Junfan Li

Langzhang Liang, Ming Yang, Yi Feng et al.

Protein sequence generation for engineering requires samples that are biophysically plausible and, when targeting a family/domain, remain recognizable members while exploring within-family diversity. Current discrete generative models typically start from uniform or masked-token noise, which discards strong position-specific constraints induced by evolution and forces the model to reconstruct conserved residues from scratch, leading to weak family control and low plausibility. We propose \emph{LineageFlow}, a Dirichlet flow-matching model that initializes generation from lineage priors derived from ancestral sequence reconstruction, turning generation into structured mutation from an evolved scaffold. Across diverse protein families, LineageFlow achieves family validity close to held-out natural sequences and improves predicted structural confidence over uniform-/mask-initialized baselines while maintaining substantial novelty and diversity. Finally, we introduce \emph{rerouting}, a single intermediate-time mutate--select--amplify intervention that enables objective-guided sampling without per-step predictor guidance and yields further gains in plausibility, including a zero-shot enzyme generation case study. Code is available at https://github.com/Jinx-byebye/LineageFlow.

Junfan Li, Shizhong Liao

In this paper, we improve the kernel alignment regret bound for online kernel learning in the regime of the Hinge loss function. Previous algorithm achieves a regret of $O((\mathcal{A}_TT\ln{T})^{\frac{1}{4}})$ at a computational complexity (space and per-round time) of $O(\sqrt{\mathcal{A}_TT\ln{T}})$, where $\mathcal{A}_T$ is called \textit{kernel alignment}. We propose an algorithm whose regret bound and computational complexity are better than previous results. Our results depend on the decay rate of eigenvalues of the kernel matrix. If the eigenvalues of the kernel matrix decay exponentially, then our algorithm enjoys a regret of $O(\sqrt{\mathcal{A}_T})$ at a computational complexity of $O(\ln^2{T})$. Otherwise, our algorithm enjoys a regret of $O((\mathcal{A}_TT)^{\frac{1}{4}})$ at a computational complexity of $O(\sqrt{\mathcal{A}_TT})$. We extend our algorithm to batch learning and obtain a $O(\frac{1}{T}\sqrt{\mathbb{E}[\mathcal{A}_T]})$ excess risk bound which improves the previous $O(1/\sqrt{T})$ bound.

Zongbo Han, Jialong Yang, Guangyu Wang et al.

Vision-language foundation models (VLMs), such as CLIP, exhibit remarkable performance across a wide range of tasks. However, deploying these models can be unreliable when significant distribution gaps exist between training and test data, while fine-tuning for diverse scenarios is often costly. Cache-based test-time adapters offer an efficient alternative by storing representative test samples to guide subsequent classifications. Yet, these methods typically employ naive cache management with limited capacity, leading to severe catastrophic forgetting when samples are inevitably dropped during updates. In this paper, we propose DOTA (DistributiOnal Test-time Adaptation), a simple yet effective method addressing this limitation. Crucially, instead of merely memorizing individual test samples, DOTA continuously estimates the underlying distribution of the test data stream. Test-time posterior probabilities are then computed using these dynamically estimated distributions via Bayes' theorem for adaptation. This distribution-centric approach enables the model to continually learn and adapt to the deployment environment. Extensive experiments validate that DOTA significantly mitigates forgetting and achieves state-of-the-art performance compared to existing methods.

Junfan Li, Shizhong Liao

The trade-off between regret and computational cost is a fundamental problem for online kernel regression, and previous algorithms worked on the trade-off can not keep optimal regret bounds at a sublinear computational complexity. In this paper, we propose two new algorithms, AOGD-ALD and NONS-ALD, which can keep nearly optimal regret bounds at a sublinear computational complexity, and give sufficient conditions under which our algorithms work. Both algorithms dynamically maintain a group of nearly orthogonal basis used to approximate the kernel mapping, and keep nearly optimal regret bounds by controlling the approximate error. The number of basis depends on the approximate error and the decay rate of eigenvalues of the kernel matrix. If the eigenvalues decay exponentially, then AOGD-ALD and NONS-ALD separately achieves a regret of $O(\sqrt{L(f)})$ and $O(\mathrm{d}_{\mathrm{eff}}(μ)\ln{T})$ at a computational complexity in $O(\ln^2{T})$. If the eigenvalues decay polynomially with degree $p\geq 1$, then our algorithms keep the same regret bounds at a computational complexity in $o(T)$ in the case of $p>4$ and $p\geq 10$, respectively. $L(f)$ is the cumulative losses of $f$ and $\mathrm{d}_{\mathrm{eff}}(μ)$ is the effective dimension of the problem. The two regret bounds are nearly optimal and are not comparable.

Junfan Li, Shizhong Liao

In this paper, we improve the regret bound for online kernel selection under bandit feedback. Previous algorithm enjoys a $O((\Vert f\Vert^2_{\mathcal{H}_i}+1)K^{\frac{1}{3}}T^{\frac{2}{3}})$ expected bound for Lipschitz loss functions. We prove two types of regret bounds improving the previous bound. For smooth loss functions, we propose an algorithm with a $O(U^{\frac{2}{3}}K^{-\frac{1}{3}}(\sum^K_{i=1}L_T(f^\ast_i))^{\frac{2}{3}})$ expected bound where $L_T(f^\ast_i)$ is the cumulative losses of optimal hypothesis in $\mathbb{H}_{i}=\{f\in\mathcal{H}_i:\Vert f\Vert_{\mathcal{H}_i}\leq U\}$. The data-dependent bound keeps the previous worst-case bound and is smaller if most of candidate kernels match well with the data. For Lipschitz loss functions, we propose an algorithm with a $O(U\sqrt{KT}\ln^{\frac{2}{3}}{T})$ expected bound asymptotically improving the previous bound. We apply the two algorithms to online kernel selection with time constraint and prove new regret bounds matching or improving the previous $O(\sqrt{T\ln{K}} +\Vert f\Vert^2_{\mathcal{H}_i}\max\{\sqrt{T},\frac{T}{\sqrt{\mathcal{R}}}\})$ expected bound where $\mathcal{R}$ is the time budget. Finally, we empirically verify our algorithms on online regression and classification tasks.

Yukun Zhang, Guanzhong Chen, Zenglin Xu et al.

Cardiovascular diseases (CVDs) are currently the leading cause of death worldwide, highlighting the critical need for early diagnosis and treatment. Machine learning (ML) methods can help diagnose CVDs early, but their performance relies on access to substantial data with high quality. However, the sensitive nature of healthcare data often restricts individual clinical institutions from sharing data to train sufficiently generalized and unbiased ML models. Federated Learning (FL) is an emerging approach, which offers a promising solution by enabling collaborative model training across multiple participants without compromising the privacy of the individual data owners. However, to the best of our knowledge, there has been limited prior research applying FL to the cardiovascular disease domain. Moreover, existing FL benchmarks and datasets are typically simulated and may fall short of replicating the complexity of natural heterogeneity found in realistic datasets that challenges current FL algorithms. To address these gaps, this paper presents the first real-world FL benchmark for cardiovascular disease detection, named FedCVD. This benchmark comprises two major tasks: electrocardiogram (ECG) classification and echocardiogram (ECHO) segmentation, based on naturally scattered datasets constructed from the CVD data of seven institutions. Our extensive experiments on these datasets reveal that FL faces new challenges with real-world non-IID and long-tail data. The code and datasets of FedCVD are available https://github.com/SMILELab-FL/FedCVD.

Zheshun Wu, Junfan Li, Zenglin Xu et al.

Machine learning techniques have garnered great interest in designing communication systems owing to their capacity in tackling with channel uncertainty. To provide theoretical guarantees for learning-based communication systems, some recent works analyze generalization bounds for devised methods based on the assumption of Independently and Identically Distributed (I.I.D.) channels, a condition rarely met in practical scenarios. In this paper, we drop the I.I.D. channel assumption and study an online optimization problem of learning to communicate over time-correlated channels. To address this issue, we further focus on two specific tasks: optimizing channel decoders for time-correlated fading channels and selecting optimal codebooks for time-correlated additive noise channels. For utilizing temporal dependence of considered channels to better learn communication systems, we develop two online optimization algorithms based on the optimistic online mirror descent framework. Furthermore, we provide theoretical guarantees for proposed algorithms via deriving sub-linear regret bound on the expected error probability of learned systems. Extensive simulation experiments have been conducted to validate that our presented approaches can leverage the channel correlation to achieve a lower average symbol error rate compared to baseline methods, consistent with our theoretical findings.

Junfan Li, Shizhong Liao, Zenglin Xu et al.

In this paper, we study the problem of online sparse linear regression (OSLR) where the algorithms are restricted to accessing only $k$ out of $d$ attributes per instance for prediction, which was proved to be NP-hard. Previous work gave polynomial-time algorithms assuming the data matrix satisfies the linear independence of features, the compatibility condition, or the restricted isometry property. We introduce a new polynomial-time algorithm, which significantly improves previous regret bounds (Ito et al., 2017) under the compatibility condition that is weaker than the other two assumptions. The improvements benefit from a tighter convergence rate of the $\ell_1$-norm error of our estimators. Our algorithm leverages the well-studied Dantzig Selector, but importantly with several novel techniques, including an algorithm-dependent sampling scheme for estimating the covariance matrix, an adaptive parameter tuning scheme, and a batching online Newton step with careful initializations. We also give novel and non-trivial analyses, including an induction method for analyzing the $\ell_1$-norm error, careful analyses on the covariance of non-independent random variables, and a decomposition on the regret. We further extend our algorithm to OSLR with additional observations where the algorithms can observe additional $k_0$ attributes after each prediction, and improve previous regret bounds (Kale et al., 2017; Ito et al., 2017).

Junfan Li, Shizhong Liao

Online kernel selection is a fundamental problem of online kernel methods.In this paper,we study online kernel selection with memory constraint in which the memory of kernel selection and online prediction procedures is limited to a fixed budget. An essential question is what is the intrinsic relationship among online learnability, memory constraint, and data complexity? To answer the question,it is necessary to show the trade-offs between regret and memory constraint.Previous work gives a worst-case lower bound depending on the data size,and shows learning is impossible within a small memory constraint.In contrast, we present distinct results by offering data-dependent upper bounds that rely on two data complexities:kernel alignment and the cumulative losses of competitive hypothesis.We propose an algorithmic framework giving data-dependent upper bounds for two types of loss functions.For the hinge loss function,our algorithm achieves an expected upper bound depending on kernel alignment.For smooth loss functions,our algorithm achieves a high-probability upper bound depending on the cumulative losses of competitive hypothesis.We also prove a matching lower bound for smooth loss functions.Our results show that if the two data complexities are sub-linear,then learning is possible within a small memory constraint.Our algorithmic framework depends on a new buffer maintaining framework and a reduction from online kernel selection to prediction with expert advice. Finally,we empirically verify the prediction performance of our algorithms on benchmark datasets.

Zheshun Wu, Zenglin Xu, Dun Zeng et al.

With the proliferation of intelligent mobile devices in wireless device-to-device (D2D) networks, decentralized federated learning (DFL) has attracted significant interest. Compared to centralized federated learning (CFL), DFL mitigates the risk of central server failures due to communication bottlenecks. However, DFL faces several challenges, such as the severe heterogeneity of data distributions in diverse environments, and the transmission outages and package errors caused by the adoption of the User Datagram Protocol (UDP) in D2D networks. These challenges often degrade the convergence of training DFL models. To address these challenges, we conduct a thorough theoretical convergence analysis for DFL and derive a convergence bound. By defining a novel quantity named unreliable links-aware neighborhood discrepancy in this convergence bound, we formulate a tractable optimization objective, and develop a novel Topology Learning method considering the Representation Discrepancy and Unreliable Links in DFL, named ToLRDUL. Intensive experiments under both feature skew and label skew settings have validated the effectiveness of our proposed method, demonstrating improved convergence speed and test accuracy, consistent with our theoretical findings.

Junfan Li, Zheshun Wu, Zenglin Xu et al.

We consider online model selection with decentralized data over $M$ clients, and study the necessity of collaboration among clients. Previous work proposed various federated algorithms without demonstrating their necessity,while we answer the question from a novel perspective of computational constraints. We prove lower bounds on the regret, and propose a federated algorithm and analyze the upper bound.Our results show (i) collaboration is unnecessary in the absence of computational constraints on clients; (ii) collaboration is necessary if the computational cost on each client is limited to $o(K)$, where $K$ is the number of candidate hypothesis spaces. We clarify the unnecessary nature of collaboration in previous federated algorithms for distributed online multi-kernel learning,and improve the regret bounds at a smaller computational and communication cost. Our algorithm relies on three new techniques including an improved Bernstein's inequality for martingale, a federated online mirror descent framework, and decoupling model selection and prediction, which might be of independent interest.

Yun Liao, Junfan Li, Shizhong Liao et al.

In this paper, we study the mistake bound of online kernel learning on a budget. We propose a new budgeted online kernel learning model, called Ahpatron, which significantly improves the mistake bound of previous work and resolves the open problem posed by Dekel, Shalev-Shwartz, and Singer (2005). We first present an aggressive variant of Perceptron, named AVP, a model without budget, which uses an active updating rule. Then we design a new budget maintenance mechanism, which removes a half of examples,and projects the removed examples onto a hypothesis space spanned by the remaining examples. Ahpatron adopts the above mechanism to approximate AVP. Theoretical analyses prove that Ahpatron has tighter mistake bounds, and experimental results show that Ahpatron outperforms the state-of-the-art algorithms on the same or a smaller budget.

Mingxi Zou, Jiaxiang Chen, Junfan Li et al.

Preference-based alignment methods (e.g., RLHF, DPO) typically optimize a single scalar objective, implicitly averaging over heterogeneous human preferences. In practice, systematic annotator and user-group disagreement makes mean-reward maximization brittle and susceptible to proxy over-optimization. We propose **Disagreement-Aware Alignment via Risk-Constrained Decoding (DARC)**, a retraining-free inference-time method that frames response selection as distributionally robust, risk-sensitive decision making. Given multiple preference samples or scalable disagreement proxies, DARC reranks candidates by maximizing a *KL-robust (entropic)* satisfaction objective, and provides simple deployment controls that cap or penalize the corresponding entropic risk premium relative to the mean, enabling explicit risk budgets without retraining. We provide theoretical characterization linking this decoding rule to principled pessimism and KL-based distributionally robust optimization. Experiments on alignment benchmarks show that DARC reduces disagreement and tail risk while maintaining competitive average quality under noisy, heterogeneous feedback.