Research Papers

Explainable AI for Bioinformatics: Methods, Tools, and Applications

Md. Rezaul Karim, Tanhim Islam, Oya Beyan +4

Artificial intelligence (AI) systems utilizing deep neural networks (DNNs) and machine learning (ML) algorithms are widely used for solving important problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNNs or ML models, which are often perceived as opaque and black-box, can make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. Additionally, in sensitive areas like healthcare, explainability and accountability are not only desirable but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable artificial intelligence (XAI) aims to overcome the opaqueness of black-box models and provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and the factors that influence their outcomes. However, most state-of-the-art interpretable ML methods are domain-agnostic and evolved from fields like computer vision, automated reasoning, or statistics, making direct application to bioinformatics problems challenging without customization and domain-specific adaptation. In this paper, we discuss the importance of explainability in the context of bioinformatics, provide an overview of model-specific and model-agnostic interpretable ML methods and tools, and outline their potential caveats and drawbacks. Besides, we discuss how to customize existing interpretable ML methods for bioinformatics problems. Nevertheless, we demonstrate how XAI methods can improve transparency through case studies in bioimaging, cancer genomics, and text mining.

The adoption of machine learning (ML) and, more specifically, deep learning (DL) applications into all major areas of our lives is underway. The development of trustworthy AI is especially important in medicine due to the large implications for patients' lives. While trustworthiness concerns various aspects including ethical, technical and privacy requirements, we focus on the importance of data quality (training/test) in DL. Since data quality dictates the behaviour of ML products, evaluating data quality will play a key part in the regulatory approval of medical AI products. We perform a systematic review following PRISMA guidelines using the databases PubMed and ACM Digital Library. We identify 2362 studies, out of which 62 records fulfil our eligibility criteria. From this literature, we synthesise the existing knowledge on data quality frameworks and combine it with the perspective of ML applications in medicine. As a result, we propose the METRIC-framework, a specialised data quality framework for medical training data comprising 15 awareness dimensions, along which developers of medical ML applications should investigate a dataset. This knowledge helps to reduce biases as a major source of unfairness, increase robustness, facilitate interpretability and thus lays the foundation for trustworthy AI in medicine. Incorporating such systematic assessment of medical datasets into regulatory approval processes has the potential to accelerate the approval of ML products and builds the basis for new standards.

Recent studies in the field of Machine Translation (MT) and Natural Language Processing (NLP) have shown that existing models amplify biases observed in the training data. The amplification of biases in language technology has mainly been examined with respect to specific phenomena, such as gender bias. In this work, we go beyond the study of gender in MT and investigate how bias amplification might affect language in a broader sense. We hypothesize that the 'algorithmic bias', i.e. an exacerbation of frequently observed patterns in combination with a loss of less frequent ones, not only exacerbates societal biases present in current datasets but could also lead to an artificially impoverished language: 'machine translationese'. We assess the linguistic richness (on a lexical and morphological level) of translations created by different data-driven MT paradigms - phrase-based statistical (PB-SMT) and neural MT (NMT). Our experiments show that there is a loss of lexical and morphological richness in the translations produced by all investigated MT paradigms for two language pairs (EN<=>FR and EN<=>ES).

Ethical Considerations in Artificial Intelligence Courses

Emanuelle Burton, Judy Goldsmith, Sven Koenig +3

The recent surge in interest in ethics in artificial intelligence may leave many educators wondering how to address moral, ethical, and philosophical issues in their AI courses. As instructors we want to develop curriculum that not only prepares students to be artificial intelligence practitioners, but also to understand the moral, ethical, and philosophical impacts that artificial intelligence will have on society. In this article we provide practical case studies and links to resources for use by AI educators. We also provide concrete suggestions on how to integrate AI ethics into a general artificial intelligence course and how to teach a stand-alone artificial intelligence ethics course.

As calls for fair and unbiased algorithmic systems increase, so too does the number of individuals working on algorithmic fairness in industry. However, these practitioners often do not have access to the demographic data they feel they need to detect bias in practice. Even with the growing variety of toolkits and strategies for working towards algorithmic fairness, they almost invariably require access to demographic attributes or proxies. We investigated this dilemma through semi-structured interviews with 38 practitioners and professionals either working in or adjacent to algorithmic fairness. Participants painted a complex picture of what demographic data availability and use look like on the ground, ranging from not having access to personal data of any kind to being legally required to collect and use demographic data for discrimination assessments. In many domains, demographic data collection raises a host of difficult questions, including how to balance privacy and fairness, how to define relevant social categories, how to ensure meaningful consent, and whether it is appropriate for private companies to infer someone's demographics. Our research suggests challenges that must be considered by businesses, regulators, researchers, and community groups in order to enable practitioners to address algorithmic bias in practice. Critically, we do not propose that the overall goal of future work should be to simply lower the barriers to collecting demographic data. Rather, our study surfaces a swath of normative questions about how, when, and whether this data should be procured, and, in cases where it is not, what should still be done to mitigate bias.

How Different Groups Prioritize Ethical Values for Responsible AI

Maurice Jakesch, Zana Buçinca, Saleema Amershi +1

Private companies, public sector organizations, and academic groups have outlined ethical values they consider important for responsible artificial intelligence technologies. While their recommendations converge on a set of central values, little is known about the values a more representative public would find important for the AI technologies they interact with and might be affected by. We conducted a survey examining how individuals perceive and prioritize responsible AI values across three groups: a representative sample of the US population (N=743), a sample of crowdworkers (N=755), and a sample of AI practitioners (N=175). Our results empirically confirm a common concern: AI practitioners' value priorities differ from those of the general public. Compared to the US-representative sample, AI practitioners appear to consider responsible AI values as less important and emphasize a different set of values. In contrast, self-identified women and black respondents found responsible AI values more important than other groups. Surprisingly, more liberal-leaning participants, rather than participants reporting experiences with discrimination, were more likely to prioritize fairness than other groups. Our findings highlight the importance of paying attention to who gets to define responsible AI.

Despite the immense societal importance of ethically designing artificial intelligence (AI), little research on the public perceptions of ethical AI principles exists. This becomes even more striking when considering that ethical AI development has the aim to be human-centric and of benefit for the whole society. In this study, we investigate how ethical principles (explainability, fairness, security, accountability, accuracy, privacy, machine autonomy) are weighted in comparison to each other. This is especially important, since simultaneously considering ethical principles is not only costly, but sometimes even impossible, as developers must make specific trade-off decisions. In this paper, we give first answers on the relative importance of ethical principles given a specific use case - the use of AI in tax fraud detection. The results of a large conjoint survey (n=1099) suggest that, by and large, German respondents found the ethical principles equally important. However, subsequent cluster analysis shows that different preference models for ethically designed systems exist among the German population. These clusters substantially differ not only in the preferred attributes, but also in the importance level of the attributes themselves. We further describe how these groups are constituted in terms of sociodemographics as well as opinions on AI. Societal implications as well as design challenges are discussed.

The ethical implications and social impacts of artificial intelligence have become topics of compelling interest to industry, researchers in academia, and the public. However, current analyses of AI in a global context are biased toward perspectives held in the U.S., and limited by a lack of research, especially outside the U.S. and Western Europe. This article summarizes the key findings of a literature review of recent social science scholarship on the social impacts of AI and related technologies in five global regions. Our team of social science researchers reviewed more than 800 academic journal articles and monographs in over a dozen languages. Our review of the literature suggests that AI is likely to have markedly different social impacts depending on geographical setting. Likewise, perceptions and understandings of AI are likely to be profoundly shaped by local cultural and social context. Recent research in U.S. settings demonstrates that AI-driven technologies have a pattern of entrenching social divides and exacerbating social inequality, particularly among historically-marginalized groups. Our literature review indicates that this pattern exists on a global scale, and suggests that low- and middle-income countries may be more vulnerable to the negative social impacts of AI and less likely to benefit from the attendant gains. We call for rigorous ethnographic research to better understand the social impacts of AI around the world. Global, on-the-ground research is particularly critical to identify AI systems that may amplify social inequality in order to mitigate potential harms. Deeper understanding of the social impacts of AI in diverse social settings is a necessary precursor to the development, implementation, and monitoring of responsible and beneficial AI technologies, and forms the basis for meaningful regulation of these technologies.

How has recent AI Ethics literature addressed topics such as fairness and justice in the context of continued social and structural power asymmetries? We trace both the historical roots and current landmark work that have been shaping the field and categorize these works under three broad umbrellas: (i) those grounded in Western canonical philosophy, (ii) mathematical and statistical methods, and (iii) those emerging from critical data/algorithm/information studies. We also survey the field and explore emerging trends by examining the rapidly growing body of literature that falls under the broad umbrella of AI Ethics. To that end, we read and annotated peer-reviewed papers published over the past four years in two premier conferences: FAccT and AIES. We organize the literature based on an annotation scheme we developed according to three main dimensions: whether the paper deals with concrete applications, use-cases, and/or people's lived experience; to what extent it addresses harmed, threatened, or otherwise marginalized groups; and if so, whether it explicitly names such groups. We note that although the goals of the majority of FAccT and AIES papers were often commendable, their consideration of the negative impacts of AI on traditionally marginalized groups remained shallow. Taken together, our conceptual analysis and the data from annotated papers indicate that the field would benefit from an increased focus on ethical analysis grounded in concrete use-cases, people's experiences, and applications as well as from approaches that are sensitive to structural and historical power asymmetries.

Toward Fairness in AI for People with Disabilities: A Research Roadmap

Anhong Guo, Ece Kamar, Jennifer Wortman Vaughan +2

AI technologies have the potential to dramatically impact the lives of people with disabilities (PWD). Indeed, improving the lives of PWD is a motivator for many state-of-the-art AI systems, such as automated speech recognition tools that can caption videos for people who are deaf and hard of hearing, or language prediction algorithms that can augment communication for people with speech or cognitive disabilities. However, widely deployed AI systems may not work properly for PWD, or worse, may actively discriminate against them. These considerations regarding fairness in AI for PWD have thus far received little attention. In this position paper, we identify potential areas of concern regarding how several AI technology categories may impact particular disability constituencies if care is not taken in their design, development, and testing. We intend for this risk assessment of how various classes of AI might interact with various classes of disability to provide a roadmap for future research that is needed to gather data, test these hypotheses, and build more inclusive algorithms.

Large Language Models (LLMs) have revolutionized natural language processing, but their susceptibility to biases poses significant challenges. This comprehensive review examines the landscape of bias in LLMs, from its origins to current mitigation strategies. We categorize biases as intrinsic and extrinsic, analyzing their manifestations in various NLP tasks. The review critically assesses a range of bias evaluation methods, including data-level, model-level, and output-level approaches, providing researchers with a robust toolkit for bias detection. We further explore mitigation strategies, categorizing them into pre-model, intra-model, and post-model techniques, highlighting their effectiveness and limitations. Ethical and legal implications of biased LLMs are discussed, emphasizing potential harms in real-world applications such as healthcare and criminal justice. By synthesizing current knowledge on bias in LLMs, this review contributes to the ongoing effort to develop fair and responsible AI systems. Our work serves as a comprehensive resource for researchers and practitioners working towards understanding, evaluating, and mitigating bias in LLMs, fostering the development of more equitable AI technologies.

In this multicultural age, language translation is one of the most performed tasks, and it is becoming increasingly AI-moderated and automated. As a novel AI system, ChatGPT claims to be proficient in such translation tasks and in this paper, we put that claim to the test. Specifically, we examine ChatGPT's accuracy in translating between English and languages that exclusively use gender-neutral pronouns. We center this study around Bengali, the 7$^{th}$ most spoken language globally, but also generalize our findings across five other languages: Farsi, Malay, Tagalog, Thai, and Turkish. We find that ChatGPT perpetuates gender defaults and stereotypes assigned to certain occupations (e.g. man = doctor, woman = nurse) or actions (e.g. woman = cook, man = go to work), as it converts gender-neutral pronouns in languages to `he' or `she'. We also observe ChatGPT completely failing to translate the English gender-neutral pronoun `they' into equivalent gender-neutral pronouns in other languages, as it produces translations that are incoherent and incorrect. While it does respect and provide appropriately gender-marked versions of Bengali words when prompted with gender information in English, ChatGPT appears to confer a higher respect to men than to women in the same occupation. We conclude that ChatGPT exhibits the same gender biases which have been demonstrated for tools like Google Translate or MS Translator, as we provide recommendations for a human centered approach for future designers of AIs that perform language translation to better accommodate such low-resource languages.