The SARS-CoV-2 coronavirus is the cause of the COVID-19 disease in humans. Like many coronaviruses, it can adapt to different hosts and evolve into different lineages. It is well-known that the major SARS-CoV-2 lineages are characterized by mutations that happen predominantly in the spike protein. Understanding the spike protein structure and how it can be perturbed is vital for understanding and determining if a lineage is of concern. These are crucial to identifying and controlling current outbreaks and preventing future pandemics. Machine learning (ML) methods are a viable solution to this effort, given the volume of available sequencing data, much of which is unaligned or even unassembled. However, such ML methods require fixed-length numerical feature vectors in Euclidean space to be applicable. Similarly, euclidean space is not considered the best choice when working with the classification and clustering tasks for biological sequences. For this purpose, we design a method that converts the protein (spike) sequences into the sequence similarity network (SSN). We can then use SSN as an input for the classical algorithms from the graph mining domain for the typical tasks such as classification and clustering to understand the data. We show that the proposed alignment-free method is able to outperform the current SOTA method in terms of clustering results. Similarly, we are able to achieve higher classification accuracy using well-known Node2Vec-based embedding compared to other baseline embedding approaches.

Contact matrices are an important ingredient in age-structured epidemic models to inform the simulated spread of the disease between sub-groups of the population. These matrices are generally derived using resource-intensive diary-based surveys and few exist in the Global South or tailored to vulnerable populations. In particular, no contact matrices exist for refugee settlements - locations under-served by epidemic models in general. In this paper we present a novel, mixed-method approach, for deriving contact matrices in populations which combines a lightweight, rapidly deployable, survey with an agent-based model of the population informed by census and behavioural data. We use this method to derive the first set of contact matrices for the Cox's Bazar refugee settlement in Bangladesh. The matrices from the refugee settlement show strong banding effects due to different age cut-offs in attendance at certain venues, such as distribution centres and religious sites, as well as the important contribution of the demographic profile of the settlement which was encoded in the model. These can have significant implications to the modelled disease dynamics. To validate our approach, we also apply our method to the population of the UK and compare our derived matrices against well-known contact matrices previously collected using traditional approaches. Overall, our findings demonstrate that our mixed-method approach can address some of the challenges of both the traditional and previously proposed agent-based approaches to deriving contact matrices, and has the potential to be rolled-out in other resource-constrained environments. This work therefore contributes to a broader aim of developing new methods and mechanisms of data collection for modelling disease spread in refugee and IDP settlements and better serving these vulnerable communities.

Numerical reasoning over hybrid data containing tables and long texts has recently received research attention from the AI community. To generate an executable reasoning program consisting of math and table operations to answer a question, state-of-the-art methods use a retriever-generator pipeline. However, their retrieval results are static, while different generation steps may rely on different sentences. To attend to the retrieved information that is relevant to each generation step, in this paper, we propose DyRRen, an extended retriever-reranker-generator framework where each generation step is enhanced by a dynamic reranking of retrieved sentences. It outperforms existing baselines on the FinQA dataset.

Participatory Artificial Intelligence (PAI) has recently gained interest by researchers as means to inform the design of technology through collective's lived experience. PAI has a greater promise than that of providing useful input to developers, it can contribute to the process of democratizing the design of technology, setting the focus on what should be designed. However, in the process of PAI there existing institutional power dynamics that hinder the realization of expansive dreams and aspirations of the relevant stakeholders. In this work we propose co-design principals for AI that address institutional power dynamics focusing on Participatory AI with youth.

How do author perceptions match up to the outcomes of the peer-review process and perceptions of others? In a top-tier computer science conference (NeurIPS 2021) with more than 23,000 submitting authors and 9,000 submitted papers, we survey the authors on three questions: (i) their predicted probability of acceptance for each of their papers, (ii) their perceived ranking of their own papers based on scientific contribution, and (iii) the change in their perception about their own papers after seeing the reviews. The salient results are: (1) Authors have roughly a three-fold overestimate of the acceptance probability of their papers: The median prediction is 70% for an approximately 25% acceptance rate. (2) Female authors exhibit a marginally higher (statistically significant) miscalibration than male authors; predictions of authors invited to serve as meta-reviewers or reviewers are similarly calibrated, but better than authors who were not invited to review. (3) Authors' relative ranking of scientific contribution of two submissions they made generally agree (93%) with their predicted acceptance probabilities, but there is a notable 7% responses where authors think their better paper will face a worse outcome. (4) The author-provided rankings disagreed with the peer-review decisions about a third of the time; when co-authors ranked their jointly authored papers, co-authors disagreed at a similar rate -- about a third of the time. (5) At least 30% of respondents of both accepted and rejected papers said that their perception of their own paper improved after the review process. The stakeholders in peer review should take these findings into account in setting their expectations from peer review.

Probabilistic circuits (PCs) are a tractable representation of probability distributions allowing for exact and efficient computation of likelihoods and marginals. There has been significant recent progress on improving the scale and expressiveness of PCs. However, PC training performance plateaus as model size increases. We discover that most capacity in existing large PC structures is wasted: fully-connected parameter layers are only sparsely used. We propose two operations: pruning and growing, that exploit the sparsity of PC structures. Specifically, the pruning operation removes unimportant sub-networks of the PC for model compression and comes with theoretical guarantees. The growing operation increases model capacity by increasing the size of the latent space. By alternatingly applying pruning and growing, we increase the capacity that is meaningfully used, allowing us to significantly scale up PC learning. Empirically, our learner achieves state-of-the-art likelihoods on MNIST-family image datasets and on Penn Tree Bank language data compared to other PC learners and less tractable deep generative models such as flow-based models and variational autoencoders (VAEs).

Scoring systems, as a type of predictive model, have significant advantages in interpretability and transparency and facilitate quick decision-making. As such, scoring systems have been extensively used in a wide variety of industries such as healthcare and criminal justice. However, the fairness issues in these models have long been criticized, and the use of big data and machine learning algorithms in the construction of scoring systems heightens this concern. In this paper, we propose a general framework to create fairness-aware, data-driven scoring systems. First, we develop a social welfare function that incorporates both efficiency and group fairness. Then, we transform the social welfare maximization problem into the risk minimization task in machine learning, and derive a fairness-aware scoring system with the help of mixed integer programming. Lastly, several theoretical bounds are derived for providing parameter selection suggestions. Our proposed framework provides a suitable solution to address group fairness concerns in the development of scoring systems. It enables policymakers to set and customize their desired fairness requirements as well as other application-specific constraints. We test the proposed algorithm with several empirical data sets. Experimental evidence supports the effectiveness of the proposed scoring system in achieving the optimal welfare of stakeholders and in balancing the needs for interpretability, fairness, and efficiency.

To mitigate the negative effects of false information more effectively, the development of automated AI (artificial intelligence) tools assisting fact-checkers is needed. Despite the existing research, there is still a gap between the fact-checking practitioners' needs and pains and the current AI research. We aspire to bridge this gap by employing methods of information behavior research to identify implications for designing better human-centered AI-based supporting tools. In this study, we conducted semi-structured in-depth interviews with Central European fact-checkers. The information behavior and requirements on desired supporting tools were analyzed using iterative bottom-up content analysis, bringing the techniques from grounded theory. The most significant needs were validated with a survey extended to fact-checkers from across Europe, in which we collected 24 responses from 20 European countries, i.e., 62% active European IFCN (International Fact-Checking Network) signatories. Our contributions are theoretical as well as practical. First, by being able to map our findings about the needs of fact-checking organizations to the relevant tasks for AI research, we have shown that the methods of information behavior research are relevant for studying the processes in the organizations and that these methods can be used to bridge the gap between the users and AI researchers. Second, we have identified fact-checkers' needs and pains focusing on so far unexplored dimensions and emphasizing the needs of fact-checkers from Central and Eastern Europe as well as from low-resource language groups which have implications for development of new resources (datasets) as well as for the focus of AI research in this domain.

Detecting opportunities and threats from massive text data is a challenging task for most. Traditionally, companies would rely mainly on structured data to detect and predict risks, losing a huge amount of information that could be extracted from unstructured text data. Fortunately, artificial intelligence came to remedy this issue by innovating in data extraction and processing techniques, allowing us to understand and make use of Natural Language data and turning it into structures that a machine can process and extract insight from. Uncertainty refers to a state of not knowing what will happen in the future. This paper aims to leverage natural language processing and machine learning techniques to model uncertainties and evaluate the risk level in each uncertainty cluster using massive text data.

Established cross-document coreference resolution (CDCR) datasets contain event-centric coreference chains of events and entities with identity relations. These datasets establish strict definitions of the coreference relations across related tests but typically ignore anaphora with more vague context-dependent loose coreference relations. In this paper, we qualitatively and quantitatively compare the annotation schemes of ECB+, a CDCR dataset with identity coreference relations, and NewsWCL50, a CDCR dataset with a mix of loose context-dependent and strict coreference relations. We propose a phrasing diversity metric (PD) that encounters for the diversity of full phrases unlike the previously proposed metrics and allows to evaluate lexical diversity of the CDCR datasets in a higher precision. The analysis shows that coreference chains of NewsWCL50 are more lexically diverse than those of ECB+ but annotating of NewsWCL50 leads to the lower inter-coder reliability. We discuss the different tasks that both CDCR datasets create for the CDCR models, i.e., lexical disambiguation and lexical diversity. Finally, to ensure generalizability of the CDCR models, we propose a direction for CDCR evaluation that combines CDCR datasets with multiple annotation schemes that focus of various properties of the coreference chains.