Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine learning and deep learning, especially in computer vision, have led to substantial improvements in analyzing large-scale high-content images at high-throughput. These efforts have facilitated understanding of compound mechanism-of-action (MOA), drug repurposing, characterization of cell morphodynamics under perturbation, and ultimately contributing to the development of novel therapeutics. In this review, we provide a comprehensive overview of the recent advances in the field of morphological profiling. We summarize the image profiling analysis workflow, survey a broad spectrum of analysis strategies encompassing feature engineering- and deep learning-based approaches, and introduce publicly available benchmark datasets. We place a particular emphasis on the application of deep learning in this pipeline, covering cell segmentation, image representation learning, and multimodal learning. Additionally, we illuminate the application of morphological profiling in phenotypic drug discovery and highlight potential challenges and opportunities in this field.
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This study investigates the possibility of mitigating the demographic biases that affect face recognition technologies through the use of synthetic data. Demographic biases have the potential to impact individuals from specific demographic groups, and can be identified by observing disparate performance of face recognition systems across demographic groups. They primarily arise from the unequal representations of demographic groups in the training data. In recent times, synthetic data have emerged as a solution to some problems that affect face recognition systems. In particular, during the generation process it is possible to specify the desired demographic and facial attributes of images, in order to control the demographic distribution of the synthesized dataset, and fairly represent the different demographic groups. We propose to fine-tune with synthetic data existing face recognition systems that present some demographic biases. We use synthetic datasets generated with GANDiffFace, a novel framework able to synthesize datasets for face recognition with controllable demographic distribution and realistic intra-class variations. We consider multiple datasets representing different demographic groups for training and evaluation. Also, we fine-tune different face recognition systems, and evaluate their demographic fairness with different metrics. Our results support the proposed approach and the use of synthetic data to mitigate demographic biases in face recognition.
GitHub Copilot is an AI-enabled tool that automates program synthesis. It has gained significant attention since its launch in 2021. Recent studies have extensively examined Copilot's capabilities in various programming tasks, as well as its security issues. However, little is known about the effect of different natural languages on code suggestion. Natural language is considered a social bias in the field of NLP, and this bias could impact the diversity of software engineering. To address this gap, we conducted an empirical study to investigate the effect of three popular natural languages (English, Japanese, and Chinese) on Copilot. We used 756 questions of varying difficulty levels from AtCoder contests for evaluation purposes. The results highlight that the capability varies across natural languages, with Chinese achieving the worst performance. Furthermore, regardless of the type of natural language, the performance decreases significantly as the difficulty of questions increases. Our work represents the initial step in comprehending the significance of natural languages in Copilot's capability and introduces promising opportunities for future endeavors.
Recent developments enable the quantification of causal control given a structural causal model (SCM). This has been accomplished by introducing quantities which encode changes in the entropy of one variable when intervening on another. These measures, named causal entropy and causal information gain, aim to address limitations in existing information theoretical approaches for machine learning tasks where causality plays a crucial role. They have not yet been properly mathematically studied. Our research contributes to the formal understanding of the notions of causal entropy and causal information gain by establishing and analyzing fundamental properties of these concepts, including bounds and chain rules. Furthermore, we elucidate the relationship between causal entropy and stochastic interventions. We also propose definitions for causal conditional entropy and causal conditional information gain. Overall, this exploration paves the way for enhancing causal machine learning tasks through the study of recently-proposed information theoretic quantities grounded in considerations about causality.
The use of multimodal imaging has led to significant improvements in the diagnosis and treatment of many diseases. Similar to clinical practice, some works have demonstrated the benefits of multimodal fusion for automatic segmentation and classification using deep learning-based methods. However, current segmentation methods are limited to fusion of modalities with the same dimensionality (e.g., 3D+3D, 2D+2D), which is not always possible, and the fusion strategies implemented by classification methods are incompatible with localization tasks. In this work, we propose a novel deep learning-based framework for the fusion of multimodal data with heterogeneous dimensionality (e.g., 3D+2D) that is compatible with localization tasks. The proposed framework extracts the features of the different modalities and projects them into the common feature subspace. The projected features are then fused and further processed to obtain the final prediction. The framework was validated on the following tasks: segmentation of geographic atrophy (GA), a late-stage manifestation of age-related macular degeneration, and segmentation of retinal blood vessels (RBV) in multimodal retinal imaging. Our results show that the proposed method outperforms the state-of-the-art monomodal methods on GA and RBV segmentation by up to 3.10% and 4.64% Dice, respectively.
Deep neural networks (DNNs), trained with gradient-based optimization and backpropagation, are currently the primary tool in modern artificial intelligence, machine learning, and data science. In many applications, DNNs are trained offline, through supervised learning or reinforcement learning, and deployed online for inference. However, training DNNs with standard backpropagation and gradient-based optimization gives no intrinsic performance guarantees or bounds on the DNN, which is essential for applications such as controls. Additionally, many offline-training and online-inference problems, such as sim2real transfer of reinforcement learning policies, experience domain shift from the training distribution to the real-world distribution. To address these stability and transfer learning issues, we propose using techniques from control theory to update DNN parameters online. We formulate the fully-connected feedforward DNN as a continuous-time dynamical system, and we propose novel last-layer update laws that guarantee desirable error convergence under various conditions on the time derivative of the DNN input vector. We further show that training the DNN under spectral normalization controls the upper bound of the error trajectories of the online DNN predictions, which is desirable when numerically differentiated quantities or noisy state measurements are input to the DNN. The proposed online DNN adaptation laws are validated in simulation to learn the dynamics of the Van der Pol system under domain shift, where parameters are varied in inference from the training dataset. The simulations demonstrate the effectiveness of using control-theoretic techniques to derive performance improvements and guarantees in DNN-based learning systems.
When is heterogeneity in the composition of an autonomous robotic team beneficial and when is it detrimental? We investigate and answer this question in the context of a minimally viable model that examines the role of heterogeneous speeds in perimeter defense problems, where defenders share a total allocated speed budget. We consider two distinct problem settings and develop strategies based on dynamic programming and on local interaction rules. We present a theoretical analysis of both approaches and our results are extensively validated using simulations. Interestingly, our results demonstrate that the viability of heterogeneous teams depends on the amount of information available to the defenders. Moreover, our results suggest a universality property: across a wide range of problem parameters the optimal ratio of the speeds of the defenders remains nearly constant.
What is learned by sophisticated neural network agents such as AlphaZero? This question is of both scientific and practical interest. If the representations of strong neural networks bear no resemblance to human concepts, our ability to understand faithful explanations of their decisions will be restricted, ultimately limiting what we can achieve with neural network interpretability. In this work we provide evidence that human knowledge is acquired by the AlphaZero neural network as it trains on the game of chess. By probing for a broad range of human chess concepts we show when and where these concepts are represented in the AlphaZero network. We also provide a behavioural analysis focusing on opening play, including qualitative analysis from chess Grandmaster Vladimir Kramnik. Finally, we carry out a preliminary investigation looking at the low-level details of AlphaZero's representations, and make the resulting behavioural and representational analyses available online.
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.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
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.
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