The use of generative artificial intelligence (AI) models is becoming ubiquitous in many fields. Though progress continues to be made, general purpose large language AI models (LLM) show a tendency to deliver creative answers, often called "hallucinations", which have slowed their application in the medical and biomedical fields where accuracy is paramount. We propose that the design and use of much smaller, domain and even task-specific LM may be a more rational and appropriate use of this technology in biomedical research. In this work we apply a very small LM by today's standards to the specialized task of predicting regulatory interactions between molecular components to fill gaps in our current understanding of intracellular pathways. Toward this we attempt to correctly posit known pathway-informed interactions recovered from manually curated pathway databases by selecting and using only the most informative examples as part of an active learning scheme. With this example we show that a small (~110 million parameters) LM based on a Bidirectional Encoder Representations from Transformers (BERT) architecture can propose molecular interactions relevant to tuberculosis persistence and transmission with over 80% accuracy using less than 25% of the ~520 regulatory relationships in question. Using information entropy as a metric for the iterative selection of new tuning examples, we also find that increased accuracy is driven by favoring the use of the incorrectly assigned statements with the highest certainty (lowest entropy). In contrast, the concurrent use of correct but least certain examples contributed little and may have even been detrimental to the learning rate.

To a ddress these gaps, prior work has sought to evaluate the cultural representations within AI generated output, b ut with few exceptions [30, 67], mostly through quantified, metricized approaches to representation such as statistical similarities and benchmark-style scoring [49, 84]. However, the use of these methods presumes that representation is an o bjective construct with an empirical, definitive ground truth that outputs can be compared against [e.g., 42, 84] [fo r a critique of ground truth, see 59]. Given limitations of these computational methods, evaluation of representation is reduced to basic recognition or factual generation of artifacts. Even when human feedback on representation is sought, it is solicited through narrow, constrained, quantitative scales from anonymized crowdworkers who often do not have th e lived experiences to evaluate nuances of cultural representation of other cultures. However, this approach to measuring representation is in contravention to decades of scholarship in the social sciences that emphasizes the subjective nature of representation, where judgments about representation in visual media are constructed in conversation with the viewer's lived experiences and the broader context within which an image is Permission to make digital or hard copies of all or part of thi s work for personal or classroom use is granted without fee pr ovided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page.

In this paper, we evaluate the performance of four randomized optimization algorithms: Randomized Hill Climbing (RHC), Simulated Annealing (SA), Genetic Algorithms (GA), and MIMIC (Mutual Information Maximizing Input Clustering), across three distinct types of problems: binary, permutation, and combinatorial. We systematically compare these algorithms using a set of benchmark fitness functions that highlight the specific challenges and requirements of each problem category. Our study analyzes each algorithm's effectiveness based on key performance metrics, including solution quality, convergence speed, computational cost, and robustness. Results show that while MIMIC and GA excel in producing high-quality solutions for binary and combinatorial problems, their computational demands vary significantly. RHC and SA, while computationally less expensive, demonstrate limited performance in complex problem landscapes. The findings offer valuable insights into the trade-offs between different optimization strategies and provide practical guidance for selecting the appropriate algorithm based on the type of problems, accuracy requirements, and computational constraints.

L-systems can be made to model and create simulations of many biological processes, such as plant development. Finding an L-system for a given process is typically solved by hand, by experts, in a massively time-consuming process. It would be significant if this could be done automatically from data, such as from sequences of images. In this paper, we are interested in inferring a particular type of L-system, deterministic context-free L-system (D0L-system) from a sequence of strings. We introduce the characteristic graph of a sequence of strings, which we then utilize to translate our problem (inferring D0L-system) in polynomial time into the maximum independent set problem (MIS) and the SAT problem. After that, we offer a classical exact algorithm and an approximate quantum algorithm for the problem.

Complex table question answering (TQA) aims to answer questions that require complex reasoning, such as multi-step or multi-category reasoning, over data represented in tabular form. Previous approaches demonstrated notable performance by leveraging either closed-source large language models (LLMs) or fine-tuned open-weight LLMs. However, fine-tuning LLMs requires high-quality training data, which is costly to obtain, and utilizing closed-source LLMs poses accessibility challenges and leads to reproducibility issues. In this paper, we propose Multi-Agent Collaboration with Tool use (MACT), a framework that requires neither closed-source models nor fine-tuning. In MACT, a planning agent and a coding agent that also make use of tools collaborate to answer questions. Our experiments on four TQA benchmarks show that MACT outperforms previous SoTA systems on three out of four benchmarks and that it performs comparably to the larger and more expensive closed-source model GPT-4 on two benchmarks, even when using only open-weight models without any fine-tuning. We conduct extensive analyses to prove the effectiveness of MACT's multi-agent collaboration in TQA.

This systematic literature review investigates perceptions, concerns, and expectations of young digital citizens regarding privacy in artificial intelligence (AI) systems, focusing on social media platforms, educational technology, gaming systems, and recommendation algorithms. Using a rigorous methodology, the review started with 2,000 papers, narrowed down to 552 after initial screening, and finally refined to 108 for detailed analysis. Data extraction focused on privacy concerns, data-sharing practices, the balance between privacy and utility, trust factors in AI, transparency expectations, and strategies to enhance user control over personal data. Findings reveal significant privacy concerns among young users, including a perceived lack of control over personal information, potential misuse of data by AI, and fears of data breaches and unauthorized access. These issues are worsened by unclear data collection practices and insufficient transparency in AI applications. The intention to share data is closely associated with perceived benefits and data protection assurances. The study also highlights the role of parental mediation and the need for comprehensive education on data privacy. Balancing privacy and utility in AI applications is crucial, as young digital citizens value personalized services but remain wary of privacy risks. Trust in AI is significantly influenced by transparency, reliability, predictable behavior, and clear communication about data usage. Strategies to improve user control over personal data include access to and correction of data, clear consent mechanisms, and robust data protection assurances. The review identifies research gaps and suggests future directions, such as longitudinal studies, multicultural comparisons, and the development of ethical AI frameworks.

Detecting and tracking code clones can ease various software development and maintenance tasks when changes in a code fragment should be propagated over all its copies. Several deep learning-based clone detection models have appeared in the literature for detecting syntactic and semantic clones, widely evaluated with the BigCloneBench dataset. However, class imbalance and the small number of semantic clones make BigCloneBench less ideal for interpreting model performance. Researchers also use other datasets such as GoogleCodeJam, OJClone, and SemanticCloneBench to understand model generalizability. To overcome the limitations of existing datasets, the GPT-assisted semantic and cross-language clone dataset GPTCloneBench has been released. However, how these models compare across datasets remains unclear. In this paper, we propose a multi-step evaluation approach for five state-of-the-art clone detection models leveraging existing benchmark datasets, including GPTCloneBench, and using mutation operators to study model ability. Specifically, we examine three highly-performing single-language models (ASTNN, GMN, CodeBERT) on BigCloneBench, SemanticCloneBench, and GPTCloneBench, testing their robustness with mutation operations. Additionally, we compare them against cross-language models (C4, CLCDSA) known for detecting semantic clones. While single-language models show high F1 scores for BigCloneBench, their performance on SemanticCloneBench varies (up to 20%). Interestingly, the cross-language model (C4) shows superior performance (around 7%) on SemanticCloneBench over other models and performs similarly on BigCloneBench and GPTCloneBench. On mutation-based datasets, C4 has more robust performance (less than 1% difference) compared to single-language models, which show high variability.

Software defect prediction is a critical aspect of software quality assurance, as it enables early identification and mitigation of defects, thereby reducing the cost and impact of software failures. Over the past few years, quantum computing has risen as an exciting technology capable of transforming multiple domains; Quantum Machine Learning (QML) is one of them. QML algorithms harness the power of quantum computing to solve complex problems with better efficiency and effectiveness than their classical counterparts. However, research into its application in software engineering to predict software defects still needs to be explored. In this study, we worked to fill the research gap by comparing the performance of three QML and five classical machine learning (CML) algorithms on the 20 software defect datasets. Our investigation reports the comparative scenarios of QML vs. CML algorithms and identifies the better-performing and consistent algorithms to predict software defects. We also highlight the challenges and future directions of employing QML algorithms in real software defect datasets based on the experience we faced while performing this investigation. The findings of this study can help practitioners and researchers further progress in this research domain by making software systems reliable and bug-free.

We introduce HiCat (Hybrid Cell Annotation using Transformative embeddings), a novel semi-supervised pipeline for annotating cell types from single-cell RNA sequencing data. HiCat fuses the strengths of supervised learning for known cell types with unsupervised learning to identify novel types. This hybrid approach incorporates both reference and query genomic data for feature engineering, enhancing the embedding learning process, increasing the effective sample size for unsupervised techniques, and improving the transferability of the supervised model trained on reference data when applied to query datasets. The pipeline follows six key steps: (1) removing batch effects using Harmony to generate a 50-dimensional principal component embedding; (2) applying UMAP for dimensionality reduction to two dimensions to capture crucial data patterns; (3) conducting unsupervised clustering of cells with DBSCAN, yielding a one-dimensional cluster membership vector; (4) merging the multi-resolution results of the previous steps into a 53-dimensional feature space that encompasses both reference and query data; (5) training a CatBoost model on the reference dataset to predict cell types in the query dataset; and (6) resolving inconsistencies between the supervised predictions and unsupervised cluster labels. When benchmarked on 10 publicly available genomic datasets, HiCat surpasses other methods, particularly in differentiating and identifying multiple new cell types. Its capacity to accurately classify novel cell types showcases its robustness and adaptability within intricate biological datasets.

Predicting software defects early in the development process not only enhances the quality and reliability of the software but also decreases the cost of development. A wide range of machine learning techniques can be employed to create software defect prediction models, but the effectiveness and accuracy of these models are often influenced by the choice of appropriate feature subset. Since finding the optimal feature subset is computationally intensive, heuristic and metaheuristic approaches are commonly employed to identify near-optimal solutions within a reasonable time frame. Recently, the quantum computing paradigm quantum annealing (QA) has been deployed to find solutions to complex optimization problems. This opens up the possibility of addressing the feature subset selection problem with a QA machine. Although several strategies have been proposed for feature subset selection using a QA machine, little exploration has been done regarding the viability of a QA machine for feature subset selection in software defect prediction. This study investigates the potential of D-Wave QA system for this task, where we formulate a mutual information (MI)-based filter approach as an optimization problem and utilize a D-Wave Quantum Processing Unit (QPU) solver as a QA solver for feature subset selection. We evaluate the performance of this approach using multiple software defect datasets from the AEEM, JIRA, and NASA projects. We also utilize a D-Wave classical solver for comparative analysis. Our experimental results demonstrate that QA-based feature subset selection can enhance software defect prediction. Although the D-Wave QPU solver exhibits competitive prediction performance with the classical solver in software defect prediction, it significantly reduces the time required to identify the best feature subset compared to its classical counterpart.