The paper addresses the problem of finding the causal direction between two associated variables. The proposed solution is to build an autoencoder of their joint distribution and to maximize its estimation capacity relative to both the marginal distributions. It is shown that the resulting two capacities cannot, in general, be equal. This leads to a new criterion for causal discovery: the higher capacity is consistent with the unconstrained choice of a distribution representing the cause while the lower capacity reflects the constraints imposed by the mechanism on the distribution of the effect. Estimation capacity is defined as the ability of the auto-encoder to represent arbitrary datasets. A regularization term forces it to decide which one of the variables to model in a more generic way i.e., while maintaining higher model capacity. The causal direction is revealed by the constraints encountered while encoding the data instead of being measured as a property of the data itself. The idea is implemented and tested using a restricted Boltzmann machine.

Whether based on models, training data or a combination, classifiers place (possibly complex) input data into one of a relatively small number of output categories. In this paper, we study the structure of the boundary--those points for which a neighbor is classified differently--in the context of an input space that is a graph, so that there is a concept of neighboring inputs, The scientific setting is a model-based naive Bayes classifier for DNA reads produced by Next Generation Sequencers. We show that the boundary is both large and complicated in structure. We create a new measure of uncertainty, called Neighbor Similarity, that compares the result for a point to the distribution of results for its neighbors. This measure not only tracks two inherent uncertainty measures for the Bayes classifier, but also can be implemented, at a computational cost, for classifiers without inherent measures of uncertainty.

Bias elimination and recent probing studies attempt to remove specific information from embedding spaces. Here it is important to remove as much of the target information as possible, while preserving any other information present. INLP is a popular recent method which removes specific information through iterative nullspace projections. Multiple iterations, however, increase the risk that information other than the target is negatively affected. We introduce two methods that find a single targeted projection: Mean Projection (MP, more efficient) and Tukey Median Projection (TMP, with theoretical guarantees). Our comparison between MP and INLP shows that (1) one MP projection removes linear separability based on the target and (2) MP has less impact on the overall space. Further analysis shows that applying random projections after MP leads to the same overall effects on the embedding space as the multiple projections of INLP. Applying one targeted (MP) projection hence is methodologically cleaner than applying multiple (INLP) projections that introduce random effects.

There is considerable interest in predicting the pathogenicity of protein variants in human genes. Due to the sparsity of high quality labels, recent approaches turn to \textit{unsupervised} learning, using Multiple Sequence Alignments (MSAs) to train generative models of natural sequence variation within each gene. These generative models then predict variant likelihood as a proxy to evolutionary fitness. In this work we instead combine this evolutionary principle with pretrained protein language models (LMs), which have already shown promising results in predicting protein structure and function. Instead of training separate models per-gene, we find that a single protein LM trained on broad sequence datasets can score pathogenicity for any gene variant zero-shot, without MSAs or finetuning. We call this unsupervised approach \textbf{VELM} (Variant Effect via Language Models), and show that it achieves scoring performance comparable to the state of the art when evaluated on clinically labeled variants of disease-related genes.

As more and more artificial intelligence (AI) technologies move from the laboratory to real-world applications, the open-set and robustness challenges brought by data from the real world have received increasing attention. Data augmentation is a widely used method to improve model performance, and some recent works have also confirmed its positive effect on the robustness of AI models. However, most of the existing data augmentation methods are heuristic, lacking the exploration of their internal mechanisms. We apply the explainable artificial intelligence (XAI) method, explore the internal mechanisms of popular data augmentation methods, analyze the relationship between game interactions and some widely used robustness metrics, and propose a new proxy for model robustness in the open-set environment. Based on the analysis of the internal mechanisms, we develop a mask-based boosting method for data augmentation that comprehensively improves several robustness measures of AI models and beats state-of-the-art data augmentation approaches. Experiments show that our method can be widely applied to many popular data augmentation methods. Different from the adversarial training, our boosting method not only significantly improves the robustness of models, but also improves the accuracy of test sets. Our code is available at \url{https://github.com/Anonymous_for_submission}.

Software-related platforms have enabled their users to collaboratively label software entities with topics. Tagging software repositories with relevant topics can be exploited for facilitating various downstream tasks. For instance, a correct and complete set of topics assigned to a repository can increase its visibility. Consequently, this improves the outcome of tasks such as browsing, searching, navigation, and organization of repositories. Unfortunately, assigned topics are usually highly noisy, and some repositories do not have well-assigned topics. Thus, there have been efforts on recommending topics for software projects, however, the semantic relationships among these topics have not been exploited so far. We propose two recommender models for tagging software projects that incorporate the semantic relationship among topics. Our approach has two main phases; (1) we first take a collaborative approach to curate a dataset of quality topics specifically for the domain of software engineering and development. We also enrich this data with the semantic relationships among these topics and encapsulate them in a knowledge graph we call SED-KGraph. Then, (2) we build two recommender systems; The first one operates only based on the list of original topics assigned to a repository and the relationships specified in our knowledge graph. The second predictive model, however, assumes there are no topics available for a repository, hence it proceeds to predict the relevant topics based on both textual information of a software project and SED-KGraph. We built SED-KGraph in a crowd-sourced project with 170 contributors from both academia and industry. The experiment results indicate that our solutions outperform baselines that neglect the semantic relationships among topics by at least 25% and 23% in terms of ASR and MAP metrics.

Few-shot learning is a rapidly evolving area of research in machine learning where the goal is to classify unlabeled data with only one or "a few" labeled exemplary samples. Neural networks are typically trained to minimize a distance metric between labeled exemplary samples and a query set. Early few-shot approaches use an episodic training process to sub-sample the training data into few-shot batches. This training process matches the sub-sampling done on evaluation. Recently, conventional supervised training coupled with a cosine distance has achieved superior performance for few-shot. Despite the diversity of few-shot approaches over the past decade, most methods still rely on the cosine or Euclidean distance layer between the latent features of the trained network. In this work, we investigate the distributions of trained few-shot features and demonstrate that they can be roughly approximated as exponential distributions. Under this assumption of an exponential distribution, we propose a new maximum log-likelihood metric for few-shot architectures. We demonstrate that the proposed metric achieves superior performance accuracy w.r.t. conventional similarity metrics (e.g., cosine, Euclidean, etc.), and achieve state-of-the-art inductive few-shot performance. Further, additional gains can be achieved by carefully combining multiple metrics and neither of our methods require post-processing feature transformations, which are common to many algorithms. Finally, we demonstrate a novel iterative algorithm designed around our maximum log-likelihood approach that achieves state-of-the-art transductive few-shot performance when the evaluation data is imbalanced. We have made our code publicly available at https://github.com/samuelhess/MLL_FSL/.

Federated learning (FL) has gained significant attention recently as a privacy-enhancing tool to jointly train a machine learning model by multiple participants. The prior work on FL has mostly studied how to protect label privacy during model training. However, model evaluation in FL might also lead to potential leakage of private label information. In this work, we propose an evaluation algorithm that can accurately compute the widely used AUC (area under the curve) metric when using the label differential privacy (DP) in FL. Through extensive experiments, we show our algorithms can compute accurate AUCs compared to the ground truth. The code is available at {\url{https://github.com/bytedance/fedlearner/tree/master/example/privacy/DPAUC}}.

Metric Elicitation (ME) is a framework for eliciting classification metrics that better align with implicit user preferences based on the task and context. The existing ME strategy so far is based on the assumption that users can most easily provide preference feedback over classifier statistics such as confusion matrices. This work examines ME, by providing a first ever implementation of the ME strategy. Specifically, we create a web-based ME interface and conduct a user study that elicits users' preferred metrics in a binary classification setting. We discuss the study findings and present guidelines for future research in this direction.

Out-of-distribution (OOD) detection is a critical task for deploying machine learning models in the open world. Distance-based methods have demonstrated promise, where testing samples are detected as OOD if they are relatively far away from in-distribution (ID) data. However, prior methods impose a strong distributional assumption of the underlying feature space, which may not always hold. In this paper, we explore the efficacy of non-parametric nearest-neighbor distance for OOD detection, which has been largely overlooked in the literature. Unlike prior works, our method does not impose any distributional assumption, hence providing stronger flexibility and generality. We demonstrate the effectiveness of nearest-neighbor-based OOD detection on several benchmarks and establish superior performance. Under the same model trained on ImageNet-1k, our method substantially reduces the false positive rate (FPR@TPR95) by 24.77% compared to a strong baseline SSD+, which uses a parametric approach Mahalanobis distance in detection. Code is available: https://github.com/deeplearning-wisc/knn-ood.