Identifying mutations of SARS-CoV-2 strains associated with their phenotypic changes is critical for pandemic prediction and prevention. We compared an explainable convolutional neural network (CNN) approach and the traditional genome-wide association study (GWAS) on the mutations associated with WHO labels of SARS-CoV-2, a proxy for virulence phenotypes. We trained a CNN classification model that can predict genomic sequences into Variants of Concern (VOCs) and then applied Shapley Additive explanations (SHAP) model to identify mutations that are important for the correct predictions. For comparison, we performed traditional GWAS to identify mutations associated with VOCs. Comparison of the two approaches shows that the explainable neural network approach can more effectively reveal known nucleotide substitutions associated with VOCs, such as those in the spike gene regions. Our results suggest that explainable neural networks for genomic sequences offer a promising alternative to the traditional genome wide analysis approaches.

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about their true capabilities. In this work, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands CodeAct, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. In addition, we evaluate OpenAI o1 with direct prompting and self-debug, which demonstrates the effectiveness of increasing inference-time compute. Still, our results underscore the limitations of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

The ability to plan a course of action that achieves a desired state of affairs has long been considered a core competence of intelligent agents and has been an integral part of AI research since its inception. With the advent of large language models (LLMs), there has been considerable interest in the question of whether or not they possess such planning abilities, but -- despite the slew of new private and open source LLMs since GPT3 -- progress has remained slow. OpenAI claims that their recent o1 (Strawberry) model has been specifically constructed and trained to escape the normal limitations of autoregressive LLMs -- making it a new kind of model: a Large Reasoning Model (LRM). In this paper, we evaluate the planning capabilities of two LRMs (o1-preview and o1-mini) on both planning and scheduling benchmarks. We see that while o1 does seem to offer significant improvements over autoregressive LLMs, this comes at a steep inference cost, while still failing to provide any guarantees over what it generates. We also show that combining o1 models with external verifiers -- in a so-called LRM-Modulo system -- guarantees the correctness of the combined system's output while further improving performance.

Large Language Model (LLM)-based recommendation systems provide more comprehensive recommendations than traditional systems by deeply analyzing content and user behavior. However, these systems often exhibit biases, favoring mainstream content while marginalizing non-traditional options due to skewed training data. This study investigates the intricate relationship between bias and LLM-based recommendation systems, with a focus on music, song, and book recommendations across diverse demographic and cultural groups. Through a comprehensive analysis conducted over different LLM-models, this paper evaluates the impact of bias on recommendation outcomes. Our findings reveal that bias is so deeply ingrained within these systems that even a simpler intervention like prompt engineering can significantly reduce bias, underscoring the pervasive nature of the issue. Moreover, factors like intersecting identities and contextual information, such as socioeconomic status, further amplify these biases, demonstrating the complexity and depth of the challenges faced in creating fair recommendations across different groups.

Traffic accidents pose a severe global public health issue, leading to 1.19 million fatalities annually, with the greatest impact on individuals aged 5 to 29 years old. This paper addresses the critical need for advanced predictive methods in road safety by conducting a comprehensive review of recent advancements in applying machine learning (ML) techniques to traffic accident analysis and prediction. It examines 191 studies from the last five years, focusing on predicting accident risk, frequency, severity, duration, as well as general statistical analysis of accident data. To our knowledge, this study is the first to provide such a comprehensive review, covering the state-of-the-art across a wide range of domains related to accident analysis and prediction. The review highlights the effectiveness of integrating diverse data sources and advanced ML techniques to improve prediction accuracy and handle the complexities of traffic data. By mapping the current landscape and identifying gaps in the literature, this study aims to guide future research towards significantly reducing traffic-related deaths and injuries by 2030, aligning with the World Health Organization (WHO) targets.

Traffic flow forecasting is a crucial first step in intelligent and proactive traffic management. Traffic flow parameters are volatile and uncertain, making traffic flow forecasting a difficult task if the appropriate forecasting model is not used. Additionally, the non-Euclidean data structure of traffic flow parameters is challenging to analyze from both spatial and temporal perspectives. State-of-the-art deep learning approaches use pure convolution, recurrent neural networks, and hybrid methods to achieve this objective efficiently. However, many of the approaches in the literature rely on complex architectures that can be difficult to train. This complexity also adds to the black-box nature of deep learning. This study introduces a novel deep learning architecture, referred to as the multigraph convolution neural network (MGCNN), for turning movement prediction at intersections. The proposed architecture combines a multigraph structure, built to model temporal variations in traffic data, with a spectral convolution operation to support modeling the spatial variations in traffic data over the graphs. The proposed model was tested using twenty days of flow and traffic control data collected from an arterial in downtown Chattanooga, TN, with ten signalized intersections. The model's ability to perform short-term predictions over 1, 2, 3, 4, and 5 minutes into the future was evaluated against four baseline state-of-the-art models. The results showed that our proposed model is superior to the other baseline models in predicting turning movements with a mean squared error (MSE) of 0.9

In this paper a multi-domain multi-task algorithm for feature selection in bulk RNAseq data is proposed. Two datasets are investigated arising from mouse host immune response to Salmonella infection. Data is collected from several strains of collaborative cross mice. Samples from the spleen and liver serve as the two domains. Several machine learning experiments are conducted and the small subset of discriminative across domains features have been extracted in each case. The algorithm proves viable and underlines the benefits of across domain feature selection by extracting new subset of discriminative features which couldn't be extracted only by one-domain approach.

This paper presents a work-in-progress on a learn-ing system that will provide robotics students with a personalized learning environment. This addresses both the scarcity of skilled robotics instructors, particularly in community colleges and the expensive demand for training equipment. The study of robotics at the college level represents a wide range of interests, experiences, and aims. This project works to provide students the flexibility to adapt their learning to their own goals and prior experience. We are developing a system to enable robotics instruction through a web-based interface that is compatible with less expensive hardware. Therefore, the free distribution of teaching materials will empower educators. This project has the potential to increase the number of robotics courses offered at both two- and four-year schools and universities. The course materials are being designed with small units and a hierarchical dependency tree in mind; students will be able to customize their course of study based on the robotics skills they have already mastered. We present an evaluation of a five module mini-course in robotics. Students indicated that they had a positive experience with the online content. They also scored the experience highly on relatedness, mastery, and autonomy perspectives, demonstrating strong motivation potential for this approach.

As power quality becomes a higher priority in the electric utility industry, the amount of disturbance event data continues to grow. Utilities do not have the required personnel to analyze each event by hand. This work presents an automated approach for analyzing power quality events recorded by digital fault recorders and power quality monitors operating within a power transmission system. The automated approach leverages rule-based analytics to examine the time and frequency domain characteristics of the voltage and current signals. Customizable thresholds are set to categorize each disturbance event. The events analyzed within this work include various faults, motor starting, and incipient instrument transformer failure. Analytics for fourteen different event types have been developed. The analytics were tested on 160 signal files and yielded an accuracy of ninety-nine percent. Continuous, nominal signal data analysis is performed using an approach coined as the cyclic histogram. The cyclic histogram process will be integrated into the digital fault recorders themselves to facilitate the detection of subtle signal variations that are too small to trigger a disturbance event and that can occur over hours or days. In addition to reducing memory requirements by a factor of 320, it is anticipated that cyclic histogram processing will aid in identifying incipient events and identifiers. This project is expected to save engineers time by automating the classification of disturbance events and increase the reliability of the transmission system by providing near real time detection and identification of disturbances as well as prevention of problems before they occur.

Smart cities operate on computational predictive frameworks that collect, aggregate, and utilize data from large-scale sensor networks. However, these frameworks are prone to multiple sources of data and algorithmic bias, which often lead to unfair prediction results. In this work, we first demonstrate that bias persists at a micro-level both temporally and spatially by studying real city data from Chattanooga, TN. To alleviate the issue of such bias, we introduce Fairguard, a micro-level temporal logic-based approach for fair smart city policy adjustment and generation in complex temporal-spatial domains. The Fairguard framework consists of two phases: first, we develop a static generator that is able to reduce data bias based on temporal logic conditions by minimizing correlations between selected attributes. Then, to ensure fairness in predictive algorithms, we design a dynamic component to regulate prediction results and generate future fair predictions by harnessing logic rules. Evaluations show that logic-enabled static Fairguard can effectively reduce the biased correlations while dynamic Fairguard can guarantee fairness on protected groups at run-time with minimal impact on overall performance.