MOTIVATION: Understanding causal effects is a fundamental goal of science and underpins our ability to make accurate predictions in unseen settings and conditions. While direct experimentation is the gold standard for measuring and validating causal effects, the field of causal graph theory offers a tantalizing alternative: extracting causal insights from observational data. Theoretical analysis has shown that this is indeed possible, given a large dataset and if certain conditions are met. However, biological datasets, frequently, do not meet such requirements but evaluation of causal discovery algorithms is typically performed on synthetic datasets, which they meet all requirements. Thus, real-life datasets are needed, in which the causal truth is reasonably known. In this work we first construct such a large-scale real-life dataset and then we perform on it a comprehensive benchmarking of various causal discovery methods. RESULTS: We find that the PC algorithm is particularly accurate at estimating causal structure, including the causal direction which is critical for biological applicability. However, PC does only produces cause-effect directionality, but not estimates of causal effects. We propose PC-NOTEARS (PCnt), a hybrid solution, which includes the PC output as an additional constraint inside the NOTEARS optimization. This approach combines PC algorithm's strengths in graph structure prediction with the NOTEARS continuous optimization to estimate causal effects accurately. PCnt achieved best aggregate performance across all structural and effect size metrics. AVAILABILITY AND IMPLEMENTATION: https://github.com/zhu-yh1/PC-NOTEARS.

In response to the explosively-increasing requirement of annotated data, Novel Class Discovery (NCD) has emerged as a promising alternative to automatically recognize unknown classes without any annotation. To this end, a model makes use of a base set to learn basic semantic discriminability that can be transferred to recognize novel classes. Most existing works handle the base and novel sets using separate objectives within a two-stage training paradigm. Despite showing competitive performance on novel classes, they fail to generalize to recognizing samples from both base and novel sets. In this paper, we focus on this generalized setting of NCD (GNCD), and propose to divide and conquer it with two groups of Compositional Experts (ComEx). Each group of experts is designed to characterize the whole dataset in a comprehensive yet complementary fashion. With their union, we can solve GNCD in an efficient end-to-end manner. We further look into the draw-back in current NCD methods, and propose to strengthen ComEx with global-to-local and local-to-local regularization. ComEx11Code: https://github.com/muliyangm/ComEx. is evaluated on four popular benchmarks, showing clear superiority towards the goal of GNCD.

In real-world recommendation systems, the preferences of users are often affected by long-term constant interests and short-term temporal needs. The recently proposed Transformer-based models have proved superior in the sequential recommendation, modeling temporal dynamics globally via the remarkable self-attention mechanism. However, all equivalent item-item interactions in original self-attention are cumbersome, failing to capture the drifting of users' local preferences, which contain abundant short-term patterns. In this paper, we propose a novel interpretable convolutional self-attention, which efficiently captures both short- and long-term patterns with a progressive attention distribution. Specifically, a down-sampling convolution module is proposed to segment the overall long behavior sequence into a series of local subsequences. Accordingly, the segments are interacted with each item in the self-attention layer to produce locality-aware contextual representations, during which the quadratic complexity in original self-attention is reduced to nearly linear complexity. Moreover, to further enhance the robust feature learning in the context of Transformers, an unsymmetrical positional encoding strategy is carefully designed. Extensive experiments are carried out on real-world datasets, \eg ML-1M, Amazon Books, and Yelp, indicating that the proposed method outperforms the state-of-the-art methods w.r.t. both effectiveness and efficiency.

Deep metric learning plays a key role in various machine learning tasks. Most of the previous works have been confined to sampling from a mini-batch, which cannot precisely characterize the global geometry of the embedding space. Although researchers have developed proxy- and classification-based methods to tackle the sampling issue, those methods inevitably incur a redundant computational cost. In this paper, we propose a novel Proxy-based deep Graph Metric Learning (ProxyGML) approach from the perspective of graph classification, which uses fewer proxies yet achieves better comprehensive performance. Specifically, multiple global proxies are leveraged to collectively approximate the original data points for each class. To efficiently capture local neighbor relationships, a small number of such proxies are adaptively selected to construct similarity subgraphs between these proxies and each data point. Further, we design a novel reverse label propagation algorithm, by which the neighbor relationships are adjusted according to ground-truth labels, so that a discriminative metric space can be learned during the process of subgraph classification. Extensive experiments carried out on widely-used CUB-200-2011, Cars196, and Stanford Online Products datasets demonstrate the superiority of the proposed ProxyGML over the state-of-the-art methods in terms of both effectiveness and efficiency. The source code is publicly available at \url{https://github.com/YuehuaZhu/ProxyGML}.