Causal Inference in Microbiomes Using Intervention Calculus

Inferring causal effects is critically important in biomedical research as it allows us to move from the typical paradigm of associational studies to causal inference, and can impact treatments and therapeutics. Association patterns can be coincidental and may lead to wrong inferences in complex systems. Microbiomes are highly complex, diverse, and dynamic environments. Microbes are key players in health and diseases. Hence knowledge of genuine causal relationships among the entities in a microbiome, and the impact of internal and external factors on microbial abundance and interactions are essential for understanding disease mechanisms and making treatment recommendations. In this paper, we investigate fundamental causal inference techniques to measure the causal effects of various entities in a microbiome. In particular, we show how to use these techniques on microbiome datasets to study the rise and impact of antibiotic-resistance in microbiomes. Our main contributions include the following. We introduce a novel pipeline for microbiome studies, new ideas for experimental design under weaker assumptions, and data augmentation by context embedding. Our pipeline is robust, different from traditional approaches, and able to predict interventional effects without any controlled experiments. Our work shows the advantages of causal inference in identifying potential pathogenic, beneficial, and antibiotic-resistant bacteria. We validate our results using results that were previously published

Unbiased Recommender Learning from Missing-Not-At-Random Implicit Feedback

Recommender systems widely use implicit feedback such as click data because of its general availability. Although the presence of clicks signals the users' preference to some extent, the lack of such clicks does not necessarily indicate a negative response from the users, as it is possible that the users were not exposed to the items (positive-unlabeled problem). This leads to a difficulty in predicting the users' preferences from implicit feedback. Previous studies addressed the positive-unlabeled problem by uniformly upweighting the loss for the positive feedback data or estimating the confidence of each data having relevance information via the EM-algorithm. However, these methods failed to address the missing-not-at-random problem in which popular or frequently recommended items are more likely to be clicked than other items even if a user does not have a considerable interest in them. To overcome these limitations, we first define an ideal loss function to be optimized to realize recommendations that maximize the relevance and propose an unbiased estimator for the ideal loss. Subsequently, we analyze the variance of the proposed unbiased estimator and further propose a clipped estimator that includes the unbiased estimator as a special case. We demonstrate that the clipped estimator is expected to improve the performance of the recommender system, by considering the bias-variance trade-off. We conduct semi-synthetic and real-world experiments and demonstrate that the proposed method largely outperforms the baselines. In particular, the proposed method works better for rare items that are less frequently observed in the training data. The findings indicate that the proposed method can better achieve the objective of recommending items with the highest relevance.Comment: accepted at WSDM'2

Debiasing Recommendation with Personal Popularity

Global popularity (GP) bias is the phenomenon that popular items are recommended much more frequently than they should be, which goes against the goal of providing personalized recommendations and harms user experience and recommendation accuracy. Many methods have been proposed to reduce GP bias but they fail to notice the fundamental problem of GP, i.e., it considers popularity from a \textit{global} perspective of \textit{all users} and uses a single set of popular items, and thus cannot capture the interests of individual users. As such, we propose a user-aware version of item popularity named \textit{personal popularity} (PP), which identifies different popular items for each user by considering the users that share similar interests. As PP models the preferences of individual users, it naturally helps to produce personalized recommendations and mitigate GP bias. To integrate PP into recommendation, we design a general \textit{personal popularity aware counterfactual} (PPAC) framework, which adapts easily to existing recommendation models. In particular, PPAC recognizes that PP and GP have both direct and indirect effects on recommendations and controls direct effects with counterfactual inference techniques for unbiased recommendations. All codes and datasets are available at \url{https://github.com/Stevenn9981/PPAC}.Comment: Accepted by WWW'24 as a research full pape

Mitigating Popularity Bias in Recommendation with Unbalanced Interactions: A Gradient Perspective

Recommender systems learn from historical user-item interactions to identify preferred items for target users. These observed interactions are usually unbalanced following a long-tailed distribution. Such long-tailed data lead to popularity bias to recommend popular but not personalized items to users. We present a gradient perspective to understand two negative impacts of popularity bias in recommendation model optimization: (i) the gradient direction of popular item embeddings is closer to that of positive interactions, and (ii) the magnitude of positive gradient for popular items are much greater than that of unpopular items. To address these issues, we propose a simple yet efficient framework to mitigate popularity bias from a gradient perspective. Specifically, we first normalize each user embedding and record accumulated gradients of users and items via popularity bias measures in model training. To address the popularity bias issues, we develop a gradient-based embedding adjustment approach used in model testing. This strategy is generic, model-agnostic, and can be seamlessly integrated into most existing recommender systems. Our extensive experiments on two classic recommendation models and four real-world datasets demonstrate the effectiveness of our method over state-of-the-art debiasing baselines.Comment: Recommendation System, Popularity Bia