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.
Breast cancer ranks as the most prevalent form of cancer diagnosed in women, and diagnosis faces several challenges, a change in the size, shape and appearance of breasts, dense breast tissue, lumps or thickening in the breast especially if in only one breast, lumps and nodules in the breast. The major challenge that faces deep learning diagnosis of breast cancer was its shape, size and position non-uniformity especially malignant cancer. This work proposed a deep learning system that increased the accuracy of classification of breast cancer types from ultrasound images. It reaches 99.29% accuracy, exceeding other previous work. First, image processing was applied to in enhance the quality of input images. Second, the image segmentation was performed using U-Net architecture. Third, many features are extracted using Mobilenet. Finally, the accuracy of proposed system was evaluated.
Synthetic Aperture Radar SAR Automatic Target Recognition ATR is a key technique of remote-sensing image recognition which can be supported by deep neural networks The existing works of SAR ATR mostly focus on improving the accuracy of the target recognition while ignoring the systems performance in terms of speed and storage which is critical to real-world applications of SAR ATR For decision-makers aiming to identify a proper deep learning model to deploy in a SAR ATR system it is important to understand the performance of different candidate deep learning models and determine the best model accordingly This paper comprehensively benchmarks several advanced deep learning models for SAR ATR with multiple distinct SAR imagery datasets Specifically we train and test five SAR image classifiers based on Residual Neural Networks ResNet18 ResNet34 ResNet50 Graph Neural Network GNN and Vision Transformer for Small-Sized Datasets (SS-ViT) We select three datasets MSTAR GBSAR and SynthWakeSAR that offer heterogeneity We evaluate and compare the five classifiers concerning their classification accuracy runtime performance in terms of inference throughput and analytical performance in terms of number of parameters number of layers model size and number of operations Experimental results show that the GNN classifier outperforms with respect to throughput and latency However it is also shown that no clear model winner emerges from all of our chosen metrics and a one model rules all case is doubtful in the domain of SAR ATR
Deep learning, in general, focuses on training a neural network from large labeled datasets. Yet, in many cases there is value in training a network just from the input at hand. This is particularly relevant in many signal and image processing problems where training data is scarce and diversity is large on the one hand, and on the other, there is a lot of structure in the data that can be exploited. Using this information is the key to deep internal-learning strategies, which may involve training a network from scratch using a single input or adapting an already trained network to a provided input example at inference time. This survey paper aims at covering deep internal-learning techniques that have been proposed in the past few years for these two important directions. While our main focus will be on image processing problems, most of the approaches that we survey are derived for general signals (vectors with recurring patterns that can be distinguished from noise) and are therefore applicable to other modalities.
Although the applications of artificial intelligence especially deep learning had greatly improved various aspects of intelligent manufacturing, they still face challenges for wide employment due to the poor generalization ability, difficulties to establish high-quality training datasets, and unsatisfactory performance of deep learning methods. The emergence of large scale foundational models(LSFMs) had triggered a wave in the field of artificial intelligence, shifting deep learning models from single-task, single-modal, limited data patterns to a paradigm encompassing diverse tasks, multimodal, and pre-training on massive datasets. Although LSFMs had demonstrated powerful generalization capabilities, automatic high-quality training dataset generation and superior performance across various domains, applications of LSFMs on intelligent manufacturing were still in their nascent stage. A systematic overview of this topic was lacking, especially regarding which challenges of deep learning can be addressed by LSFMs and how these challenges can be systematically tackled. To fill this gap, this paper systematically expounded current statue of LSFMs and their advantages in the context of intelligent manufacturing. and compared comprehensively with the challenges faced by current deep learning models in various intelligent manufacturing applications. We also outlined the roadmaps for utilizing LSFMs to address these challenges. Finally, case studies of applications of LSFMs in real-world intelligent manufacturing scenarios were presented to illustrate how LSFMs could help industries, improve their efficiency.
The continuous development of artificial intelligence has a profound impact on biomedicine and other fields, providing new research ideas and technical methods. Brain-inspired computing is an important intersection between multimodal technology and biomedical field. Focusing on the application scenarios of decoding text and speech from brain signals in human-computer interaction, this paper presents a comprehensive review of the brain-inspired computing models based on deep learning (DL), tracking its evolution, application value, challenges and potential research trends. We first reviews its basic concepts and development history, and divides its evolution into two stages: recent machine learning and current deep learning, emphasizing the importance of each stage in the research of brain-inspired computing for human-computer interaction. In addition, the latest progress of deep learning in different tasks of brain-inspired computing for human-computer interaction is reviewed from five perspectives, including datasets and different brain signals, and the application of key technologies in the model is elaborated in detail. Despite significant advances in brain-inspired computational models, challenges remain to fully exploit their capabilities, and we provide insights into possible directions for future academic research. For more detailed information, please visit our GitHub page: https://github.com/ultracoolHub/brain-inspired-computing.
Climate downscaling is a crucial technique within climate research, serving to project low-resolution (LR) climate data to higher resolutions (HR). Previous research has demonstrated the effectiveness of deep learning for downscaling tasks. However, most deep learning models for climate downscaling may not perform optimally for high scaling factors (i.e., 4x, 8x) due to their limited ability to capture the intricate details required for generating HR climate data. Furthermore, climate data behaves differently from image data, necessitating a nuanced approach when employing deep generative models. In response to these challenges, this paper presents a deep generative model for downscaling climate data, specifically precipitation on a regional scale. We employ a denoising diffusion probabilistic model (DDPM) conditioned on multiple LR climate variables. The proposed model is evaluated using precipitation data from the Community Earth System Model (CESM) v1.2.2 simulation. Our results demonstrate significant improvements over existing baselines, underscoring the effectiveness of the conditional diffusion model in downscaling climate data.
I study the price dynamics of non-fungible tokens (NFTs) and propose a deep learning framework for dynamic valuation of NFTs. I use data from the Ethereum blockchain and OpenSea to train a deep learning model on historical trades, market trends, and traits/rarity features of Bored Ape Yacht Club NFTs. After hyperparameter tuning, the model is able to predict the price of NFTs with high accuracy. I propose an application framework for this model using zero-knowledge machine learning (zkML) and discuss its potential use cases in the context of decentralized finance (DeFi) applications.
Following the technological advancements in medicine, the operation rooms are evolving into intelligent environments. The context-aware systems (CAS) can comprehensively interpret the surgical state, enable real-time warning, and support decision-making, especially for novice surgeons. These systems can automatically analyze surgical videos and perform indexing, documentation, and post-operative report generation. The ever-increasing demand for such automatic systems has sparked machine-learning-based approaches for surgical video analysis. This thesis addresses the significant challenges in cataract surgery video analysis to pave the way for building efficient context-aware systems. The main contributions of this thesis are five folds: (1) This thesis demonstrates that spatio-temporal localization of the relevant content can considerably improve phase recognition accuracy. (2) This thesis proposes a novel deep-learning-based framework for relevance-based compression to enable real-time streaming and adaptive storage of cataract surgery videos. (3) Several convolutional modules are proposed to boost the networks' semantic interpretation performance in challenging conditions. These challenges include blur and reflection distortion, transparency, deformability, color and texture variation, blunt edges, and scale variation. (4) This thesis proposes and evaluates the first framework for automatic irregularity detection in cataract surgery videos. (5) To alleviate the requirement for manual pixel-based annotations, this thesis proposes novel strategies for self-supervised representation learning adapted to semantic segmentation.
Deep learning has revolutionized autonomous driving by enabling vehicles to perceive and interpret their surroundings with remarkable accuracy. This progress is attributed to various deep learning models, including Mediated Perception, Behavior Reflex, and Direct Perception, each offering unique advantages and challenges in enhancing autonomous driving capabilities. However, there is a gap in research addressing integrating these approaches and understanding their relevance in diverse driving scenarios. This study introduces three distinct neural network models corresponding to Mediated Perception, Behavior Reflex, and Direct Perception approaches. We explore their significance across varying driving conditions, shedding light on the strengths and limitations of each approach. Our architecture fuses information from the base, future latent vector prediction, and auxiliary task networks, using global routing commands to select appropriate action sub-networks. We aim to provide insights into effectively utilizing diverse modeling strategies in autonomous driving by conducting experiments and evaluations. The results show that the ensemble model performs better than the individual approaches, suggesting that each modality contributes uniquely toward the performance of the overall model. Moreover, by exploring the significance of each modality, this study offers a roadmap for future research in autonomous driving, emphasizing the importance of leveraging multiple models to achieve robust performance.
As the use of Lithium-ion batteries continues to grow, it becomes increasingly important to be able to predict their remaining useful life. This work aims to compare the relative performance of different machine learning algorithms, both traditional machine learning and deep learning, in order to determine the best-performing algorithms for battery cycle life prediction based on minimal data. We investigated 14 different machine learning models that were fed handcrafted features based on statistical data and split into 3 feature groups for testing. For deep learning models, we tested a variety of neural network models including different configurations of standard Recurrent Neural Networks, Gated Recurrent Units, and Long Short Term Memory with and without attention mechanism. Deep learning models were fed multivariate time series signals based on the raw data for each battery across the first 100 cycles. Our experiments revealed that the machine learning algorithms on handcrafted features performed particularly well, resulting in 10-20% average mean absolute percentage error. The best-performing algorithm was the Random Forest Regressor, which gave a minimum 9.8% mean absolute percentage error. Traditional machine learning models excelled due to their capability to comprehend general data set trends. In comparison, deep learning models were observed to perform particularly poorly on raw, limited data. Algorithms like GRU and RNNs that focused on capturing medium-range data dependencies were less adept at recognizing the gradual, slow trends critical for this task. Our investigation reveals that implementing machine learning models with hand-crafted features proves to be more effective than advanced deep learning models for predicting the remaining useful Lithium-ion battery life with limited data availability.
Speech recognition has become an important task in the development of machine learning and artificial intelligence. In this study, we explore the important task of keyword spotting using speech recognition machine learning and deep learning techniques. We implement feature engineering by converting raw waveforms to Mel Frequency Cepstral Coefficients (MFCCs), which we use as inputs to our models. We experiment with several different algorithms such as Hidden Markov Model with Gaussian Mixture, Convolutional Neural Networks and variants of Recurrent Neural Networks including Long Short-Term Memory and the Attention mechanism. In our experiments, RNN with BiLSTM and Attention achieves the best performance with an accuracy of 93.9 %
This review presents a comprehensive exploration of hybrid and ensemble deep learning models within Natural Language Processing (NLP), shedding light on their transformative potential across diverse tasks such as Sentiment Analysis, Named Entity Recognition, Machine Translation, Question Answering, Text Classification, Generation, Speech Recognition, Summarization, and Language Modeling. The paper systematically introduces each task, delineates key architectures from Recurrent Neural Networks (RNNs) to Transformer-based models like BERT, and evaluates their performance, challenges, and computational demands. The adaptability of ensemble techniques is emphasized, highlighting their capacity to enhance various NLP applications. Challenges in implementation, including computational overhead, overfitting, and model interpretation complexities, are addressed alongside the trade-off between interpretability and performance. Serving as a concise yet invaluable guide, this review synthesizes insights into tasks, architectures, and challenges, offering a holistic perspective for researchers and practitioners aiming to advance language-driven applications through ensemble deep learning in NLP.
Mobile traffic data in urban regions shows differentiated patterns during different hours of the day. The exploitation of these patterns enables highly accurate mobile traffic prediction for proactive network management. However, recent Deep Learning (DL) driven studies have only exploited spatiotemporal features and have ignored the geographical correlations, causing high complexity and erroneous mobile traffic predictions. This paper addresses these limitations by proposing an enhanced mobile traffic prediction scheme that combines the clustering strategy of daily mobile traffic peak time and novel multi Temporal Convolutional Network with a Long Short Term Memory (multi TCN-LSTM) model. The mobile network cells that exhibit peak traffic during the same hour of the day are clustered together. Our experiments on large-scale real-world mobile traffic data show up to 28% performance improvement compared to state-of-the-art studies, which confirms the efficacy and viability of the proposed approach.
We study the understanding of deep neural networks from the scope in which they are trained on. While the accuracy of these models is usually impressive on the aggregate level, they still make mistakes, sometimes on cases that appear to be trivial. Moreover, these models are not reliable in realizing what they do not know leading to failures such as adversarial vulnerability and out-of-distribution failures. Here, we propose a measure for quantifying the ambiguity of inputs for any given model with regard to the scope of its training. We define the ambiguity based on the geometric arrangements of the decision boundaries and the convex hull of training set in the feature space learned by the trained model, and demonstrate that a single ambiguity measure may detect a considerable portion of mistakes of a model on in-distribution samples, adversarial inputs, as well as out-of-distribution inputs. Using our ambiguity measure, a model may abstain from classification when it encounters ambiguous inputs leading to a better model accuracy not just on a given testing set, but on the inputs it may encounter at the world at large. In pursuit of this measure, we develop a theoretical framework that can identify the unknowns of the model in relation to its scope. We put this in perspective with the confidence of the model and develop formulations to identify the regions of the domain which are unknown to the model, yet the model is guaranteed to have high confidence.
Nowadays, the prevailing detectors of steganographic communication in digital images mainly consist of three steps, i.e., residual computation, feature extraction, and binary classification. In this paper, we present an alternative approach to steganalysis of digital images based on convolutional neural network (CNN), which is shown to be able to well replicate and optimize these key steps in a unified framework and learn hierarchical representations directly from raw images. The proposed CNN has a quite different structure from the ones used in conventional computer vision tasks. Rather than a random strategy, the weights in the first layer of the proposed CNN are initialized with the basic high-pass filter set used in the calculation of residual maps in a spatial rich model (SRM), which acts as a regularizer to suppress the image content effectively. To better capture the structure of embedding signals, which usually have extremely low SNR (stego signal to image content), a new activation function called a truncated linear unit is adopted in our CNN model. Finally, we further boost the performance of the proposed CNN-based steganalyzer by incorporating the knowledge of selection channel. Three state-of-the-art steganographic algorithms in spatial domain, e.g., WOW, S-UNIWARD, and HILL, are used to evaluate the effectiveness of our model. Compared to SRM and its selection-channel-aware variant maxSRMd2, our model achieves superior performance across all tested algorithms for a wide variety of payloads.
Reproducing published deep learning papers to validate their conclusions can be difficult due to sources of irreproducibility. We investigate the impact that implementation factors have on the results and how they affect reproducibility of deep learning studies. Three deep learning experiments were ran five times each on 13 different hardware environments and four different software environments. The analysis of the 780 combined results showed that there was a greater than 6% accuracy range on the same deterministic examples introduced from hardware or software environment variations alone. To account for these implementation factors, researchers should run their experiments multiple times in different hardware and software environments to verify their conclusions are not affected.
Semantic communication has emerged as a promising approach for improving efficient transmission in the next generation of wireless networks. Inspired by the success of semantic communication in different areas, we aim to provide a new semantic communication scheme from the semantic level. In this paper, we propose a novel DL-based semantic communication system for video transmission, which compacts semantic-related information to improve transmission efficiency. In particular, we utilize the Bi-optical flow to estimate residual information of inter-frame details. We also propose a feature choice module and a feature fusion module to drop semantically redundant features while paying more attention to the important semantic-related content. We employ a frame prediction module to reconstruct semantic features of the prediction frame from the received signal at the receiver. To enhance the system's robustness, we propose a noise attention module that assigns different importance weights to the extracted features. Simulation results indicate that our proposed method outperforms existing approaches in terms of transmission efficiency, achieving about 33.3\% reduction in the number of transmitted symbols while improving the peak signal-to-noise ratio (PSNR) performance by an average of 0.56dB.
Deep learning has proven to successfully learn variations in tissue and cell morphology. Training of such models typically relies on expensive manual annotations. Here we conjecture that spatially resolved gene expression, e.i., the transcriptome, can be used as an alternative to manual annotations. In particular, we trained five convolutional neural networks with patches of different size extracted from locations defined by spatially resolved gene expression. The network is trained to classify tissue morphology related to two different genes, general tissue, as well as background, on an image of fluorescence stained nuclei in a mouse brain coronal section. Performance is evaluated on an independent tissue section from a different mouse brain, reaching an average Dice score of 0.51. Results may indicate that novel techniques for spatially resolved transcriptomics together with deep learning may provide a unique and unbiased way to find genotype-phenotype relationships.
This paper investigates the feasibility of machine learning (ML)-based pilotless spatial multiplexing in multiple-input and multiple-output (MIMO) communication systems. Especially, it is shown that by training the transmitter and receiver jointly, the transmitter can learn such constellation shapes for the spatial streams which facilitate completely blind separation and detection by the simultaneously learned receiver. To the best of our knowledge, this is the first time ML-based spatial multiplexing without channel estimation pilots is demonstrated. The results show that the learned pilotless scheme can outperform a conventional pilot-based system by as much as 15-20% in terms of spectral efficiency, depending on the modulation order and signal-to-noise ratio.