arXiv subjects

Rui Kuang

Publications and source records attributed to Rui Kuang.

10 recordsLinked to original sources

arXiv2026

PerturbRx: Learning Treatment-Conditioned Latent Transitions for Patient Drug Response Prediction

Scarce data and tumor heterogeneity limit patient-level cancer treatment-response prediction. Existing approaches predict response from pretreatment molecular profiles and drug representations, without explicitly modeling the molecular changes expected under treatment. We propose PerturbRx, a treatment-conditioned representation learning framework that learns intervention-induced latent transitions and uses them as patient-drug response features. PerturbRx trains a drug- and dose-conditioned transition predictor from context-matched but cell-unpaired control and treated single-cell populations, then freezes and transfers the predictor to pretreatment patient profiles without requiring post-treatment measurements. The transition is combined with patient and drug representations to predict response. Across TCGA and patient-derived xenograft benchmarks, PerturbRx achieves the strongest aggregate predictive performance among the evaluated methods. These results support perturbation-pretrained latent transitions as useful representations for patient-level drug-response prediction.

q-bio.QM↗

arXiv2026

The-Hausdorff-dimension-of-the-survivor-set

Let $ 1<\beta< 2 $, the sequence $\alpha(\beta)=\alpha(\beta)_1\alpha(\beta)_2\dotsb $ be the quasi-greedy $ \beta $-expansion of $ 1 $, and $ t\in [0,1) $ be a bifurcation parameter. The $\beta$-transformation is defined to be $T_{\beta}(x)=\beta x (mod 1) $ for $x\in [0,1)$. The Hausdorff dimension of the survivor set $K(t)=\{x\in [0,1)\colon T_{\beta}^k(x)\not\in (0,t), \forall k\geq0\} $ is equal to $ -\frac{\ln\lambda}{\ln\beta} $ under the condition that $ \sum_{i=k}^{\infty}\frac{\alpha(\beta)_i }{\beta^i}\geq t $ for any $ k\geq 1 $, where $ \lambda\in (0,1) $ is the smallest positive solution of the equation $\sum_{n=1}^{\infty}(\alpha(\beta)_n-t_n)x^n=1$ with $(t_n) $ being the quasi-greedy $\beta$-expansion of $t$. And the local H\"older exponent of the Hausdorff dimension function of $K(t) $ is larger than the value of the function itself.

math.DS↗

arXiv2024

DrugAgent: Reliable Multi-Agent Integration of Conflicting Biomedical Evidence for Drug-Target Interaction Assessment

Workflows in drug-target interaction (DTI) assessment require integrating heterogeneous data from predictive models, curated resources, and observations from experimental literature. This evidence can be incomplete or conflicting. DrugAgent is a large language model (LLM)-based multi-agent system focused on DTI evidence integration that integrates outputs from machine learning, knowledge graph, and retrieval-augmented generation (RAG) agents. DrugAgent converts agent outputs into interpretable representations, then summarizes conflict across the evidence. We evaluated DrugAgent on kinase screening data of 900 pairs spanning 178 kinases and 42 inhibitors, and an androgen receptor antagonist screening benchmark. On the kinase dataset, LLM-as-a-Judge evaluation indicated outputs were faithful to input evidence in 98.8% of cases. Biological plausibility of returned summarization was high (scores 3-4 out of 5) across ground-truth classes: 79% of Weak activity labels cases (81% for Moderate/77% Strong); Strong cases received higher scores than Weak/Moderate. Label stability showed 98% agreement across runs. Results on the antagonist benchmark were consistent with the kinase dataset. Retrieved literature provided the greatest benefit when direct drug-target evidence was available, highlighting the importance of evidence availability for RAG-based integration. DrugAgent provides heterogeneous evidence-grounded DTI assessment, complementing standalone DTI prediction. We provide strategies to model agreement, conflict, and uncertainty in biomedical evidence integration. Code: https://github.com/sciluna/DrugAgent.

cs.AI↗

arXiv2024

drGT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network

For translational impact, both accurate drug response prediction and biological plausibility of predictive features are needed. We present drGT, a heterogeneous graph deep learning model over drugs, genes, and cell lines that couples prediction with mechanism-oriented interpretability via attention coefficients (ACs). We assess both predictive generalization (random, unseen-drug, unseen-cell, and zero-shot splits) and biological plausibility (use of text-mined PubMed gene-drug co-mentions and comparison to a structure-based DTI predictor) on GDSC, NCI60, and CTRP datasets. Across benchmarks, drGT consistently delivers top regression performance while maintaining competitive classification accuracy for drug sensitivity. Under random 5-fold cross-validation, drGT attains an AUROC of up to 0.945 (3rd overall) and an $R^2$ up to 0.690, outperforming all baselines on regression. In leave-one-out tests for unseen cell lines and drugs, drGT achieves AUROCs of 0.706 and 0.844, and $R^2$ values of 0.692 and 0.022, the only model yielding positive $R^2$ for unseen drugs. In zero-shot prediction, drGT achieves an AUROC of 0.786 and a regression $R^2$ of 0.334, both representing the highest scores among all models. For interpretability, AC-derived drug-gene links recover known biology: among 976 drugs with known DTIs, 36.9% of predicted links match established DTIs, and 63.7% are supported by either PubMed abstracts or a structure-based predictive model. Enrichment analyses of AC-prioritized genes reveal drug-perturbed biological processes, providing pathway-level explanations. drGT advances predictive generalization and mechanism-centered interpretability, offering state-of-the-art regression accuracy and literature-supported biological hypotheses that demonstrate the use of graph learning from heterogeneous input data for biological discovery. Code: https://github.com/sciluna/drGT

cs.LG↗

arXiv2023

Shadowable points of free semigroup actions

The shadowable points of dynamical systems has been well-studied by Morales \cite{MR3535492}. This paper aims to generalize the main results obtained by Morales to free semigroup actions. To this end, we introduce the notion of shadowable points of a free semigroup action. Let $G$ be a free semigroup generated by finite continuous self-maps acting on compact metric space. We will prove the following results for $G$ on compact metric spaces. The set of shadowable points of $G$ is a Borel set. $G$ has the pseudo-orbit tracing property (POTP) if and only if every point is a shadowable point of $G$. The chain recurrent and non-wandering sets of $G$ coincide when every chain recurrent point is a shadowable point of $G$. The space $X$ is totally disconnected at every shadowable point of $G$ under certain condition.

math.DS↗

arXiv2018

Scalable Label Propagation for Multi-relational Learning on the Tensor Product of Graphs

Multi-relational learning on knowledge graphs infers high-order relations among the entities across the graphs. This learning task can be solved by label propagation on the tensor product of the knowledge graphs to learn the high-order relations as a tensor. In this paper, we generalize a widely used label propagation model to the normalized tensor product graph, and propose an optimization formulation and a scalable Low-rank Tensor-based Label Propagation algorithm (LowrankTLP) to infer multi-relations for two learning tasks, hyperlink prediction and multiple graph alignment. The optimization formulation minimizes the upper bound of the noisy tensor estimation error for multiple graph alignment, by learning with a subset of the eigen-pairs in the spectrum of the normalized tensor product graph. We also provide a data-dependent transductive Rademacher bound for binary hyperlink prediction. We accelerate LowrankTLP with parallel tensor computation which enables label propagation on a tensor product of 100 graphs each of size 1000 in less than half hour in the simulation. LowrankTLP was also applied to predicting the author-paper-venue hyperlinks in publication records, alignment of segmented regions across up to 26 CT-scan images and alignment of protein-protein interaction networks across multiple species. The experiments demonstrate that LowrankTLP indeed well approximates the original label propagation with better scalability and accuracy.

cs.LG↗

arXiv2017

Low-rank Label Propagation for Semi-supervised Learning with 100 Millions Samples

The success of semi-supervised learning crucially relies on the scalability to a huge amount of unlabelled data that are needed to capture the underlying manifold structure for better classification. Since computing the pairwise similarity between the training data is prohibitively expensive in most kinds of input data, currently, there is no general ready-to-use semi-supervised learning method/tool available for learning with tens of millions or more data points. In this paper, we adopted the idea of two low-rank label propagation algorithms, GLNP (Global Linear Neighborhood Propagation) and Kernel Nyström Approximation, and implemented the parallelized version of the two algorithms accelerated with Nesterov's accelerated projected gradient descent for Big-data Label Propagation (BigLP). The parallel algorithms are tested on five real datasets ranging from 7000 to 10,000,000 in size and a simulation dataset of 100,000,000 samples. In the experiments, the implementation can scale up to datasets with 100,000,000 samples and hundreds of features and the algorithms also significantly improved the prediction accuracy when only a very small percentage of the data is labeled. The results demonstrate that the BigLP implementation is highly scalable to big data and effective in utilizing the unlabeled data for semi-supervised learning.

cs.LG↗

arXiv2015

Network-based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification.

cs.CE↗

arXiv2015

Predicting Small Group Accretion in Social Networks: A topology based incremental approach

Small Group evolution has been of central importance in social sciences and also in the industry for understanding dynamics of team formation. While most of research works studying groups deal at a macro level with evolution of arbitrary size communities, in this paper we restrict ourselves to studying evolution of small group (size $\leq20$) which is governed by contrasting sociological phenomenon. Given a previous history of group collaboration between a set of actors, we address the problem of predicting likely future group collaborations. Unfortunately, predicting groups requires choosing from $n \choose r$ possibilities (where $r$ is group size and $n$ is total number of actors), which becomes computationally intractable as group size increases. However, our statistical analysis of a real world dataset has shown that two processes: an external actor joining an existing group (incremental accretion (IA)) or collaborating with a subset of actors of an exiting group (subgroup accretion (SA)), are largely responsible for future group formation. This helps to drastically reduce the $n\choose r$ possibilities. We therefore, model the attachment of a group for different actors outside this group. In this paper, we have built three topology based prediction models to study these phenomena. The performance of these models is evaluated using extensive experiments over DBLP dataset. Our prediction results shows that the proposed models are significantly useful for future group predictions both for IA and SA.

cs.SI↗

arXiv2011

Inferring Disease and Gene Set Associations with Rank Coherence in Networks

A computational challenge to validate the candidate disease genes identified in a high-throughput genomic study is to elucidate the associations between the set of candidate genes and disease phenotypes. The conventional gene set enrichment analysis often fails to reveal associations between disease phenotypes and the gene sets with a short list of poorly annotated genes, because the existing annotations of disease causative genes are incomplete. We propose a network-based computational approach called rcNet to discover the associations between gene sets and disease phenotypes. Assuming coherent associations between the genes ranked by their relevance to the query gene set, and the disease phenotypes ranked by their relevance to the hidden target disease phenotypes of the query gene set, we formulate a learning framework maximizing the rank coherence with respect to the known disease phenotype-gene associations. An efficient algorithm coupling ridge regression with label propagation, and two variants are introduced to find the optimal solution of the framework. We evaluated the rcNet algorithms and existing baseline methods with both leave-one-out cross-validation and a task of predicting recently discovered disease-gene associations in OMIM. The experiments demonstrated that the rcNet algorithms achieved the best overall rankings compared to the baselines. To further validate the reproducibility of the performance, we applied the algorithms to identify the target diseases of novel candidate disease genes obtained from recent studies of GWAS, DNA copy number variation analysis, and gene expression profiling. The algorithms ranked the target disease of the candidate genes at the top of the rank list in many cases across all the three case studies. The rcNet algorithms are available as a webtool for disease and gene set association analysis at http://compbio.cs.umn.edu/dgsa_rcNet.

q-bio.GN↗