-art performance with just 25\% of the original training data.
The dominant sequence transduction models are based on complex recurrent or convolutional neural networks in an encoder-decoder configuration. The best performing models also connect the encoder and decoder through an attention mechanism. We propose a new simple network architecture, the Transformer, based solely on attention mechanisms, dispensing with recurrence and convolutions entirely. Experiments on two machine translation tasks show these models to be superior in quality while being more parallelizable and requiring significantly less time to train. Our model achieves 28.4 BLEU on the WMT 2014 English-to-German translation task, improving over the existing best results, including ensembles by over 2 BLEU. On the WMT 2014 English-to-French translation task, our model establishes a new single-model state-of-the-art BLEU score of 41.8 after training for 3.5 days on eight GPUs, a small fraction of the training costs of the best models from the literature. We show that the Transformer generalizes well to other tasks by applying it successfully to English constituency parsing both with large and limited training data.