Zhirong Yang

Tong Yu, Lei Cheng, Ruslan Khalitov et al.

Self-supervised pretraining (SSP) has been recognized as a method to enhance prediction accuracy in various downstream tasks. However, its efficacy for DNA sequences remains somewhat constrained. This limitation stems primarily from the fact that most existing SSP approaches in genomics focus on masked language modeling of individual sequences, neglecting the crucial aspect of encoding statistics across multiple sequences. To overcome this challenge, we introduce an innovative deep neural network model, which incorporates collaborative learning between a `student' and a `teacher' subnetwork. In this model, the student subnetwork employs masked learning on nucleotides and progressively adapts its parameters to the teacher subnetwork through an exponential moving average approach. Concurrently, both subnetworks engage in contrastive learning, deriving insights from two augmented representations of the input sequences. This self-distillation process enables our model to effectively assimilate both contextual information from individual sequences and distributional data across the sequence population. We validated our approach with preliminary pretraining using the human reference genome, followed by applying it to 20 downstream inference tasks. The empirical results from these experiments demonstrate that our novel method significantly boosts inference performance across the majority of these tasks. Our code is available at https://github.com/wiedersehne/FinDNA.

Zhirong Yang, Yuwei Chen, Jukka Corander

Cluster visualization is an essential task for nonlinear dimensionality reduction as a data analysis tool. It is often believed that Student t-Distributed Stochastic Neighbor Embedding (t-SNE) can show clusters for well clusterable data, with a smaller Kullback-Leibler divergence corresponding to a better quality. There was even theoretical proof for the guarantee of this property. However, we point out that this is not necessarily the case -- t-SNE may leave clustering patterns hidden despite strong signals present in the data. Extensive empirical evidence is provided to support our claim. First, several real-world counter-examples are presented, where t-SNE fails even if the input neighborhoods are well clusterable. Tuning hyperparameters in t-SNE or using better optimization algorithms does not help solve this issue because a better t-SNE learning objective can correspond to a worse cluster embedding. Second, we check the assumptions in the clustering guarantee of t-SNE and find they are often violated for real-world data sets.

Ruslan Khalitov, Tong Yu, Lei Cheng et al.

Square matrices appear in many machine learning problems and models. Optimization over a large square matrix is expensive in memory and in time. Therefore an economic approximation is needed. Conventional approximation approaches factorize the square matrix into a number matrices of much lower ranks. However, the low-rank constraint is a performance bottleneck if the approximated matrix is intrinsically high-rank or close to full rank. In this paper, we propose to approximate a large square matrix with a product of sparse full-rank matrices. In the approximation, our method needs only $N(\log N)^2$ non-zero numbers for an $N\times N$ full matrix. We present both non-parametric and parametric ways to find the factorization. In the former, we learn the factorizing matrices directly, and in the latter, we train neural networks to map input data to the non-zero matrix entries. The sparse factorization method is tested for a variety of synthetic and real-world square matrices. The experimental results demonstrate that our method gives a better approximation when the approximated matrix is sparse and high-rank. Based on this finding, we use our parametric method as a scalable attention architecture that performs strongly in learning tasks for long sequential data and defeats Transformer and its several variants.

Zhirong Yang, Yuwei Chen, Denis Sedov et al.

Neighbor Embedding (NE) aims to preserve pairwise similarities between data items and has been shown to yield an effective principle for data visualization. However, even the best existing NE methods such as Stochastic Neighbor Embedding (SNE) may leave large-scale patterns hidden, for example clusters, despite strong signals being present in the data. To address this, we propose a new cluster visualization method based on the Neighbor Embedding principle. We first present a family of Neighbor Embedding methods that generalizes SNE by using non-normalized Kullback-Leibler divergence with a scale parameter. In this family, much better cluster visualizations often appear with a parameter value different from the one corresponding to SNE. We also develop an efficient software that employs asynchronous stochastic block coordinate descent to optimize the new family of objective functions. Our experimental results demonstrate that the method consistently and substantially improves the visualization of data clusters compared with the state-of-the-art NE approaches.

Denis Sedov, Zhirong Yang

Word embedding, which encodes words into vectors, is an important starting point in natural language processing and commonly used in many text-based machine learning tasks. However, in most current word embedding approaches, the similarity in embedding space is not optimized in the learning. In this paper we propose a novel neighbor embedding method which directly learns an embedding simplex where the similarities between the mapped words are optimal in terms of minimal discrepancy to the input neighborhoods. Our method is built upon two-step random walks between words via topics and thus able to better reveal the topics among the words. Experiment results indicate that our method, compared with another existing word embedding approach, is more favorable for various queries.

Yao Lu, Zhirong Yang, Juho Kannala et al.

Inferring the relations between two images is an important class of tasks in computer vision. Examples of such tasks include computing optical flow and stereo disparity. We treat the relation inference tasks as a machine learning problem and tackle it with neural networks. A key to the problem is learning a representation of relations. We propose a new neural network module, contrast association unit (CAU), which explicitly models the relations between two sets of input variables. Due to the non-negativity of the weights in CAU, we adopt a multiplicative update algorithm for learning these weights. Experiments show that neural networks with CAUs are more effective in learning five fundamental image transformations than conventional neural networks.

Yao Lu, Jukka Corander, Zhirong Yang

Stochastic Neighbor Embedding (SNE) methods minimize the divergence between the similarity matrix of a high-dimensional data set and its counterpart from a low-dimensional embedding, leading to widely applied tools for data visualization. Despite their popularity, the current SNE methods experience a crowding problem when the data include highly imbalanced similarities. This implies that the data points with higher total similarity tend to get crowded around the display center. To solve this problem, we introduce a fast normalization method and normalize the similarity matrix to be doubly stochastic such that all the data points have equal total similarities. Furthermore, we show empirically and theoretically that the doubly stochasticity constraint often leads to embeddings which are approximately spherical. This suggests replacing a flat space with spheres as the embedding space. The spherical embedding eliminates the discrepancy between the center and the periphery in visualization, which efficiently resolves the crowding problem. We compared the proposed method (DOSNES) with the state-of-the-art SNE method on three real-world datasets and the results clearly indicate that our method is more favorable in terms of visualization quality.

Onur Dikmen, Zhirong Yang, Erkki Oja

Information divergence that measures the difference between two nonnegative matrices or tensors has found its use in a variety of machine learning problems. Examples are Nonnegative Matrix/Tensor Factorization, Stochastic Neighbor Embedding, topic models, and Bayesian network optimization. The success of such a learning task depends heavily on a suitable divergence. A large variety of divergences have been suggested and analyzed, but very few results are available for an objective choice of the optimal divergence for a given task. Here we present a framework that facilitates automatic selection of the best divergence among a given family, based on standard maximum likelihood estimation. We first propose an approximated Tweedie distribution for the beta-divergence family. Selecting the best beta then becomes a machine learning problem solved by maximum likelihood. Next, we reformulate alpha-divergence in terms of beta-divergence, which enables automatic selection of alpha by maximum likelihood with reuse of the learning principle for beta-divergence. Furthermore, we show the connections between gamma and beta-divergences as well as Rényi and alpha-divergences, such that our automatic selection framework is extended to non-separable divergences. Experiments on both synthetic and real-world data demonstrate that our method can quite accurately select information divergence across different learning problems and various divergence families.

Zhirong Yang, Erkki Oja

Clustering analysis by nonnegative low-rank approximations has achieved remarkable progress in the past decade. However, most approximation approaches in this direction are still restricted to matrix factorization. We propose a new low-rank learning method to improve the clustering performance, which is beyond matrix factorization. The approximation is based on a two-step bipartite random walk through virtual cluster nodes, where the approximation is formed by only cluster assigning probabilities. Minimizing the approximation error measured by Kullback-Leibler divergence is equivalent to maximizing the likelihood of a discriminative model, which endows our method with a solid probabilistic interpretation. The optimization is implemented by a relaxed Majorization-Minimization algorithm that is advantageous in finding good local minima. Furthermore, we point out that the regularized algorithm with Dirichlet prior only serves as initialization. Experimental results show that the new method has strong performance in clustering purity for various datasets, especially for large-scale manifold data.