Cellular reprogramming can be used for both the prevention and cure of different diseases. However, the efficiency of discovering reprogramming strategies with classical wet-lab experiments is hindered by lengthy time commitments and high costs. In this study, we develop a novel computational framework based on deep reinforcement learning that facilitates the identification of reprogramming strategies. For this aim, we formulate a control problem in the context of cellular reprogramming for the frameworks of BNs and PBNs under the asynchronous update mode. Furthermore, we introduce the notion of a pseudo-attractor and a procedure for identification of pseudo-attractor state during training. Finally, we devise a computational framework for solving the control problem, which we test on a number of different models.
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The fusion of causal models with deep learning introducing increasingly intricate data sets, such as the causal associations within images or between textual components, has surfaced as a focal research area. Nonetheless, the broadening of original causal concepts and theories to such complex, non-statistical data has been met with serious challenges. In response, our study proposes redefinitions of causal data into three distinct categories from the standpoint of causal structure and representation: definite data, semi-definite data, and indefinite data. Definite data chiefly pertains to statistical data used in conventional causal scenarios, while semi-definite data refers to a spectrum of data formats germane to deep learning, including time-series, images, text, and others. Indefinite data is an emergent research sphere inferred from the progression of data forms by us. To comprehensively present these three data paradigms, we elaborate on their formal definitions, differences manifested in datasets, resolution pathways, and development of research. We summarize key tasks and achievements pertaining to definite and semi-definite data from myriad research undertakings, present a roadmap for indefinite data, beginning with its current research conundrums. Lastly, we classify and scrutinize the key datasets presently utilized within these three paradigms.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
The dominating NLP paradigm of training a strong neural predictor to perform one task on a specific dataset has led to state-of-the-art performance in a variety of applications (eg. sentiment classification, span-prediction based question answering or machine translation). However, it builds upon the assumption that the data distribution is stationary, ie. that the data is sampled from a fixed distribution both at training and test time. This way of training is inconsistent with how we as humans are able to learn from and operate within a constantly changing stream of information. Moreover, it is ill-adapted to real-world use cases where the data distribution is expected to shift over the course of a model's lifetime. The first goal of this thesis is to characterize the different forms this shift can take in the context of natural language processing, and propose benchmarks and evaluation metrics to measure its effect on current deep learning architectures. We then proceed to take steps to mitigate the effect of distributional shift on NLP models. To this end, we develop methods based on parametric reformulations of the distributionally robust optimization framework. Empirically, we demonstrate that these approaches yield more robust models as demonstrated on a selection of realistic problems. In the third and final part of this thesis, we explore ways of efficiently adapting existing models to new domains or tasks. Our contribution to this topic takes inspiration from information geometry to derive a new gradient update rule which alleviate catastrophic forgetting issues during adaptation.
Due to their increasing spread, confidence in neural network predictions became more and more important. However, basic neural networks do not deliver certainty estimates or suffer from over or under confidence. Many researchers have been working on understanding and quantifying uncertainty in a neural network's prediction. As a result, different types and sources of uncertainty have been identified and a variety of approaches to measure and quantify uncertainty in neural networks have been proposed. This work gives a comprehensive overview of uncertainty estimation in neural networks, reviews recent advances in the field, highlights current challenges, and identifies potential research opportunities. It is intended to give anyone interested in uncertainty estimation in neural networks a broad overview and introduction, without presupposing prior knowledge in this field. A comprehensive introduction to the most crucial sources of uncertainty is given and their separation into reducible model uncertainty and not reducible data uncertainty is presented. The modeling of these uncertainties based on deterministic neural networks, Bayesian neural networks, ensemble of neural networks, and test-time data augmentation approaches is introduced and different branches of these fields as well as the latest developments are discussed. For a practical application, we discuss different measures of uncertainty, approaches for the calibration of neural networks and give an overview of existing baselines and implementations. Different examples from the wide spectrum of challenges in different fields give an idea of the needs and challenges regarding uncertainties in practical applications. Additionally, the practical limitations of current methods for mission- and safety-critical real world applications are discussed and an outlook on the next steps towards a broader usage of such methods is given.
As soon as abstract mathematical computations were adapted to computation on digital computers, the problem of efficient representation, manipulation, and communication of the numerical values in those computations arose. Strongly related to the problem of numerical representation is the problem of quantization: in what manner should a set of continuous real-valued numbers be distributed over a fixed discrete set of numbers to minimize the number of bits required and also to maximize the accuracy of the attendant computations? This perennial problem of quantization is particularly relevant whenever memory and/or computational resources are severely restricted, and it has come to the forefront in recent years due to the remarkable performance of Neural Network models in computer vision, natural language processing, and related areas. Moving from floating-point representations to low-precision fixed integer values represented in four bits or less holds the potential to reduce the memory footprint and latency by a factor of 16x; and, in fact, reductions of 4x to 8x are often realized in practice in these applications. Thus, it is not surprising that quantization has emerged recently as an important and very active sub-area of research in the efficient implementation of computations associated with Neural Networks. In this article, we survey approaches to the problem of quantizing the numerical values in deep Neural Network computations, covering the advantages/disadvantages of current methods. With this survey and its organization, we hope to have presented a useful snapshot of the current research in quantization for Neural Networks and to have given an intelligent organization to ease the evaluation of future research in this area.
We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.
Many natural language processing tasks solely rely on sparse dependencies between a few tokens in a sentence. Soft attention mechanisms show promising performance in modeling local/global dependencies by soft probabilities between every two tokens, but they are not effective and efficient when applied to long sentences. By contrast, hard attention mechanisms directly select a subset of tokens but are difficult and inefficient to train due to their combinatorial nature. In this paper, we integrate both soft and hard attention into one context fusion model, "reinforced self-attention (ReSA)", for the mutual benefit of each other. In ReSA, a hard attention trims a sequence for a soft self-attention to process, while the soft attention feeds reward signals back to facilitate the training of the hard one. For this purpose, we develop a novel hard attention called "reinforced sequence sampling (RSS)", selecting tokens in parallel and trained via policy gradient. Using two RSS modules, ReSA efficiently extracts the sparse dependencies between each pair of selected tokens. We finally propose an RNN/CNN-free sentence-encoding model, "reinforced self-attention network (ReSAN)", solely based on ReSA. It achieves state-of-the-art performance on both Stanford Natural Language Inference (SNLI) and Sentences Involving Compositional Knowledge (SICK) datasets.
While it is nearly effortless for humans to quickly assess the perceptual similarity between two images, the underlying processes are thought to be quite complex. Despite this, the most widely used perceptual metrics today, such as PSNR and SSIM, are simple, shallow functions, and fail to account for many nuances of human perception. Recently, the deep learning community has found that features of the VGG network trained on the ImageNet classification task has been remarkably useful as a training loss for image synthesis. But how perceptual are these so-called "perceptual losses"? What elements are critical for their success? To answer these questions, we introduce a new Full Reference Image Quality Assessment (FR-IQA) dataset of perceptual human judgments, orders of magnitude larger than previous datasets. We systematically evaluate deep features across different architectures and tasks and compare them with classic metrics. We find that deep features outperform all previous metrics by huge margins. More surprisingly, this result is not restricted to ImageNet-trained VGG features, but holds across different deep architectures and levels of supervision (supervised, self-supervised, or even unsupervised). Our results suggest that perceptual similarity is an emergent property shared across deep visual representations.
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