arXiv subjects

Minghua Deng

Publications and source records attributed to Minghua Deng.

18 recordsLinked to original sources

arXiv2026

A Correlation-Free Test for High-Dimensional Elliptical Distributions

Elliptical distributions provide a flexible and widely used extension of multivariate normal distribution. They play a critical role in many statistical procedures when dealing with high-dimensional data. However, goodness-of-fit testing for elliptical distributions remains challenging when the dimension is comparable to or larger than the sample size. In this work, we propose a correlation-free test for high-dimensional elliptical distributions. We establish high-dimensional Gaussian approximation for the test statistic under general correlation structures, allowing the dimension to grow as $\log p=o(n^{1/14})$ under finite moment conditions, without using the inverse sample covariance matrix. We further develop Gaussian multiplier bootstrap test procedure and prove its theoretical validity. Numerical studies demonstrate stable finite-sample behavior and favorable power against a range of alternatives. Applications to real datasets illustrate practical utility of the proposed test.

stat.ME↗

arXiv2026

CogniFold: Always-On Proactive Memory via Cognitive Folding

Existing agent memory remains predominantly reactive and retrieval-based, lacking the capacity to autonomously organize experience into persistent cognitive structure. Toward genuinely autonomous agents, we introduce CogniFold, a brain-inspired "always-on" agent memory designed for the next generation of proactive assistants. CogniFold continuously folds fragmented event streams into self-emerging cognitive structures, bootstrapping progressively higher-level cognition from incoming events and accumulated knowledge. We ground this by extending Complementary Learning Systems (CLS) theory from two layers (hippocampus, neocortex) to three, adding a prefrontal intent layer. Emulating the prefrontal cortex as the locus of intentional control and decision-making, CogniFold achieves this through graph-topology self-organization: cognitive structures proactively assemble under the stream, merge when semantically similar, decay when stale, relink through associative recall, and surface intents when concept-cluster density crosses a threshold. We evaluate structural formation using CogEval-Bench, demonstrating that CogniFold uniquely produces memory structures that match cognitive expectations and concept emergence. Furthermore, across eight downstream benchmarks -- two probing long-term conversational memory (LoCoMo, LongMemEval) and six spanning other cognitive domains -- we validate that CogniFold simultaneously performs robustly on conventional memory tasks. Our code is available at https://github.com/OpenNorve/CogniFold.

cs.AI↗

arXiv2024

Improving Tree Probability Estimation with Stochastic Optimization and Variance Reduction

Probability estimation of tree topologies is one of the fundamental tasks in phylogenetic inference. The recently proposed subsplit Bayesian networks (SBNs) provide a powerful probabilistic graphical model for tree topology probability estimation by properly leveraging the hierarchical structure of phylogenetic trees. However, the expectation maximization (EM) method currently used for learning SBN parameters does not scale up to large data sets. In this paper, we introduce several computationally efficient methods for training SBNs and show that variance reduction could be the key for better performance. Furthermore, we also introduce the variance reduction technique to improve the optimization of SBN parameters for variational Bayesian phylogenetic inference (VBPI). Extensive synthetic and real data experiments demonstrate that our methods outperform previous baseline methods on the tasks of tree topology probability estimation as well as Bayesian phylogenetic inference using SBNs.

q-bio.PE↗

arXiv2023

Criterion-based Heterogeneous Collaborative Filtering for Multi-behavior Implicit Recommendation

Recent years have witnessed the explosive growth of interaction behaviors in multimedia information systems, where multi-behavior recommender systems have received increasing attention by leveraging data from various auxiliary behaviors such as tip and collect. Among various multi-behavior recommendation methods, non-sampling methods have shown superiority over negative sampling methods. However, two observations are usually ignored in existing state-of-the-art non-sampling methods based on binary regression: (1) users have different preference strengths for different items, so they cannot be measured simply by binary implicit data; (2) the dependency across multiple behaviors varies for different users and items. To tackle the above issue, we propose a novel non-sampling learning framework named Criterion-guided Heterogeneous Collaborative Filtering (CHCF). CHCF introduces both upper and lower thresholds to indicate selection criteria, which will guide user preference learning. Besides, CHCF integrates criterion learning and user preference learning into a unified framework, which can be trained jointly for the interaction prediction of the target behavior. We further theoretically demonstrate that the optimization of Collaborative Metric Learning can be approximately achieved by the CHCF learning framework in a non-sampling form effectively. Extensive experiments on three real-world datasets show the effectiveness of CHCF in heterogeneous scenarios.

cs.IR↗

arXiv2023

TGNN: A Joint Semi-supervised Framework for Graph-level Classification

This paper studies semi-supervised graph classification, a crucial task with a wide range of applications in social network analysis and bioinformatics. Recent works typically adopt graph neural networks to learn graph-level representations for classification, failing to explicitly leverage features derived from graph topology (e.g., paths). Moreover, when labeled data is scarce, these methods are far from satisfactory due to their insufficient topology exploration of unlabeled data. We address the challenge by proposing a novel semi-supervised framework called Twin Graph Neural Network (TGNN). To explore graph structural information from complementary views, our TGNN has a message passing module and a graph kernel module. To fully utilize unlabeled data, for each module, we calculate the similarity of each unlabeled graph to other labeled graphs in the memory bank and our consistency loss encourages consistency between two similarity distributions in different embedding spaces. The two twin modules collaborate with each other by exchanging instance similarity knowledge to fully explore the structure information of both labeled and unlabeled data. We evaluate our TGNN on various public datasets and show that it achieves strong performance.

cs.LG↗

arXiv2023

Neighborhood Consensus Contrastive Learning for Backward-Compatible Representation

In object re-identification (ReID), the development of deep learning techniques often involves model updates and deployment. It is unbearable to re-embedding and re-index with the system suspended when deploying new models. Therefore, backward-compatible representation is proposed to enable "new" features to be compared with "old" features directly, which means that the database is active when there are both "new" and "old" features in it. Thus we can scroll-refresh the database or even do nothing on the database to update. The existing backward-compatible methods either require a strong overlap between old and new training data or simply conduct constraints at the instance level. Thus they are difficult in handling complicated cluster structures and are limited in eliminating the impact of outliers in old embeddings, resulting in a risk of damaging the discriminative capability of new features. In this work, we propose a Neighborhood Consensus Contrastive Learning (NCCL) method. With no assumptions about the new training data, we estimate the sub-cluster structures of old embeddings. A new embedding is constrained with multiple old embeddings in both embedding space and discrimination space at the sub-class level. The effect of outliers diminished, as the multiple samples serve as "mean teachers". Besides, we also propose a scheme to filter the old embeddings with low credibility, further improving the compatibility robustness. Our method ensures backward compatibility without impairing the accuracy of the new model. And it can even improve the new model's accuracy in most scenarios.

cs.CV↗

arXiv2022

A Survey on Deep Hashing Methods

Nearest neighbor search aims to obtain the samples in the database with the smallest distances from them to the queries, which is a basic task in a range of fields, including computer vision and data mining. Hashing is one of the most widely used methods for its computational and storage efficiency. With the development of deep learning, deep hashing methods show more advantages than traditional methods. In this survey, we detailedly investigate current deep hashing algorithms including deep supervised hashing and deep unsupervised hashing. Specifically, we categorize deep supervised hashing methods into pairwise methods, ranking-based methods, pointwise methods as well as quantization according to how measuring the similarities of the learned hash codes. Moreover, deep unsupervised hashing is categorized into similarity reconstruction-based methods, pseudo-label-based methods and prediction-free self-supervised learning-based methods based on their semantic learning manners. We also introduce three related important topics including semi-supervised deep hashing, domain adaption deep hashing and multi-modal deep hashing. Meanwhile, we present some commonly used public datasets and the scheme to measure the performance of deep hashing algorithms. Finally, we discuss some potential research directions in conclusion.

cs.CV↗

arXiv2021

ARGO: Modeling Heterogeneity in E-commerce Recommendation

Nowadays, E-commerce is increasingly integrated into our daily lives. Meanwhile, shopping process has also changed incrementally from one behavior (purchase) to multiple behaviors (such as view, carting and purchase). Therefore, utilizing interaction data of auxiliary behavior data draws a lot of attention in the E-commerce recommender systems. However, all existing models ignore two kinds of intrinsic heterogeneity which are helpful to capture the difference of user preferences and the difference of item attributes. First (intra-heterogeneity), each user has multiple social identities with otherness, and these different identities can result in quite different interaction preferences. Second (inter-heterogeneity), each item can transfer an item-specific percentage of score from low-level behavior to high-level behavior for the gradual relationship among multiple behaviors. Thus, the lack of consideration of these heterogeneities damages recommendation rank performance. To model the above heterogeneities, we propose a novel method named intra- and inter-heterogeneity recommendation model (ARGO). Specifically, we embed each user into multiple vectors representing the user's identities, and the maximum of identity scores indicates the interaction preference. Besides, we regard the item-specific transition percentage as trainable transition probability between different behaviors. Extensive experiments on two real-world datasets show that ARGO performs much better than the state-of-the-art in multi-behavior scenarios.

cs.IR↗

arXiv2021

Statistical computation methods for microbiome compositional data network inference

Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential to an understanding of the organization and complex interplay of microbial communities, as well as the structure and dynamics of various ecosystems. A common and essential approach toward this objective involves the inference of microbiome interaction networks. Although network inference methods in other fields have been studied before, applying these methods to estimate microbiome associations based on compositional data will not yield valid results. On the one hand, features of microbiome data such as compositionality, sparsity and high-dimensionality challenge the data normalization and the design of computational methods. On the other hand, several issues like microbial community heterogeneity, external environmental interference and biological concerns also make it more difficult to deal with the network inference. In this paper, we provide a comprehensive review of emerging microbiome interaction network inference methods. According to various assumptions and research targets, estimated networks are divided into four main categories: correlation networks, conditional correlation networks, mixture networks and differential networks. Their scope of applications, advantages and limitations are presented in this review. Since real microbial interactions can be complex and dynamic, no unifying method has captured all the aspects of interest to date. In addition, we discuss the challenges now confronting current microbial associations study and future prospects. Finally, we highlight that the research in microbial network inference requires the joint promotion of statistical computation methods and experimental techniques.

stat.AP↗

arXiv2021

CIMON: Towards High-quality Hash Codes

Recently, hashing is widely used in approximate nearest neighbor search for its storage and computational efficiency. Most of the unsupervised hashing methods learn to map images into semantic similarity-preserving hash codes by constructing local semantic similarity structure from the pre-trained model as the guiding information, i.e., treating each point pair similar if their distance is small in feature space. However, due to the inefficient representation ability of the pre-trained model, many false positives and negatives in local semantic similarity will be introduced and lead to error propagation during the hash code learning. Moreover, few of the methods consider the robustness of models, which will cause instability of hash codes to disturbance. In this paper, we propose a new method named {\textbf{C}}omprehensive s{\textbf{I}}milarity {\textbf{M}}ining and c{\textbf{O}}nsistency lear{\textbf{N}}ing (CIMON). First, we use global refinement and similarity statistical distribution to obtain reliable and smooth guidance. Second, both semantic and contrastive consistency learning are introduced to derive both disturb-invariant and discriminative hash codes. Extensive experiments on several benchmark datasets show that the proposed method outperforms a wide range of state-of-the-art methods in both retrieval performance and robustness.

cs.CV↗

arXiv2021

DNA-GCN: Graph convolutional networks for predicting DNA-protein binding

Predicting DNA-protein binding is an important and classic problem in bioinformatics. Convolutional neural networks have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. However, none of the studies has utilized graph convolutional networks for motif inference. In this work, we propose to use graph convolutional networks for motif inference. We build a sequence k-mer graph for the whole dataset based on k-mer co-occurrence and k-mer sequence relationship and then learn DNA Graph Convolutional Network (DNA-GCN) for the whole dataset. Our DNA-GCN is initialized with a one-hot representation for all nodes, and it then jointly learns the embeddings for both k-mers and sequences, as supervised by the known labels of sequences. We evaluate our model on 50 datasets from ENCODE. DNA-GCN shows its competitive performance compared with the baseline model. Besides, we analyze our model and design several different architectures to help fit different datasets.

q-bio.GN↗

arXiv2021

Deep Unsupervised Hashing by Distilled Smooth Guidance

Hashing has been widely used in approximate nearest neighbor search for its storage and computational efficiency. Deep supervised hashing methods are not widely used because of the lack of labeled data, especially when the domain is transferred. Meanwhile, unsupervised deep hashing models can hardly achieve satisfactory performance due to the lack of reliable similarity signals. To tackle this problem, we propose a novel deep unsupervised hashing method, namely Distilled Smooth Guidance (DSG), which can learn a distilled dataset consisting of similarity signals as well as smooth confidence signals. To be specific, we obtain the similarity confidence weights based on the initial noisy similarity signals learned from local structures and construct a priority loss function for smooth similarity-preserving learning. Besides, global information based on clustering is utilized to distill the image pairs by removing contradictory similarity signals. Extensive experiments on three widely used benchmark datasets show that the proposed DSG consistently outperforms the state-of-the-art search methods.

cs.CV↗

arXiv2021

Graph Contrastive Clustering

Recently, some contrastive learning methods have been proposed to simultaneously learn representations and clustering assignments, achieving significant improvements. However, these methods do not take the category information and clustering objective into consideration, thus the learned representations are not optimal for clustering and the performance might be limited. Towards this issue, we first propose a novel graph contrastive learning framework, which is then applied to the clustering task and we come up with the Graph Constrastive Clustering~(GCC) method. Different from basic contrastive clustering that only assumes an image and its augmentation should share similar representation and clustering assignments, we lift the instance-level consistency to the cluster-level consistency with the assumption that samples in one cluster and their augmentations should all be similar. Specifically, on the one hand, the graph Laplacian based contrastive loss is proposed to learn more discriminative and clustering-friendly features. On the other hand, a novel graph-based contrastive learning strategy is proposed to learn more compact clustering assignments. Both of them incorporate the latent category information to reduce the intra-cluster variance while increasing the inter-cluster variance. Experiments on six commonly used datasets demonstrate the superiority of our proposed approach over the state-of-the-art methods.

cs.CV↗

arXiv2018

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

Accurate prediction of inter-residue contacts of a protein is important to calcu- lating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective to inferring inter-residue contacts. The Markov ran- dom field (MRF) technique, although being widely used for contact prediction, suffers from the following dilemma: the actual likelihood function of MRF is accurate but time-consuming to calculate, in contrast, approximations to the actual likelihood, say pseudo-likelihood, are efficient to calculate but inaccu- rate. Thus, how to achieve both accuracy and efficiency simultaneously remains a challenge. In this study, we present such an approach (called clmDCA) for contact prediction. Unlike plmDCA using pseudo-likelihood, i.e., the product of conditional probability of individual residues, our approach uses composite- likelihood, i.e., the product of conditional probability of all residue pairs. Com- posite likelihood has been theoretically proved as a better approximation to the actual likelihood function than pseudo-likelihood. Meanwhile, composite likelihood is still efficient to maximize, thus ensuring the efficiency of clmDCA. We present comprehensive experiments on popular benchmark datasets, includ- ing PSICOV dataset and CASP-11 dataset, to show that: i) clmDCA alone outperforms the existing MRF-based approaches in prediction accuracy. ii) When equipped with deep learning technique for refinement, the prediction ac- curacy of clmDCA was further significantly improved, suggesting the suitability of clmDCA for subsequent refinement procedure. We further present successful application of the predicted contacts to accurately build tertiary structures for proteins in the PSICOV dataset. Accessibility: The software clmDCA and a server are publicly accessible through http://protein.ict.ac.cn/clmDCA/.

q-bio.BM↗

arXiv2017

Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning

Background. Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary structure prediction. However, direct angle prediction from sequence alone is challenging. Method. In this study, we present a novel method to predict real-valued angles by combining clustering and deep learning. That is, we first generate certain clusters of angles (each assigned a label) and then apply a deep residual neural network to predict the label posterior probability. Finally, we output real-valued prediction by a mixture of the clusters with their predicted probabilities. At the same time, we also estimate the bound of the prediction errors at each residue from the predicted label probabilities. Result. In this article, we present a novel method (named RaptorX-Angle) to predict real-valued angles by combining clustering and deep learning. Tested on a subset of PDB25 and the targets in the latest two Critical Assessment of protein Structure Prediction (CASP), our method outperforms the existing state-of-art method SPIDER2 in terms of Pearson Correlation Coefficient (PCC) and Mean Absolute Error (MAE). Our result also shows approximately linear relationship between the real prediction errors and our estimated bounds. That is, the real prediction error can be well approximated by our estimated bounds. Conclusions. Our study provides an alternative and more accurate prediction of dihedral angles, which may facilitate protein structure prediction and functional study.

q-bio.BM↗

arXiv2017

Differential Network Analysis via the Lasso Penalized D-Trace Loss

Biological networks often change under different environmental and genetic conditions. Understanding how these networks change becomes an important problem in biological studies. In this paper, we model the network change as the difference of two precision matrices and propose a novel loss function for estimating the precision matrix difference. Under a new irrepresentability condition, we show that the new loss function with the lasso penalty can give consistent estimates in high-dimensional setting for sub-Gaussian and polynomial-tailed distributions. An efficient algorithm is developed based on the alternating direction method to solve the optimization problem. Simulation studies and a real data analysis about colorectal cancer show that the proposed method outperforms other available methods.

stat.ME↗

arXiv2015

Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics

Next Generation Sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential. A plausible model for this underlying distribution of word counts is given through modelling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data. Here we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution, using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate them using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results, and that the clustering results that use a MC of the estimated order give a plausible clustering of the species.

q-bio.GN↗

arXiv2006

Stochastic Model of Yeast Cell Cycle Network

Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we propose and study a stochastic model for the network regulating the cell cycle of the budding yeast. The stochasticity in the model is controlled by a temperature-like parameter $β$. Our simulation results show that both the biological stationary state and the biological pathway are stable for a wide range of "temperature". There is, however, a sharp transition-like behavior at $β_c$, below which the dynamics is dominated by noise. We also define a pseudo energy landscape for the system in which the biological pathway can be seen as a deep valley.

q-bio.MN↗