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We propose a method to represent bipartite networks using graph embeddings tailored to tackle the challenges of studying ecological networks, such as the ones linking plants and pollinators, where many covariates need to be accounted for, in particular to control for sampling bias. We adapt the variational graph auto-encoder approach to the bipartite case, which enables us to generate embeddings in a latent space where the two sets of nodes are positioned based on their probability of connection. We translate the fairness framework commonly considered in sociology in order to address sampling bias in ecology. By incorporating the Hilbert-Schmidt independence criterion (HSIC) as an additional penalty term in the loss we optimize, we ensure that the structure of the latent space is independent of continuous variables, which are related to the sampling process. Finally, we show how our approach can change our understanding of ecological networks when applied to the Spipoll data set, a citizen science monitoring program of plant-pollinator interactions to which many observers contribute, making it prone to sampling bias.

The approximate nearest neighbor search (ANNS) is a fundamental and essential component in data mining and information retrieval, with graph-based methodologies demonstrating superior performance compared to alternative approaches. Extensive research efforts have been dedicated to improving search efficiency by developing various graph-based indices, such as HNSW (Hierarchical Navigable Small World). However, the performance of HNSW and most graph-based indices become unacceptable when faced with a large number of real-time deletions, insertions, and updates. Furthermore, during update operations, HNSW can result in some data points becoming unreachable, a situation we refer to as the `unreachable points phenomenon'. This phenomenon could significantly affect the search accuracy of the graph in certain situations. To address these issues, we present efficient measures to overcome the shortcomings of HNSW, specifically addressing poor performance over long periods of delete and update operations and resolving the issues caused by the unreachable points phenomenon. Our proposed MN-RU algorithm effectively improves update efficiency and suppresses the growth rate of unreachable points, ensuring better overall performance and maintaining the integrity of the graph. Our results demonstrate that our methods outperform existing approaches. Furthermore, since our methods are based on HNSW, they can be easily integrated with existing indices widely used in the industrial field, making them practical for future real-world applications. Code is available at \url{//github.com/xwt1/MN-RU.git}

A signed graph offers richer information than an unsigned graph, since it describes both collaborative and competitive relationships in social networks. In this paper, we study the opinion dynamics on a signed graph, based on the Friedkin-Johnsen model. We first interpret the equilibrium opinion in terms of a defined random walk on an augmented signed graph, by representing the equilibrium opinion of every node as a combination of all nodes' internal opinions, with the coefficient of the internal opinion for each node being the difference of two absorbing probabilities. We then quantify some relevant social phenomena and express them in terms of the $\ell_2$ norms of vectors. We also design a nearly-linear time signed Laplacian solver for assessing these quantities, by establishing a connection between the absorbing probability of random walks on a signed graph and that on an associated unsigned graph. We further study the opinion optimization problem by changing the initial opinions of a fixed number of nodes, which can be optimally solved in cubic time. We provide a nearly-linear time algorithm with error guarantee to approximately solve the problem. Finally, we execute extensive experiments on sixteen real-life signed networks, which show that both of our algorithms are effective and efficient, and are scalable to massive graphs with over 20 million nodes.

Anomaly synthesis strategies can effectively enhance unsupervised anomaly detection. However, existing strategies have limitations in the coverage and controllability of anomaly synthesis, particularly for weak defects that are very similar to normal regions. In this paper, we propose Global and Local Anomaly co-Synthesis Strategy (GLASS), a novel unified framework designed to synthesize a broader coverage of anomalies under the manifold and hypersphere distribution constraints of Global Anomaly Synthesis (GAS) at the feature level and Local Anomaly Synthesis (LAS) at the image level. Our method synthesizes near-in-distribution anomalies in a controllable way using Gaussian noise guided by gradient ascent and truncated projection. GLASS achieves state-of-the-art results on the MVTec AD (detection AUROC of 99.9\%), VisA, and MPDD datasets and excels in weak defect detection. The effectiveness and efficiency have been further validated in industrial applications for woven fabric defect detection. The code and dataset are available at: \url{//github.com/cqylunlun/GLASS}.

Recommendation systems capable of providing diverse sets of results are a focus of increasing importance, with motivations ranging from fairness to novelty and other aspects of optimizing user experience. One form of diversity of recent interest is calibration, the notion that personalized recommendations should reflect the full distribution of a user's interests, rather than a single predominant category -- for instance, a user who mainly reads entertainment news but also wants to keep up with news on the environment and the economy would prefer to see a mixture of these genres, not solely entertainment news. Existing work has formulated calibration as a subset selection problem; this line of work observes that the formulation requires the unrealistic assumption that all recommended items receive equal consideration from the user, but leaves as an open question the more realistic setting in which user attention decays as they move down the list of results. In this paper, we consider calibration with decaying user attention under two different models. In both models, there is a set of underlying genres that items can belong to. In the first setting, where items are represented by fine-grained mixtures of genre percentages, we provide a $(1-1/e)$-approximation algorithm by extending techniques for constrained submodular optimization. In the second setting, where items are coarsely binned into a single genre each, we surpass the $(1-1/e)$ barrier imposed by submodular maximization and give a $2/3$-approximate greedy algorithm. Our work thus addresses the problem of capturing ordering effects due to decaying attention, allowing for the extension of near-optimal calibration from recommendation sets to recommendation lists.

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

Beyond estimating parameters of interest from data, one of the key goals of statistical inference is to properly quantify uncertainty in these estimates. In Bayesian inference, this uncertainty is provided by the posterior distribution, the computation of which typically involves an intractable high-dimensional integral. Among available approximation methods, sampling-based approaches come with strong theoretical guarantees but scale poorly to large problems, while variational approaches scale well but offer few theoretical guarantees. In particular, variational methods are known to produce overconfident estimates of posterior uncertainty and are typically non-identifiable, with many latent variable configurations generating equivalent predictions. Here, we address these challenges by showing how diffusion-based models (DBMs), which have recently produced state-of-the-art performance in generative modeling tasks, can be repurposed for performing calibrated, identifiable Bayesian inference. By exploiting a previously established connection between the stochastic and probability flow ordinary differential equations (pfODEs) underlying DBMs, we derive a class of models, inflationary flows, that uniquely and deterministically map high-dimensional data to a lower-dimensional Gaussian distribution via ODE integration. This map is both invertible and neighborhood-preserving, with controllable numerical error, with the result that uncertainties in the data are correctly propagated to the latent space. We demonstrate how such maps can be learned via standard DBM training using a novel noise schedule and are effective at both preserving and reducing intrinsic data dimensionality. The result is a class of highly expressive generative models, uniquely defined on a low-dimensional latent space, that afford principled Bayesian inference.

This paper suggests a statistical framework for describing the relations between the physical and conceptual entities of a brain-like model. Features and concept instances are put into context, where the paper suggests that features may be the electrical wiring, although chemical connections are also possible. With this idea, the actual length of the connection is important, because it is related to firing rates and neuron synchronization, but the signal type is less important. The paper then suggests that concepts are neuron groups that link feature sets and concept instances are determined by chemical signals from those groups. Therefore, features become the static horizontal framework of the neural system and concepts are vertically interconnected combinations of these. With regards to functionality, the neuron is then considered to be functional and the more horizontal memory structures can be glial. This would also suggest that features can be distributed entities and not concentrated to a single area.

Aspect based sentiment analysis (ABSA) can provide more detailed information than general sentiment analysis, because it aims to predict the sentiment polarities of the given aspects or entities in text. We summarize previous approaches into two subtasks: aspect-category sentiment analysis (ACSA) and aspect-term sentiment analysis (ATSA). Most previous approaches employ long short-term memory and attention mechanisms to predict the sentiment polarity of the concerned targets, which are often complicated and need more training time. We propose a model based on convolutional neural networks and gating mechanisms, which is more accurate and efficient. First, the novel Gated Tanh-ReLU Units can selectively output the sentiment features according to the given aspect or entity. The architecture is much simpler than attention layer used in the existing models. Second, the computations of our model could be easily parallelized during training, because convolutional layers do not have time dependency as in LSTM layers, and gating units also work independently. The experiments on SemEval datasets demonstrate the efficiency and effectiveness of our models.

Multi-relation Question Answering is a challenging task, due to the requirement of elaborated analysis on questions and reasoning over multiple fact triples in knowledge base. In this paper, we present a novel model called Interpretable Reasoning Network that employs an interpretable, hop-by-hop reasoning process for question answering. The model dynamically decides which part of an input question should be analyzed at each hop; predicts a relation that corresponds to the current parsed results; utilizes the predicted relation to update the question representation and the state of the reasoning process; and then drives the next-hop reasoning. Experiments show that our model yields state-of-the-art results on two datasets. More interestingly, the model can offer traceable and observable intermediate predictions for reasoning analysis and failure diagnosis.