Mingyang Zhou

Mingyang Zhou, Zichao Yan, Elliot Layne et al. · mila

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Ming-Yang Zhou, Zhao Zhuo, Hao Liao et al.

Controlling complex networks is of paramount importance in science and engineering. Despite recent efforts to improve controllability and synchronous strength, little attention has been paid to the speed of pinning synchronizability (rate of convergence in pinning control) and the corresponding pinning node selection. To address this issue, we propose a hypothesis to restrict the control cost, then build a linear matrix inequality related to the speed of pinning controllability. By solving the inequality, we obtain both the speed of pinning controllability and optimal control strength (feedback gains in pinning control) for all nodes. Interestingly, some low-degree nodes are able to achieve large feedback gains, which suggests that they have high influence on controlling system. In addition, when choosing nodes with high feedback gains as pinning nodes, the controlling speed of real systems is remarkably enhanced compared to that of traditional large-degree and large-betweenness selections. Thus, the proposed approach provides a novel way to investigate the speed of pinning controllability and can evoke other effective heuristic pinning node selections for large-scale systems.

Mingyang Zhou, Luowei Zhou, Shuohang Wang et al.

Vision-and-language pre-training has achieved impressive success in learning multimodal representations between vision and language. To generalize this success to non-English languages, we introduce UC2, the first machine translation-augmented framework for cross-lingual cross-modal representation learning. To tackle the scarcity problem of multilingual captions for image datasets, we first augment existing English-only datasets with other languages via machine translation (MT). Then we extend the standard Masked Language Modeling and Image-Text Matching training objectives to multilingual setting, where alignment between different languages is captured through shared visual context (i.e, using image as pivot). To facilitate the learning of a joint embedding space of images and all languages of interest, we further propose two novel pre-training tasks, namely Masked Region-to-Token Modeling (MRTM) and Visual Translation Language Modeling (VTLM), leveraging MT-enhanced translated data. Evaluation on multilingual image-text retrieval and multilingual visual question answering benchmarks demonstrates that our proposed framework achieves new state-of-the-art on diverse non-English benchmarks while maintaining comparable performance to monolingual pre-trained models on English tasks.

Kaihui Liang, Austin Chau, Yu Li et al.

Gunrock 2.0 is built on top of Gunrock with an emphasis on user adaptation. Gunrock 2.0 combines various neural natural language understanding modules, including named entity detection, linking, and dialog act prediction, to improve user understanding. Its dialog management is a hierarchical model that handles various topics, such as movies, music, and sports. The system-level dialog manager can handle question detection, acknowledgment, error handling, and additional functions, making downstream modules much easier to design and implement. The dialog manager also adapts its topic selection to accommodate different users' profile information, such as inferred gender and personality. The generation model is a mix of templates and neural generation models. Gunrock 2.0 is able to achieve an average rating of 3.73 at its latest build from May 29th to June 4th.

Hao Liao, Jiao Wu, Mingyang Zhou et al.

The goal of the ranking problem in networks is to rank nodes from best to worst, according to a chosen criterion. In this work, we focus on ranking the nodes according to their quality. The problem of ranking the nodes in bipartite networks is valuable for many real-world applications. For instance, high-quality products can be promoted on an online shop or highly reputed restaurants attract more people on venues review platforms. However, many classical ranking algorithms share a common drawback: they tend to rank older movies higher than newer movies, though some newer movies may have a high quality. This time bias originates from the fact that older nodes in a network tend to have more connections than newer ones. In the study, we develop a ranking method using a rebalance approach to diminish the time bias of the rankings in bipartite graphs.

Dian Yu, Michelle Cohn, Yi Mang Yang et al.

Gunrock is the winner of the 2018 Amazon Alexa Prize, as evaluated by coherence and engagement from both real users and Amazon-selected expert conversationalists. We focus on understanding complex sentences and having in-depth conversations in open domains. In this paper, we introduce some innovative system designs and related validation analysis. Overall, we found that users produce longer sentences to Gunrock, which are directly related to users' engagement (e.g., ratings, number of turns). Additionally, users' backstory queries about Gunrock are positively correlated to user satisfaction. Finally, we found dialog flows that interleave facts and personal opinions and stories lead to better user satisfaction.

Mingyang Zhou, Runxiang Cheng, Yong Jae Lee et al.

We introduce a novel multimodal machine translation model that utilizes parallel visual and textual information. Our model jointly optimizes the learning of a shared visual-language embedding and a translator. The model leverages a visual attention grounding mechanism that links the visual semantics with the corresponding textual semantics. Our approach achieves competitive state-of-the-art results on the Multi30K and the Ambiguous COCO datasets. We also collected a new multilingual multimodal product description dataset to simulate a real-world international online shopping scenario. On this dataset, our visual attention grounding model outperforms other methods by a large margin.

Aaron Gerow, Mingyang Zhou, Stan Matwin et al.

Bipartite data is common in data engineering and brings unique challenges, particularly when it comes to clustering tasks that impose on strong structural assumptions. This work presents an unsupervised method for assessing similarity in bipartite data. Similar to some co-clustering methods, the method is based on regular equivalence in graphs. The algorithm uses spectral properties of a bipartite adjacency matrix to estimate similarity in both dimensions. The method is reflexive in that similarity in one dimension is used to inform similarity in the other. Reflexive regular equivalence can also use the structure of transitivities -- in a network sense -- the contribution of which is controlled by the algorithm's only free-parameter, $α$. The method is completely unsupervised and can be used to validate assumptions of co-similarity, which are required but often untested, in co-clustering analyses. Three variants of the method with different normalizations are tested on synthetic data. The method is found to be robust to noise and well-suited to asymmetric co-similar structure, making it particularly informative for cluster analysis and recommendation in bipartite data of unknown structure. In experiments, the convergence and speed of the algorithm are found to be stable for different levels of noise. Real-world data from a network of malaria genes are analyzed, where the similarity produced by the reflexive method is shown to out-perform other measures' ability to correctly classify genes.