An Explainable Artificial Intelligence Software Tool for Weight Management Experts (PRIMO): Mixed Methods Study.

BACKGROUND: Predicting the likelihood of success of weight loss interventions using machine learning (ML) models may enhance intervention effectiveness by enabling timely and dynamic modification of intervention components for nonresponders to treatment. However, a lack of understanding and trust in these ML models impacts adoption among weight management experts. Recent advances in the field of explainable artificial intelligence enable the interpretation of ML models, yet it is unknown whether they enhance model understanding, trust, and adoption among weight management experts. OBJECTIVE: This study aimed to build and evaluate an ML model that can predict 6-month weight loss success (ie, ≥7% weight loss) from 5 engagement and diet-related features collected over the initial 2 weeks of an intervention, to assess whether providing ML-based explanations increases weight management experts' agreement with ML model predictions, and to inform factors that influence the understanding and trust of ML models to advance explainability in early prediction of weight loss among weight management experts. METHODS: We trained an ML model using the random forest (RF) algorithm and data from a 6-month weight loss intervention (N=419). We leveraged findings from existing explainability metrics to develop Prime Implicant Maintenance of Outcome (PRIMO), an interactive tool to understand predictions made by the RF model. We asked 14 weight management experts to predict hypothetical participants' weight loss success before and after using PRIMO. We compared PRIMO with 2 other explainability methods, one based on feature ranking and the other based on conditional probability. We used generalized linear mixed-effects models to evaluate participants' agreement with ML predictions and conducted likelihood ratio tests to examine the relationship between explainability methods and outcomes for nested models. We conducted guided interviews and thematic analysis to study the impact of our tool on experts' understanding and trust in the model. RESULTS: Our RF model had 81% accuracy in the early prediction of weight loss success. Weight management experts were significantly more likely to agree with the model when using PRIMO (χ2=7.9; P=.02) compared with the other 2 methods with odds ratios of 2.52 (95% CI 0.91-7.69) and 3.95 (95% CI 1.50-11.76). From our study, we inferred that our software not only influenced experts' understanding and trust but also impacted decision-making. Several themes were identified through interviews: preference for multiple explanation types, need to visualize uncertainty in explanations provided by PRIMO, and need for model performance metrics on similar participant test instances. CONCLUSIONS: Our results show the potential for weight management experts to agree with the ML-based early prediction of success in weight loss treatment programs, enabling timely and dynamic modification of intervention components to enhance intervention effectiveness. Our findings provide methods for advancing the understandability and trust of ML models among weight management experts.

Optimal algorithms for haplotype assembly from whole-genome sequence data.

MOTIVATION: Haplotype inference is an important step for many types of analyses of genetic variation in the human genome. Traditional approaches for obtaining haplotypes involve collecting genotype information from a population of individuals and then applying a haplotype inference algorithm. The development of high-throughput sequencing technologies allows for an alternative strategy to obtain haplotypes by combining sequence fragments. The problem of 'haplotype assembly' is the problem of assembling the two haplotypes for a chromosome given the collection of such fragments, or reads, and their locations in the haplotypes, which are pre-determined by mapping the reads to a reference genome. Errors in reads significantly increase the difficulty of the problem and it has been shown that the problem is NP-hard even for reads of length 2. Existing greedy and stochastic algorithms are not guaranteed to find the optimal solutions for the haplotype assembly problem. RESULTS: In this article, we proposed a dynamic programming algorithm that is able to assemble the haplotypes optimally with time complexity O(m x 2(k) x n), where m is the number of reads, k is the length of the longest read and n is the total number of SNPs in the haplotypes. We also reduce the haplotype assembly problem into the maximum satisfiability problem that can often be solved optimally even when k is large. Taking advantage of the efficiency of our algorithm, we perform simulation experiments demonstrating that the assembly of haplotypes using reads of length typical of the current sequencing technologies is not practical. However, we demonstrate that the combination of this approach and the traditional haplotype phasing approaches allow us to practically construct haplotypes containing both common and rare variants.