Yingyu Lin

Yingyu Lin, Yi-An Ma, Yu-Xiang Wang et al.

Posterior sampling, i.e., exponential mechanism to sample from the posterior distribution, provides $\varepsilon$-pure differential privacy (DP) guarantees and does not suffer from potentially unbounded privacy breach introduced by $(\varepsilon,δ)$-approximate DP. In practice, however, one needs to apply approximate sampling methods such as Markov chain Monte Carlo (MCMC), thus re-introducing the unappealing $δ$-approximation error into the privacy guarantees. To bridge this gap, we propose the Approximate SAample Perturbation (abbr. ASAP) algorithm which perturbs an MCMC sample with noise proportional to its Wasserstein-infinity ($W_\infty$) distance from a reference distribution that satisfies pure DP or pure Gaussian DP (i.e., $δ=0$). We then leverage a Metropolis-Hastings algorithm to generate the sample and prove that the algorithm converges in $W_\infty$ distance. We show that by combining our new techniques with a localization step, we obtain the first nearly linear-time algorithm that achieves the optimal rates in the DP-ERM problem with strongly convex and smooth losses.

Xunpeng Huang, Yingyu Lin, Nikki Lijing Kuang et al.

Continuous diffusion models have demonstrated remarkable performance in data generation across various domains, yet their efficiency remains constrained by two critical limitations: (1) the local adjacency structure of the forward Markov process, which restricts long-range transitions in the data space, and (2) inherent biases introduced during the simulation of time-inhomogeneous reverse denoising processes. To address these challenges, we propose Quantized Transition Diffusion (QTD), a novel approach that integrates data quantization with discrete diffusion dynamics. Our method first transforms the continuous data distribution $p_*$ into a discrete one $q_*$ via histogram approximation and binary encoding, enabling efficient representation in a structured discrete latent space. We then design a continuous-time Markov chain (CTMC) with Hamming distance-based transitions as the forward process, which inherently supports long-range movements in the original data space. For reverse-time sampling, we introduce a \textit{truncated uniformization} technique to simulate the reverse CTMC, which can provably provide unbiased generation from $q_*$ under minimal score assumptions. Through a novel KL dynamic analysis of the reverse CTMC, we prove that QTD can generate samples with $O(d\ln^2(d/ε))$ score evaluations in expectation to approximate the $d$--dimensional target distribution $p_*$ within an $ε$ error tolerance. Our method not only establishes state-of-the-art inference efficiency but also advances the theoretical foundations of diffusion-based generative modeling by unifying discrete and continuous diffusion paradigms.

Yingyu Lin, Erchi Wang, Yi-An Ma et al.

We propose a framework to convert $(\varepsilon, δ)$-approximate Differential Privacy (DP) mechanisms into $(\varepsilon', 0)$-pure DP mechanisms under certain conditions, a process we call ``purification.'' This algorithmic technique leverages randomized post-processing with calibrated noise to eliminate the $δ$ parameter while achieving near-optimal privacy-utility tradeoff for pure DP. It enables a new design strategy for pure DP algorithms: first run an approximate DP algorithm with certain conditions, and then purify. This approach allows one to leverage techniques such as strong composition and propose-test-release that require $δ>0$ in designing pure-DP methods with $δ=0$. We apply this framework in various settings, including Differentially Private Empirical Risk Minimization (DP-ERM), stability-based release, and query release tasks. To the best of our knowledge, this is the first work with a statistically and computationally efficient reduction from approximate DP to pure DP. Finally, we illustrate the use of this reduction for proving lower bounds under approximate DP constraints with explicit dependence in $δ$, avoiding the sophisticated fingerprinting code construction.

Huiwei Zhou, Zhuang Liu, Shixian Ning et al.

Automatically extracting Protein-Protein Interactions (PPI) from biomedical literature provides additional support for precision medicine efforts. This paper proposes a novel memory network-based model (MNM) for PPI extraction, which leverages prior knowledge about protein-protein pairs with memory networks. The proposed MNM captures important context clues related to knowledge representations learned from knowledge bases. Both entity embeddings and relation embeddings of prior knowledge are effective in improving the PPI extraction model, leading to a new state-of-the-art performance on the BioCreative VI PPI dataset. The paper also shows that multiple computational layers over an external memory are superior to long short-term memory networks with the local memories.

Huiwei Zhou, Zhuang Liu1, Shixian Ning et al.

Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot make full use of the prior knowledge in knowledge bases (KB). KBs contain huge amounts of structured information about entities and relationships, therefore plays a pivotal role in PPI extraction. This paper proposes a knowledge-aware attention network (KAN) to fuse prior knowledge about protein-protein pairs and context information for PPI extraction. The proposed model first adopts a diagonal-disabled multi-head attention mechanism to encode context sequence along with knowledge representations learned from KB. Then a novel multi-dimensional attention mechanism is used to select the features that can best describe the encoded context. Experiment results on the BioCreative VI PPI dataset show that the proposed approach could acquire knowledge-aware dependencies between different words in a sequence and lead to a new state-of-the-art performance.

Huiwei Zhou, Shixian Ning, Yunlong Yang et al.

Chemical-disease relation (CDR) extraction is significantly important to various areas of biomedical research and health care. Nowadays, many large-scale biomedical knowledge bases (KBs) containing triples about entity pairs and their relations have been built. KBs are important resources for biomedical relation extraction. However, previous research pays little attention to prior knowledge. In addition, the dependency tree contains important syntactic and semantic information, which helps to improve relation extraction. So how to effectively use it is also worth studying. In this paper, we propose a novel convolutional attention network (CAN) for CDR extraction. Firstly, we extract the shortest dependency path (SDP) between chemical and disease pairs in a sentence, which includes a sequence of words, dependency directions, and dependency relation tags. Then the convolution operations are performed on the SDP to produce deep semantic dependency features. After that, an attention mechanism is employed to learn the importance/weight of each semantic dependency vector related to knowledge representations learned from KBs. Finally, in order to combine dependency information and prior knowledge, the concatenation of weighted semantic dependency representations and knowledge representations is fed to the softmax layer for classification. Experiments on the BioCreative V CDR dataset show that our method achieves comparable performance with the state-of-the-art systems, and both dependency information and prior knowledge play important roles in CDR extraction task.

Huiwei Zhou, Yunlong Yang, Shixian Ning et al.

Automatically extracting the relationships between chemicals and diseases is significantly important to various areas of biomedical research and health care. Biomedical experts have built many large-scale knowledge bases (KBs) to advance the development of biomedical research. KBs contain huge amounts of structured information about entities and relationships, therefore plays a pivotal role in chemical-disease relation (CDR) extraction. However, previous researches pay less attention to the prior knowledge existing in KBs. This paper proposes a neural network-based attention model (NAM) for CDR extraction, which makes full use of context information in documents and prior knowledge in KBs. For a pair of entities in a document, an attention mechanism is employed to select important context words with respect to the relation representations learned from KBs. Experiments on the BioCreative V CDR dataset show that combining context and knowledge representations through the attention mechanism, could significantly improve the CDR extraction performance while achieve comparable results with state-of-the-art systems.