Linfeng Liu

Gabriel Appleby, Linfeng Liu, Li-Ping Liu

Spatial interpolation is a class of estimation problems where locations with known values are used to estimate values at other locations, with an emphasis on harnessing spatial locality and trends. Traditional Kriging methods have strong Gaussian assumptions, and as a result, often fail to capture complexities within the data. Inspired by the recent progress of graph neural networks, we introduce Kriging Convolutional Networks (KCN), a method of combining the advantages of Graph Convolutional Networks (GCN) and Kriging. Compared to standard GCNs, KCNs make direct use of neighboring observations when generating predictions. KCNs also contain the Kriging method as a specific configuration. We further improve the model's performance by adding attention. Empirically, we show that this model outperforms GCNs and Kriging in several applications. The implementation of KCN using PyTorch is publicized at the GitHub repository: https://github.com/tufts-ml/kcn-torch.

Linfeng Liu, Xu Han, Dawei Zhou et al.

Subgraph similarity search, one of the core problems in graph search, concerns whether a target graph approximately contains a query graph. The problem is recently touched by neural methods. However, current neural methods do not consider pruning the target graph, though pruning is critically important in traditional calculations of subgraph similarities. One obstacle to applying pruning in neural methods is {the discrete property of pruning}. In this work, we convert graph pruning to a problem of node relabeling and then relax it to a differentiable problem. Based on this idea, we further design a novel neural network to approximate a type of subgraph distance: the subgraph edit distance (SED). {In particular, we construct the pruning component using a neural structure, and the entire model can be optimized end-to-end.} In the design of the model, we propose an attention mechanism to leverage the information about the query graph and guide the pruning of the target graph. Moreover, we develop a multi-head pruning strategy such that the model can better explore multiple ways of pruning the target graph. The proposed model establishes new state-of-the-art results across seven benchmark datasets. Extensive analysis of the model indicates that the proposed model can reasonably prune the target graph for SED computation. The implementation of our algorithm is released at our Github repo: https://github.com/tufts-ml/Prune4SED.

Linfeng Liu, Siyu Liu, Lu Zhang et al.

Accurate medical classification requires a large number of multi-modal data, and in many cases, different feature types. Previous studies have shown promising results when using multi-modal data, outperforming single-modality models when classifying diseases such as Alzheimer's Disease (AD). However, those models are usually not flexible enough to handle missing modalities. Currently, the most common workaround is discarding samples with missing modalities which leads to considerable data under-utilization. Adding to the fact that labeled medical images are already scarce, the performance of data-driven methods like deep learning can be severely hampered. Therefore, a multi-modal method that can handle missing data in various clinical settings is highly desirable. In this paper, we present Multi-Modal Mixing Transformer (3MAT), a disease classification transformer that not only leverages multi-modal data but also handles missing data scenarios. In this work, we test 3MT for AD and Cognitively normal (CN) classification and mild cognitive impairment (MCI) conversion prediction to progressive MCI (pMCI) or stable MCI (sMCI) using clinical and neuroimaging data. The model uses a novel Cascaded Modality Transformer architecture with cross-attention to incorporate multi-modal information for more informed predictions. We propose a novel modality dropout mechanism to ensure an unprecedented level of modality independence and robustness to handle missing data scenarios. The result is a versatile network that enables the mixing of arbitrary numbers of modalities with different feature types and also ensures full data utilization missing data scenarios. The model is trained and evaluated on the ADNI dataset with the SOTRA performance and further evaluated with the AIBL dataset with missing data.

Linfeng Liu, Junyan Lyu, Siyu Liu et al.

The prediction of mild cognitive impairment (MCI) conversion to Alzheimer's disease (AD) is important for early treatment to prevent or slow the progression of AD. To accurately predict the MCI conversion to stable MCI or progressive MCI, we propose Triformer, a novel transformer-based framework with three specialized transformers to incorporate multi-model data. Triformer uses I) an image transformer to extract multi-view image features from medical scans, II) a clinical transformer to embed and correlate multi-modal clinical data, and III) a modality fusion transformer that produces an accurate prediction based on fusing the outputs from the image and clinical transformers. Triformer is evaluated on the Alzheimer's Disease Neuroimaging Initiative (ANDI)1 and ADNI2 datasets and outperforms previous state-of-the-art single and multi-modal methods.

Linfeng Liu, Hongqiu Wu, Hai Zhao

This paper studies Chinese Spelling Correction (CSC), which aims to detect and correct the potential spelling errors in a given sentence. Current state-of-the-art methods regard CSC as a sequence tagging task and fine-tune BERT-based models on sentence pairs. However, we note a critical flaw in the process of tagging one character to another, that the correction is excessively conditioned on the error. This is opposite from human mindset, where individuals rephrase the complete sentence based on its semantics, rather than solely on the error patterns memorized before. Such a counter-intuitive learning process results in the bottleneck of generalizability and transferability of machine spelling correction. To address this, we propose Rephrasing Language Model (ReLM), where the model is trained to rephrase the entire sentence by infilling additional slots, instead of character-to-character tagging. This novel training paradigm achieves the new state-of-the-art results across fine-tuned and zero-shot CSC benchmarks, outperforming previous counterparts by a large margin. Our method also learns transferable language representation when CSC is jointly trained with other tasks.

Siyu Liu, Linfeng Liu, Xuan Vinh et al.

In medical image analysis, the subtle visual characteristics of many diseases are challenging to discern, particularly due to the lack of paired data. For example, in mild Alzheimer's Disease (AD), brain tissue atrophy can be difficult to observe from pure imaging data, especially without paired AD and Cognitively Normal ( CN ) data for comparison. This work presents Disease Discovery GAN ( DiDiGAN), a weakly-supervised style-based framework for discovering and visualising subtle disease features. DiDiGAN learns a disease manifold of AD and CN visual characteristics, and the style codes sampled from this manifold are imposed onto an anatomical structural "blueprint" to synthesise paired AD and CN magnetic resonance images (MRIs). To suppress non-disease-related variations between the generated AD and CN pairs, DiDiGAN leverages a structural constraint with cycle consistency and anti-aliasing to enforce anatomical correspondence. When tested on the Alzheimer's Disease Neuroimaging Initiative ( ADNI) dataset, DiDiGAN showed key AD characteristics (reduced hippocampal volume, ventricular enlargement, and atrophy of cortical structures) through synthesising paired AD and CN scans. The qualitative results were backed up by automated brain volume analysis, where systematic pair-wise reductions in brain tissue structures were also measured

Hongqiu Wu, Linfeng Liu, Hai Zhao et al.

Beyond the great cognitive powers showcased by language models, it is crucial to scrutinize whether their reasoning capabilities stem from strong generalization or merely exposure to relevant data. As opposed to constructing increasingly complex logic, this paper probes into the boolean logic, the root capability of a logical reasoner. We find that any pre-trained language models even including large language models only behave like a random selector in the face of multi-nested boolean logic, a task that humans can handle with ease. To empower language models with this fundamental capability, this paper proposes a new self-supervised learning method \textit{Curriculum Logical Reasoning} (\textsc{Clr}), where we augment the training data with nested boolean logic chain step-by-step, and program the training from simpler logical patterns gradually to harder ones. This new training paradigm allows language models to effectively generalize to much harder and longer-hop logic, which can hardly be learned through naive training. Furthermore, we show that boolean logic is a great foundation for improving the subsequent general logical tasks.

Fabian Paischer, Liu Yang, Linfeng Liu et al.

In sequential recommendation, models recommend items based on user's interaction history. To this end, current models usually incorporate information such as item descriptions and user intent or preferences. User preferences are usually not explicitly given in open-source datasets, and thus need to be approximated, for example via large language models (LLMs). Current approaches leverage approximated user preferences only during training and rely solely on the past interaction history for recommendations, limiting their ability to dynamically adapt to changing preferences, potentially reinforcing echo chambers. To address this issue, we propose a new paradigm, namely preference discerning, which explicitly conditions a generative recommendation model on user preferences in natural language within its context. To evaluate preference discerning, we introduce a novel benchmark that provides a holistic evaluation across various scenarios, including preference steering and sentiment following. Upon evaluating current state-of-the-art methods on our benchmark, we discover that their ability to dynamically adapt to evolving user preferences is limited. To address this, we propose a new method named Mender ($\textbf{M}$ultimodal Prefer$\textbf{en}$ce $\textbf{D}$iscern$\textbf{er}$), which achieves state-of-the-art performance in our benchmark. Our results show that Mender effectively adapts its recommendation guided by human preferences, even if not observed during training, paving the way toward more flexible recommendation models.

Ran Jiang, Sanfeng Zhang, Linfeng Liu et al.

To enhance the security of text CAPTCHAs, various methods have been employed, such as adding the interference lines on the text, randomly distorting the characters, and overlapping multiple characters. These methods partly increase the difficulty of automated segmentation and recognition attacks. However, facing the rapid development of the end-to-end breaking algorithms, their security has been greatly weakened. The diffusion model is a novel image generation model that can generate the text images with deep fusion of characters and background images. In this paper, an image-click CAPTCHA scheme called Diff-CAPTCHA is proposed based on denoising diffusion models. The background image and characters of the CAPTCHA are treated as a whole to guide the generation process of a diffusion model, thus weakening the character features available for machine learning, enhancing the diversity of character features in the CAPTCHA, and increasing the difficulty of breaking algorithms. To evaluate the security of Diff-CAPTCHA, this paper develops several attack methods, including end-to-end attacks based on Faster R-CNN and two-stage attacks, and Diff-CAPTCHA is compared with three baseline schemes, including commercial CAPTCHA scheme and security-enhanced CAPTCHA scheme based on style transfer. The experimental results show that diffusion models can effectively enhance CAPTCHA security while maintaining good usability in human testing.

Linfeng Liu, Michael C. Hughes, Soha Hassoun et al.

Recent works leveraging Graph Neural Networks to approach graph matching tasks have shown promising results. Recent progress in learning discrete distributions poses new opportunities for learning graph matching models. In this work, we propose a new model, Stochastic Iterative Graph MAtching (SIGMA), to address the graph matching problem. Our model defines a distribution of matchings for a graph pair so the model can explore a wide range of possible matchings. We further introduce a novel multi-step matching procedure, which learns how to refine a graph pair's matching results incrementally. The model also includes dummy nodes so that the model does not have to find matchings for nodes without correspondence. We fit this model to data via scalable stochastic optimization. We conduct extensive experiments across synthetic graph datasets as well as biochemistry and computer vision applications. Across all tasks, our results show that SIGMA can produce significantly improved graph matching results compared to state-of-the-art models. Ablation studies verify that each of our components (stochastic training, iterative matching, and dummy nodes) offers noticeable improvement.

Linfeng Liu, Michael C. Hughes, Li-Ping Liu

We propose a new model, the Neighbor Mixture Model (NMM), for modeling node labels in a graph. This model aims to capture correlations between the labels of nodes in a local neighborhood. We carefully design the model so it could be an alternative to a Markov Random Field but with more affordable computations. In particular, drawing samples and evaluating marginal probabilities of single labels can be done in linear time. To scale computations to large graphs, we devise a variational approximation without introducing extra parameters. We further use graph neural networks (GNNs) to parameterize the NMM, which reduces the number of learnable parameters while allowing expressive representation learning. The proposed model can be either fit directly to large observed graphs or used to enable scalable inference that preserves correlations for other distributions such as deep generative graph models. Across a diverse set of node classification, image denoising, and link prediction tasks, we show our proposed NMM advances the state-of-the-art in modeling real-world labeled graphs.

Linfeng Liu, Liping Liu

Inference for GP models with non-Gaussian noises is computationally expensive when dealing with large datasets. Many recent inference methods approximate the posterior distribution with a simpler distribution defined on a small number of inducing points. The inference is accurate only when data points have strong correlation with these inducing points. In this paper, we consider the inference problem in a different direction: GP function values in the posterior are mostly correlated in short distance. We construct a variational distribution such that the inference for a data point considers only its neighborhood. With this construction, the variational lower bound is highly decomposible, hence we can run stochastic optimization with very small batches. We then train Graph Convolutional Networks as a reusable model to identify variational parameters for each data point. Model reuse greatly reduces the number of parameters and the number of iterations needed in optimization. The proposed method significantly speeds up the inference and often gets more accurate results than previous methods.