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In this study, we propose HOPER (HOlistic ProtEin Representation), a novel multimodal learning framework designed to enhance protein function prediction (PFP) in low-data settings. The challenge of predicting protein functions is compounded by the limited availability of labeled data. Traditional machine learning models already struggle in such cases, and while deep learning models excel with abundant data, they also face difficulties when data is scarce. HOPER addresses this issue by integrating three distinct modalities - protein sequences, biomedical text, and protein-protein interaction (PPI) networks - to create a comprehensive protein representation. The model utilizes autoencoders to generate holistic embeddings, which are then employed for PFP tasks using transfer learning. HOPER outperforms existing methods on a benchmark dataset across all Gene Ontology categories, i.e., molecular function, biological process, and cellular component. Additionally, we demonstrate its practical utility by identifying new immune-escape proteins in lung adenocarcinoma, offering insights into potential therapeutic targets. Our results highlight the effectiveness of multimodal representation learning for overcoming data limitations in biological research, potentially enabling more accurate and scalable protein function prediction. HOPER source code and datasets are available at https://github.com/kansil/HOPER

The eXTP mission is a major project of the Chinese Academy of Sciences (CAS), with a large involvement of Europe. Its scientific payload includes four instruments: SFA, PFA, LAD and WFM. They offer an unprecedented simultaneous wide-band Xray timing and polarimetry sensitivity. A large European consortium is contributing to the eXTP study, both for the science and the instrumentation. Europe is expected to provide two of the four instruments: LAD and WFM; the LAD is led by Italy and the WFM by Spain. The WFM for eXTP is based on the design originally proposed for the LOFT ESA M3 mission, that underwent a Phase A feasibility study. It will be a wide field of view X-ray monitor instrument working in the 2-50 keV energy range, achieved with large-area Silicon Drift Detectors (SDDs), similar to the ones used for the LAD but with better spatial resolution. The WFM will consist of 3 pairs of coded mask cameras with a total combined field of view (FoV) of 90x180 degrees at zero response and a source localisation accuracy of ~1 arc min. The main goal of the WFM is to provide triggers for the target of opportunity observations of the SFA, PFA and LAD, in order to perform the core science programme, dedicated to the study of matter under extreme conditions of density, gravity and magnetism. In addition, the unprecedented combination of large field of view and imaging capability, down to 2 keV, of the WFM will allow eXTP to make important discoveries of the variable and transient X-ray sky, and provide X-ray coverage of a broad range of astrophysical objects covered under 'observatory science', such as gamma-ray bursts, fast radio bursts, gravitational wave electromagnetic counterparts. In this paper we provide an overview of the WFM instrument, explaining its design, configuration, and anticipated performance., Comment: 15 pages, 13 figures, Proceedings of SPIE 13093, Space Telescopes and Instrumentation 2024: Ultraviolet to Gamma Ray; Proceedings Volume 13093, Space Telescopes and Instrumentation 2024: Ultraviolet to Gamma Ray; 130931Y (2024); doi: 10.1117/12.3020020

Unit testing is an essential component of software testing, with the assert statements playing an important role in determining whether the tested function operates as expected. Although research has explored automated test case generation, generating meaningful assert statements remains an ongoing challenge. While several studies have investigated assert statement generation in Java, limited work addresses this task in popular dynamically-typed programming languages like Python. In this paper, we introduce Chat-like execution-based Asserts Prediction (\tool), a novel Large Language Model-based approach for generating meaningful assert statements for Python projects. \tool utilizes the persona, Chain-of-Thought, and one-shot learning techniques in the prompt design, and conducts rounds of communication with LLM and Python interpreter to generate meaningful assert statements. We also present a Python assert statement dataset mined from GitHub. Our evaluation demonstrates that \tool achieves 64.7\% accuracy for single assert statement generation and 62\% for overall assert statement generation, outperforming the existing approaches. We also analyze the mismatched assert statements, which may still share the same functionality and discuss the potential help \tool could offer to the automated Python unit test generation. The findings indicate that \tool has the potential to benefit the SE community through more practical usage scenarios.

AI leaders and companies have much to offer to AI/ML practitioners to support them in addressing and mitigating biases in the AI/ML systems they develop. AI/ML practitioners need to receive the necessary resources and support from experts to develop unbiased AI/ML systems. However, our studies have revealed a discrepancy between practitioners' understanding of 'AI/ML bias' and the definitions of tech companies and researchers. This indicates a misalignment that needs addressing. Efforts should be made to match practitioners' understanding of AI/ML bias with the definitions developed by tech companies and researchers. These efforts could yield a significant return on investment by aiding AI/ML practitioners in developing unbiased AI/ML systems., Comment: 6 pages, 1 table, 1 figure

The rise in the use of AI/ML applications across industries has sparked more discussions about the fairness of AI/ML in recent times. While prior research on the fairness of AI/ML exists, there is a lack of empirical studies focused on understanding the perspectives and experiences of AI practitioners in developing a fair AI/ML system. Understanding AI practitioners' perspectives and experiences on the fairness of AI/ML systems are important because they are directly involved in its development and deployment and their insights can offer valuable real-world perspectives on the challenges associated with ensuring fairness in AI/ML systems. We conducted semi-structured interviews with 22 AI practitioners to investigate their understanding of what a 'fair AI/ML' is, the challenges they face in developing a fair AI/ML system, the consequences of developing an unfair AI/ML system, and the strategies they employ to ensure AI/ML system fairness. We developed a framework showcasing the relationship between AI practitioners' understanding of 'fair AI/ML' system and (i) their challenges in its development, (ii) the consequences of developing an unfair AI/ML system, and (iii) strategies used to ensure AI/ML system fairness. By exploring AI practitioners' perspectives and experiences, this study provides actionable insights to enhance AI/ML fairness, which may promote fairer systems, reduce bias, and foster public trust in AI technologies. Additionally, we also identify areas for further investigation and offer recommendations to aid AI practitioners and AI companies in navigating fairness., Comment: 46 pages, 8 figures, 2 tables

Deep Learning (DL) models have rapidly advanced, focusing on achieving high performance through testing model accuracy and robustness. However, it is unclear whether DL projects, as software systems, are tested thoroughly or functionally correct when there is a need to treat and test them like other software systems. Therefore, we empirically study the unit tests in open-source DL projects, analyzing 9,129 projects from GitHub. We find that: 1) unit tested DL projects have positive correlation with the open-source project metrics and have a higher acceptance rate of pull requests, 2) 68% of the sampled DL projects are not unit tested at all, 3) the layer and utilities (utils) of DL models have the most unit tests. Based on these findings and previous research outcomes, we built a mapping taxonomy between unit tests and faults in DL projects. We discuss the implications of our findings for developers and researchers and highlight the need for unit testing in open-source DL projects to ensure their reliability and stability. The study contributes to this community by raising awareness of the importance of unit testing in DL projects and encouraging further research in this area., Comment: ACM Transactions on Software Engineering and Methodology (2023)

Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets across multiple conditions. Researchers then must infer kinases responsible for changes in phosphosites of each substrate. However, tools that infer kinase-substrate interactions (KSIs) are not optimized to interactively explore the resulting large and complex networks, significant phosphosites, and states. There is thus an unmet need for a tool that facilitates user-friendly analysis, interactive exploration, visualization, and communication of phosphoproteomics datasets. We present PhosNetVis, a web-based tool for researchers of all computational skill levels to easily infer, generate and interactively explore KSI networks in 2D or 3D by streamlining phosphoproteomics data analysis steps within a single tool. PhostNetVis lowers barriers for researchers in rapidly generating high-quality visualizations to gain biological insights from their phosphoproteomics datasets. It is available at: https://gumuslab.github.io/PhosNetVis/, Comment: Added new author, added references, changed fig1 and fig4

India has enacted an intricate affirmative action program through a reservation system since the 1950s. Notably, in 2008, a historic judgment by the Supreme Court of India (SCI) in the case of Ashoka Kumar Thakur vs. Union of India mandated a 27 percent reservation to the Other Backward Classes (OBC). The SCI's ruling suggested implementing the OBC reservation as a soft reserve without defining a procedural framework. The SCI recommended a maximum of 10 points difference between the cutoff scores of the open-category and OBC positions. We show that this directive conflicts with India's fundamental Supreme Court mandates on reservation policy. Moreover, we show that the score-elevated reserve policy proposed by S\"onmez and Yenmez (2022) is inconsistent with this directive.

Since 1950, India has instituted an intricate affirmative action program through a meticulously designed reservation system. This system incorporates vertical and horizontal reservations to address historically marginalized groups' socioeconomic imbalances. Vertical reservations designate specific quotas of available positions in publicly funded educational institutions and government employment for Scheduled Castes, Scheduled Tribes, Other Backward Classes, and Economically Weaker Sections. Concurrently, horizontal reservations are employed within each vertical category to allocate positions for additional subgroups, such as women and individuals with disabilities. In educational admissions, the legal framework recommended that unfilled positions reserved for the OBC category revert to unreserved status. Moreover, we document that individuals from vertically reserved categories have more complicated preferences over institution-vertical category position pairs, even though authorities only elicit their preferences over institutions. To address these challenges, the present paper proposes a novel class of choice rules, termed the Generalized Lexicographic (GL) choice rules. This class is comprehensive, subsuming the most salient priority structures discussed in the extant matching literature. Utilizing the GL choice rules and the deferred acceptance mechanism, we present a robust framework that generates equitable and effective solutions for resource allocation problems in the Indian context.