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.

The escalating volume of academic literature presents a formidable challenge in staying updated with the newest research developments. Addressing this, this study introduces a pioneering AI-based tool, configured specifically to streamline the efficiency of the article selection phase in Systematic Literature Reviews (SLRs). Utilizing the robust capabilities of OpenAI's GPT-4 Assistant API, the tool successfully homogenizes the article selection process across a broad array of academic disciplines. Implemented through a tripartite approach consisting of data preparation, AI-mediated article assessment, and structured result presentation, this tool significantly accelerates the time-consuming task of literature reviews. Importantly, this tool could be highly beneficial in fields such as management and economics, where the SLR process involves substantial human judgment. The adoption of a standard GPT model can substantially reduce potential biases and enhance the speed and precision of the SLR selection phase. This not only amplifies researcher productivity and accuracy but also denotes a considerable stride forward in the way academic research is conducted amidst the surging body of scholarly publications.

Pathology images of histopathology can be acquired from camera-mounted microscopes or whole slide scanners. Utilizing similarity calculations to match patients based on these images holds significant potential in research and clinical contexts. Recent advancements in search technologies allow for nuanced quantification of cellular structures across diverse tissue types, facilitating comparisons and enabling inferences about diagnosis, prognosis, and predictions for new patients when compared against a curated database of diagnosed and treated cases. In this paper, we comprehensively review the latest developments in image search technologies for histopathology, offering a concise overview tailored for computational pathology researchers seeking effective, fast and efficient image search methods in their work.

Clustering algorithms aim to organize data into groups or clusters based on the inherent patterns and similarities within the data. They play an important role in today's life, such as in marketing and e-commerce, healthcare, data organization and analysis, and social media. Numerous clustering algorithms exist, with ongoing developments introducing new ones. Each algorithm possesses its own set of strengths and weaknesses, and as of now, there is no universally applicable algorithm for all tasks. In this work, we analyzed existing clustering algorithms and classify mainstream algorithms across five different dimensions: underlying principles and characteristics, data point assignment to clusters, dataset capacity, predefined cluster numbers and application area. This classification facilitates researchers in understanding clustering algorithms from various perspectives and helps them identify algorithms suitable for solving specific tasks. Finally, we discussed the current trends and potential future directions in clustering algorithms. We also identified and discussed open challenges and unresolved issues in the field.

As Large Language Models and Natural Language Processing (NLP) technology rapidly develop and spread into daily life, it becomes crucial to anticipate how their use could harm people. One problem that has received a lot of attention in recent years is that this technology has displayed harmful biases, from generating derogatory stereotypes to producing disparate outcomes for different social groups. Although a lot of effort has been invested in assessing and mitigating these biases, our methods of measuring the biases of NLP models have serious problems and it is often unclear what they actually measure. In this paper, we provide an interdisciplinary approach to discussing the issue of NLP model bias by adopting the lens of psychometrics -- a field specialized in the measurement of concepts like bias that are not directly observable. In particular, we will explore two central notions from psychometrics, the construct validity and the reliability of measurement tools, and discuss how they can be applied in the context of measuring model bias. Our goal is to provide NLP practitioners with methodological tools for designing better bias measures, and to inspire them more generally to explore tools from psychometrics when working on bias measurement tools.

In this article, we review the literature on statistical theories of neural networks from three perspectives. In the first part, results on excess risks for neural networks are reviewed in the nonparametric framework of regression or classification. These results rely on explicit constructions of neural networks, leading to fast convergence rates of excess risks, in that tools from the approximation theory are adopted. Through these constructions, the width and depth of the networks can be expressed in terms of sample size, data dimension, and function smoothness. Nonetheless, their underlying analysis only applies to the global minimizer in the highly non-convex landscape of deep neural networks. This motivates us to review the training dynamics of neural networks in the second part. Specifically, we review papers that attempt to answer ``how the neural network trained via gradient-based methods finds the solution that can generalize well on unseen data.'' In particular, two well-known paradigms are reviewed: the Neural Tangent Kernel (NTK) paradigm, and Mean-Field (MF) paradigm. In the last part, we review the most recent theoretical advancements in generative models including Generative Adversarial Networks (GANs), diffusion models, and in-context learning (ICL) in the Large Language Models (LLMs). The former two models are known to be the main pillars of the modern generative AI era, while ICL is a strong capability of LLMs in learning from a few examples in the context. Finally, we conclude the paper by suggesting several promising directions for deep learning theory.

Artificial intelligence (AI) has acquired notorious relevance in modern computing as it effectively solves complex tasks traditionally done by humans. AI provides methods to represent and infer knowledge, efficiently manipulate texts and learn from vast amount of data. These characteristics are applicable in many activities that human find laborious or repetitive, as is the case of the analysis of scientific literature. Manually preparing and writing a systematic literature review (SLR) takes considerable time and effort, since it requires planning a strategy, conducting the literature search and analysis, and reporting the findings. Depending on the area under study, the number of papers retrieved can be of hundreds or thousands, meaning that filtering those relevant ones and extracting the key information becomes a costly and error-prone process. However, some of the involved tasks are repetitive and, therefore, subject to automation by means of AI. In this paper, we present a survey of AI techniques proposed in the last 15 years to help researchers conduct systematic analyses of scientific literature. We describe the tasks currently supported, the types of algorithms applied, and available tools proposed in 34 primary studies. This survey also provides a historical perspective of the evolution of the field and the role that humans can play in an increasingly automated SLR process.

In an era characterized by the pervasive integration of artificial intelligence into decision-making processes across diverse industries, the demand for trust has never been more pronounced. This thesis embarks on a comprehensive exploration of bias and fairness, with a particular emphasis on their ramifications within the banking sector, where AI-driven decisions bear substantial societal consequences. In this context, the seamless integration of fairness, explainability, and human oversight is of utmost importance, culminating in the establishment of what is commonly referred to as "Responsible AI". This emphasizes the critical nature of addressing biases within the development of a corporate culture that aligns seamlessly with both AI regulations and universal human rights standards, particularly in the realm of automated decision-making systems. Nowadays, embedding ethical principles into the development, training, and deployment of AI models is crucial for compliance with forthcoming European regulations and for promoting societal good. This thesis is structured around three fundamental pillars: understanding bias, mitigating bias, and accounting for bias. These contributions are validated through their practical application in real-world scenarios, in collaboration with Intesa Sanpaolo. This collaborative effort not only contributes to our understanding of fairness but also provides practical tools for the responsible implementation of AI-based decision-making systems. In line with open-source principles, we have released Bias On Demand and FairView as accessible Python packages, further promoting progress in the field of AI fairness.

In the rapidly evolving domain of Natural Language Generation (NLG) evaluation, introducing Large Language Models (LLMs) has opened new avenues for assessing generated content quality, e.g., coherence, creativity, and context relevance. This survey aims to provide a thorough overview of leveraging LLMs for NLG evaluation, a burgeoning area that lacks a systematic analysis. We propose a coherent taxonomy for organizing existing LLM-based evaluation metrics, offering a structured framework to understand and compare these methods. Our detailed exploration includes critically assessing various LLM-based methodologies, as well as comparing their strengths and limitations in evaluating NLG outputs. By discussing unresolved challenges, including bias, robustness, domain-specificity, and unified evaluation, this survey seeks to offer insights to researchers and advocate for fairer and more advanced NLG evaluation techniques.

Given the complexity and lack of transparency in deep neural networks (DNNs), extensive efforts have been made to make these systems more interpretable or explain their behaviors in accessible terms. Unlike most reviews, which focus on algorithmic and model-centric perspectives, this work takes a "data-centric" view, examining how data collection, processing, and analysis contribute to explainable AI (XAI). We categorize existing work into three categories subject to their purposes: interpretations of deep models, referring to feature attributions and reasoning processes that correlate data points with model outputs; influences of training data, examining the impact of training data nuances, such as data valuation and sample anomalies, on decision-making processes; and insights of domain knowledge, discovering latent patterns and fostering new knowledge from data and models to advance social values and scientific discovery. Specifically, we distill XAI methodologies into data mining operations on training and testing data across modalities, such as images, text, and tabular data, as well as on training logs, checkpoints, models and other DNN behavior descriptors. In this way, our study offers a comprehensive, data-centric examination of XAI from a lens of data mining methods and applications.