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Qixin Zhang

Qixin Zhang contributes to research discovery and scholarly infrastructure.

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Machine Learning Artificial Intelligence math.OC Computation and Language Software Engineering

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preprint2026arXiv

CMKL: Modality-Aware Continual Learning for Evolving Biomedical Knowledge Graphs

Biomedical knowledge graphs are increasingly large, dynamic, and multimodal, driven by rapid advances in biotechnology such as high-throughput sequencing. Machine learning models can infer previously unobserved biomedical relationships and characterize biomedical entities in these graphs, but existing knowledge graph embedding methods and their continual learning extensions either assume static graph structure or fail to exploit multimodal information under evolving data distributions. They also apply uniform regularization across all model parameters, ignoring that different modalities may exhibit distinct forgetting dynamics as the graph evolves. We propose the Continual Multimodal Knowledge Graph Learner (CMKL), a CL framework for biomedical KGs that natively encodes structure, text, and molecules, fuses them through a Mixture-of-Experts (MoE) router, and protects previously learned knowledge with standard EWC regularization and a K-means-diverse multimodal replay buffer. We evaluate CMKL on a 129K-entity biomedical continual benchmark with 10 tasks. On continual biomedical entity classification, CMKL reaches AP 0.591 versus 0.370 for the strongest structural baseline, a 60% gain that is driven by access to multimodal features and preserved across the sequence with near-zero forgetting (AF 0.008). On continual relationship prediction, CMKL reaches AP $0.062$, matching Naive Sequential and EWC (0.058) within seed noise and outperforming Joint Training (0.047, p=0.045) and LKGE (0.039). A frozen-text ablation reaches AP 0.136, more than double any jointly trained model, yet that signal is unreachable by margin-ranking gradients: the greedy-modality asymmetry lives at the representation level, not the fusion level, and MoE routing manages it by suppressing the unreachable modality without forcing it through a learned bottleneck. Code: github.com/yradwan147/cmkl-neurips2026

preprint2026arXiv

Discovering Physical Directions in Weight Space: Composing Neural PDE Experts

Recent advances in neural operators have made partial differential equation (PDE) surrogate modeling increasingly scalable and transferable through large-scale pretraining and in-context adaptation. However, after a shared operator is fine-tuned to multiple regimes within a continuous physical family, it remains unclear whether the resulting weight-space updates merely form isolated regime experts or reveal reusable physical structure. Starting from a shared family anchor, we fine-tune low- and high-regime endpoint experts and show that their updates can be separated into a family-shared adaptation and a direction aligned with the underlying physical parameter. This separation reinterprets endpoint experts as finite-difference probes of a local physical direction in weight space, explaining why static averaging can interpolate between regimes but attenuates endpoint-specific physics. Building on this perspective, we propose Calibration-Conditioned Merge (CCM), a post-hoc coordinate readout method for composing neural PDE experts along this physical direction. Given physical metadata, a calibrated coordinate mapping, or a short observed rollout prefix, CCM infers the target composition coordinate and deploys a single merged checkpoint for the remaining rollout. We evaluate CCM on the reaction--diffusion system, viscosity-parameterized two-dimensional Navier--Stokes equations, and radial dam-break dynamics. Across these benchmarks, CCM achieves its strongest gains in extrapolative regimes, reducing out-of-distribution rollout error relative to the family anchor by 54.2%, 42.8%, and 13.8%, respectively. Further experiments across FNO scales, a DPOT-style backbone, and ablations confirm that endpoint fine-tuning is not arbitrary checkpoint drift, but reveals a calibratable physical direction for training-free transfer across PDE regimes.

preprint2026arXiv

Efficient Differentiable Causal Discovery via Reliable Super-Structure Learning

Recently, differentiable causal discovery has emerged as a promising approach to improve the accuracy and efficiency of existing methods. However, when applied to high-dimensional data or data with latent confounders, these methods, often based on off-the-shelf continuous optimization algorithms, struggle with the vast search space, the complexity of the objective function, and the nontrivial nature of graph-theoretical constraints. As a result, there has been a surge of interest in leveraging super-structures to guide the optimization process. Nonetheless, learning an appropriate super-structure at the right level of granularity, and doing so efficiently across various settings, presents significant challenges. In this paper, we propose ALVGL, a novel and general enhancement to the differentiable causal discovery pipeline. ALVGL employs a sparse and low-rank decomposition to learn the precision matrix of the data. We design an ADMM procedure to optimize this decomposition, identifying components in the precision matrix that are most relevant to the underlying causal structure. These components are then combined to construct a super-structure that is provably a superset of the true causal graph. This super-structure is used to initialize a standard differentiable causal discovery method with a more focused search space, thereby improving both optimization efficiency and accuracy. We demonstrate the versatility of ALVGL by instantiating it across a range of structural causal models, including both Gaussian and non-Gaussian settings, with and without unmeasured confounders. Extensive experiments on synthetic and real-world datasets show that ALVGL not only achieves state-of-the-art accuracy but also significantly improves optimization efficiency, making it a reliable and effective solution for differentiable causal discovery.

preprint2026arXiv

Learning Multi-Relational Graph Representations for DNA Methylation-Based Biological Age Estimation

Aging clocks aim to estimate biological age, a measure of physiological state distinct from chronological age, from observable biomarkers, and are widely used for health assessment and disease analysis. DNA methylation is a particularly informative biomarker due to its stability and strong association with aging, and recent learning-based approaches have improved predictive performance. However, most existing methods treat CpG sites as independent features, overlooking the complex and heterogeneous biological relationships among them. We propose RelAge-GNN, a multi-relational graph neural network framework for DNA methylation-based age prediction. Our method constructs three complementary graphs capturing co-methylation patterns, genomic co-localization, and gene-level associations among CpG sites. Each graph is modeled by an independent GNN branch, and a learnable gating mechanism adaptively fuses the resulting representations. Experiments on large-scale datasets show that RelAge-GNN achieves competitive accuracy and stronger correlation with chronological age compared to state-of-the-art methods. Moreover, the model exhibits improved sensitivity in detecting age acceleration across diverse disease cohorts, highlighting its potential utility for disease characterization. Finally, through post hoc interpretability analyses, we quantify the contributions of different relational structures and CpG sites, providing biologically meaningful insights and suggesting potential directions for aging-related research. Our code is available at: https://anonymous.4open.science/r/RelAge-GNN-F1E3/.

preprint2026arXiv

Reasoning over Precedents Alongside Statutes: Case-Augmented Deliberative Alignment for LLM Safety

Ensuring that Large Language Models (LLMs) adhere to safety principles without refusing benign requests remains a significant challenge. While OpenAI introduces deliberative alignment (DA) to enhance the safety of its o-series models through reasoning over detailed ``code-like'' safety rules, the effectiveness of this approach in open-source LLMs, which typically lack advanced reasoning capabilities, is understudied. In this work, we systematically evaluate the impact of explicitly specifying extensive safety codes versus demonstrating them through illustrative cases. We find that referencing explicit codes inconsistently improves harmlessness and systematically degrades helpfulness, whereas training on case-augmented simple codes yields more robust and generalized safety behaviors. By guiding LLMs with case-augmented reasoning instead of extensive code-like safety rules, we avoid rigid adherence to narrowly enumerated rules and enable broader adaptability. Building on these insights, we propose CADA, a case-augmented deliberative alignment method for LLMs utilizing reinforcement learning on self-generated safety reasoning chains. CADA effectively enhances harmlessness, improves robustness against attacks, and reduces over-refusal while preserving utility across diverse benchmarks, offering a practical alternative to rule-only DA for improving safety while maintaining helpfulness.

preprint2026arXiv

TERGAD: Structure-Aware Text-Enhanced Representations for Graph Anomaly Detection

Graph Anomaly Detection (GAD) aims to identify atypical graph entities, such as nodes, edges, or substructures, that deviate significantly from the majority. While existing text-rich approaches typically integrate structural context into the data representation pipeline using raw textual features, they often neglect the structural context of nodes. This limitation hinders their ability to detect sophisticated anomalies arising from inconsistencies between a node's inherent content and its topological role. To bridge this gap, we propose TERGAD (Structure-aware Text-enhanced Representations for Graph Anomaly Detection), A novel data augmentation framework that enriches structural semantics for GAD via the semantic reasoning capabilities of Large Language Models (LLMs). Specifically, TERGAD translates node-level topological properties into descriptive natural language narratives, which are subsequently processed by an LLM to derive high-level semantic embeddings. These embeddings are then adaptively fused with original node attributes through a gated dual-branch autoencoder to jointly reconstruct both graph structure and node features. The anomaly score is computed based on the integrated reconstruction error, effectively capturing deviations in both observable attributes and LLM-informed semantic expectations. Extensive experiments on six real-world datasets demonstrate that TERGAD consistently outperforms state-of-the-art baselines. Furthermore, our ablation studies validate the indispensable role of structural semantic guidance and the efficacy of the gated fusion mechanism. Code is available at https://github.com/Kantorakitty/TERGAD-main.

preprint2022arXiv

Communication-Efficient Decentralized Online Continuous DR-Submodular Maximization

Maximizing a monotone submodular function is a fundamental task in machine learning, economics, and statistics. In this paper, we present two communication-efficient decentralized online algorithms for the monotone continuous DR-submodular maximization problem, both of which reduce the number of per-function gradient evaluations and per-round communication complexity from $T^{3/2}$ to $1$. The first one, One-shot Decentralized Meta-Frank-Wolfe (Mono-DMFW), achieves a $(1-1/e)$-regret bound of $O(T^{4/5})$. As far as we know, this is the first one-shot and projection-free decentralized online algorithm for monotone continuous DR-submodular maximization. Next, inspired by the non-oblivious boosting function \citep{zhang2022boosting}, we propose the Decentralized Online Boosting Gradient Ascent (DOBGA) algorithm, which attains a $(1-1/e)$-regret of $O(\sqrt{T})$. To the best of our knowledge, this is the first result to obtain the optimal $O(\sqrt{T})$ against a $(1-1/e)$-approximation with only one gradient inquiry for each local objective function per step. Finally, various experimental results confirm the effectiveness of the proposed methods.

preprint2022arXiv

MNL-Bandits under Inventory and Limited Switches Constraints

Optimizing the assortment of products to display to customers is a key to increasing revenue for both offline and online retailers. To trade-off between exploring customers' preference and exploiting customers' choices learned from data, in this paper, by adopting the Multi-Nomial Logit (MNL) choice model to capture customers' choices over products, we study the problem of optimizing assortments over a planning horizon $T$ for maximizing the profit of the retailer. To make the problem setting more practical, we consider both the inventory constraint and the limited switches constraint, where the retailer cannot use up the resource inventory before time $T$ and is forbidden to switch the assortment shown to customers too many times. Such a setting suits the case when an online retailer wants to dynamically optimize the assortment selection for a population of customers. We develop an efficient UCB-like algorithm to optimize the assortments while learning customers' choices from data. We prove that our algorithm can achieve a sub-linear regret bound $\tilde{O}\left(T^{1-α/2}\right)$ if $O(T^α)$ switches are allowed. %, and our regret bound is optimal with respect to $T$. Extensive numerical experiments show that our algorithm outperforms baselines and the gap between our algorithm's performance and the theoretical upper bound is small.

preprint2022arXiv

Online Learning for Non-monotone Submodular Maximization: From Full Information to Bandit Feedback

In this paper, we revisit the online non-monotone continuous DR-submodular maximization problem over a down-closed convex set, which finds wide real-world applications in the domain of machine learning, economics, and operations research. At first, we present the Meta-MFW algorithm achieving a $1/e$-regret of $O(\sqrt{T})$ at the cost of $T^{3/2}$ stochastic gradient evaluations per round. As far as we know, Meta-MFW is the first algorithm to obtain $1/e$-regret of $O(\sqrt{T})$ for the online non-monotone continuous DR-submodular maximization problem over a down-closed convex set. Furthermore, in sharp contrast with ODC algorithm \citep{thang2021online}, Meta-MFW relies on the simple online linear oracle without discretization, lifting, or rounding operations. Considering the practical restrictions, we then propose the Mono-MFW algorithm, which reduces the per-function stochastic gradient evaluations from $T^{3/2}$ to 1 and achieves a $1/e$-regret bound of $O(T^{4/5})$. Next, we extend Mono-MFW to the bandit setting and propose the Bandit-MFW algorithm which attains a $1/e$-regret bound of $O(T^{8/9})$. To the best of our knowledge, Mono-MFW and Bandit-MFW are the first sublinear-regret algorithms to explore the one-shot and bandit setting for online non-monotone continuous DR-submodular maximization problem over a down-closed convex set, respectively. Finally, we conduct numerical experiments on both synthetic and real-world datasets to verify the effectiveness of our methods.

preprint2022arXiv

Stochastic Continuous Submodular Maximization: Boosting via Non-oblivious Function

In this paper, we revisit Stochastic Continuous Submodular Maximization in both offline and online settings, which can benefit wide applications in machine learning and operations research areas. We present a boosting framework covering gradient ascent and online gradient ascent. The fundamental ingredient of our methods is a novel non-oblivious function $F$ derived from a factor-revealing optimization problem, whose any stationary point provides a $(1-e^{-γ})$-approximation to the global maximum of the $γ$-weakly DR-submodular objective function $f\in C^{1,1}_L(\mathcal{X})$. Under the offline scenario, we propose a boosting gradient ascent method achieving $(1-e^{-γ}-ε^{2})$-approximation after $O(1/ε^2)$ iterations, which improves the $(\frac{γ^2}{1+γ^2})$ approximation ratio of the classical gradient ascent algorithm. In the online setting, for the first time we consider the adversarial delays for stochastic gradient feedback, under which we propose a boosting online gradient algorithm with the same non-oblivious function $F$. Meanwhile, we verify that this boosting online algorithm achieves a regret of $O(\sqrt{D})$ against a $(1-e^{-γ})$-approximation to the best feasible solution in hindsight, where $D$ is the sum of delays of gradient feedback. To the best of our knowledge, this is the first result to obtain $O(\sqrt{T})$ regret against a $(1-e^{-γ})$-approximation with $O(1)$ gradient inquiry at each time step, when no delay exists, i.e., $D=T$. Finally, numerical experiments demonstrate the effectiveness of our boosting methods.

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