Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after cardiovascular diseases. Gene expression can play a fundamental role in the early detection of cancer, as it is indicative of the biochemical processes in tissue and cells, as well as the genetic characteristics of an organism. Deoxyribonucleic Acid (DNA) microarrays and Ribonucleic Acid (RNA)- sequencing methods for gene expression data allow quantifying the expression levels of genes and produce valuable data for computational analysis. This study reviews recent progress in gene expression analysis for cancer classification using machine learning methods. Both conventional and deep learning-based approaches are reviewed, with an emphasis on the ap-plication of deep learning models due to their comparative advantages for identifying gene patterns that are distinctive for various types of cancers. Relevant works that employ the most commonly used deep neural network architectures are covered, including multi-layer perceptrons, convolutional, recurrent, graph, and transformer networks. This survey also presents an overview of the data collection methods for gene expression analysis and lists important datasets that are commonly used for supervised machine learning for this task. Furthermore, reviewed are pertinent techniques for feature engineering and data preprocessing that are typically used to handle the high dimensionality of gene expression data, caused by a large number of genes present in data samples. The paper concludes with a discussion of future research directions for machine learning-based gene expression analysis for cancer classification.

Text classification is a fundamental task in natural language processing (NLP). Several recent studies show the success of deep learning on text processing. Convolutional neural network (CNN), as a popular deep learning model, has shown remarkable success in the task of text classification. In this paper, new baseline models have been studied for text classification using CNN. In these models, documents are fed to the network as a three-dimensional tensor representation to provide sentence-level analysis. Applying such a method enables the models to take advantage of the positional information of the sentences in the text. Besides, analysing adjacent sentences allows extracting additional features. The proposed models have been compared with the state-of-the-art models using several datasets. The results have shown that the proposed models have better performance, particularly in the longer documents.

Variational autoencoders (VAEs) are a popular framework for modeling complex data distributions; they can be efficiently trained via variational inference by maximizing the evidence lower bound (ELBO), at the expense of a gap to the exact (log-)marginal likelihood. While VAEs are commonly used for disentangled representation learning, it is unclear why ELBO maximization would yield such representations, since unregularized maximum likelihood estimation generally cannot invert the data-generating process without additional assumptions. Yet, VAEs often succeed at this task. We seek to elucidate this apparent paradox by studying nonlinear VAEs in the limit of near-deterministic decoders. We first prove that, in this regime, the optimal encoder approximately inverts the decoder--a commonly used but unproven conjecture--which we refer to as self-consistency. Leveraging self-consistency, we show that the ELBO converges to a regularized log-likelihood. This allows VAEs to perform what has recently been termed independent mechanism analysis (IMA): it adds an inductive bias towards decoders with column-orthogonal Jacobians, which helps recovering the true latent factors. The gap between ELBO and log-likelihood is therefore welcome, since it bears unanticipated benefits for nonlinear representation learning. In experiments on synthetic and image data, we show that VAEs uncover the true latent factors when the data generating process satisfies the IMA assumption.

Artificial intelligence and machine learning algorithms have become ubiquitous. Although they offer a wide range of benefits, their adoption in decision-critical fields is limited by their lack of interpretability, particularly with textual data. Moreover, with more data available than ever before, it has become increasingly important to explain automated predictions. Generally, users find it difficult to understand the underlying computational processes and interact with the models, especially when the models fail to generate the outcomes or explanations, or both, correctly. This problem highlights the growing need for users to better understand the models' inner workings and gain control over their actions. This dissertation focuses on two fundamental challenges of addressing this need. The first involves explanation generation: inferring high-quality explanations from text documents in a scalable and data-driven manner. The second challenge consists in making explanations actionable, and we refer to it as critiquing. This dissertation examines two important applications in natural language processing and recommendation tasks. Overall, we demonstrate that interpretability does not come at the cost of reduced performance in two consequential applications. Our framework is applicable to other fields as well. This dissertation presents an effective means of closing the gap between promise and practice in artificial intelligence.

Conversational information seeking (CIS) is concerned with a sequence of interactions between one or more users and an information system. Interactions in CIS are primarily based on natural language dialogue, while they may include other types of interactions, such as click, touch, and body gestures. This monograph provides a thorough overview of CIS definitions, applications, interactions, interfaces, design, implementation, and evaluation. This monograph views CIS applications as including conversational search, conversational question answering, and conversational recommendation. Our aim is to provide an overview of past research related to CIS, introduce the current state-of-the-art in CIS, highlight the challenges still being faced in the community. and suggest future directions.

Existing deep neural networks for histopathology image synthesis cannot generate image styles that align with different organs, and cannot produce accurate boundaries of clustered nuclei. To address these issues, we propose a style-guided instance-adaptive normalization (SIAN) approach to synthesize realistic color distributions and textures for histopathology images from different organs. SIAN contains four phases, semantization, stylization, instantiation, and modulation. The first two phases synthesize image semantics and styles by using semantic maps and learned image style vectors. The instantiation module integrates geometrical and topological information and generates accurate nuclei boundaries. We validate the proposed approach on a multiple-organ dataset, Extensive experimental results demonstrate that the proposed method generates more realistic histopathology images than four state-of-the-art approaches for five organs. By incorporating synthetic images from the proposed approach to model training, an instance segmentation network can achieve state-of-the-art performance.

We introduce CriticSMC, a new algorithm for planning as inference built from a composition of sequential Monte Carlo with learned Soft-Q function heuristic factors. These heuristic factors, obtained from parametric approximations of the marginal likelihood ahead, more effectively guide SMC towards the desired target distribution, which is particularly helpful for planning in environments with hard constraints placed sparsely in time. Compared with previous work, we modify the placement of such heuristic factors, which allows us to cheaply propose and evaluate large numbers of putative action particles, greatly increasing inference and planning efficiency. CriticSMC is compatible with informative priors, whose density function need not be known, and can be used as a model-free control algorithm. Our experiments on collision avoidance in a high-dimensional simulated driving task show that CriticSMC significantly reduces collision rates at a low computational cost while maintaining realism and diversity of driving behaviors across vehicles and environment scenarios.

Autonomous navigation and path-planning around non-cooperative space objects is an enabling technology for on-orbit servicing and space debris removal systems. The navigation task includes the determination of target object motion, the identification of target object features suitable for grasping, and the identification of collision hazards and other keep-out zones. Given this knowledge, chaser spacecraft can be guided towards capture locations without damaging the target object or without unduly the operations of a servicing target by covering up solar arrays or communication antennas. One way to autonomously achieve target identification, characterization and feature recognition is by use of artificial intelligence algorithms. This paper discusses how the combination of cameras and machine learning algorithms can achieve the relative navigation task. The performance of two deep learning-based object detection algorithms, Faster Region-based Convolutional Neural Networks (R-CNN) and You Only Look Once (YOLOv5), is tested using experimental data obtained in formation flight simulations in the ORION Lab at Florida Institute of Technology. The simulation scenarios vary the yaw motion of the target object, the chaser approach trajectory, and the lighting conditions in order to test the algorithms in a wide range of realistic and performance limiting situations. The data analyzed include the mean average precision metrics in order to compare the performance of the object detectors. The paper discusses the path to implementing the feature recognition algorithms and towards integrating them into the spacecraft Guidance Navigation and Control system.

Recent advances in probabilistic generative modeling have motivated learning Structural Causal Models (SCM) from observational datasets using deep conditional generative models, also known as Deep Structural Causal Model (DSCM). If successful, DSCMs can be utilized for causal estimation tasks, e.g., for answering counterfactual queries (Pawlowski et al. (2020)). In this work, we warn practitioners about non-identifiability of counterfactual inference from observational data, even in the absence of unobserved confounding and assuming known causal structure. We prove counterfactual identifiability of monotonic generation mechanisms with single dimensional exogenous variables. For general generation mechanisms with multi-dimensional exogenous variables, we provide an impossibility result for counterfactual identifiability, motivating the need for parametric assumptions. As a practical approach, we propose a method for estimating worst-case errors of learned DSCMs' counterfactual predictions. The size of this error can be an essential metric for deciding whether or not DSCMs are a viable approach for counterfactual inference in a specific problem setting. In evaluation, our method confirms negligible counterfactual errors for an identifiable Structural Causal Model (SCM) from prior work, and also provides informative error bounds on counterfactual errors for a non-identifiable synthetic SCM.

Accurately modeling complex, multimodal distributions is necessary for optimal decision-making, but doing so for rotations in three-dimensions, i.e., the SO(3) group, is challenging due to the curvature of the rotation manifold. The recently described implicit-PDF (IPDF) is a simple, elegant, and effective approach for learning arbitrary distributions on SO(3) up to a given precision. However, inference with IPDF requires $N$ forward passes through the network's final multilayer perceptron (where $N$ places an upper bound on the likelihood that can be calculated by the model), which is prohibitively slow for those without the computational resources necessary to parallelize the queries. In this paper, I introduce AQuaMaM, a neural network capable of both learning complex distributions on the rotation manifold and calculating exact likelihoods for query rotations in a single forward pass. Specifically, AQuaMaM autoregressively models the projected components of unit quaternions as mixtures of uniform distributions that partition their geometrically-restricted domain of values. When trained on an "infinite" toy dataset with ambiguous viewpoints, AQuaMaM rapidly converges to a sampling distribution closely matching the true data distribution. In contrast, the sampling distribution for IPDF dramatically diverges from the true data distribution, despite IPDF approaching its theoretical minimum evaluation loss during training. When trained on a constructed dataset of 500,000 renders of a die in different rotations, AQuaMaM reaches a test log-likelihood 14% higher than IPDF. Further, compared to IPDF, AQuaMaM uses 24% fewer parameters, has a prediction throughput 52$\times$ faster on a single GPU, and converges in a similar amount of time during training.