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In this study, we address the challenge of using energy-based models to produce high-quality, label-specific data in complex structured datasets, such as population genetics, RNA or protein sequences data. Traditional training methods encounter difficulties due to inefficient Markov chain Monte Carlo mixing, which affects the diversity of synthetic data and increases generation times. To address these issues, we use a novel training algorithm that exploits non-equilibrium effects. This approach, applied on the Restricted Boltzmann Machine, improves the model's ability to correctly classify samples and generate high-quality synthetic data in only a few sampling steps. The effectiveness of this method is demonstrated by its successful application to four different types of data: handwritten digits, mutations of human genomes classified by continental origin, functionally characterized sequences of an enzyme protein family, and homologous RNA sequences from specific taxonomies.

Spatially dependent data arises in many applications, and Gaussian processes are a popular modelling choice for these scenarios. While Bayesian analyses of these problems have proven to be successful, selecting prior distributions for these complex models remains a difficult task. In this work, we propose a principled approach for setting prior distributions on model variance components by placing a prior distribution on a measure of model fit. In particular, we derive the distribution of the prior coefficient of determination. Placing a beta prior distribution on this measure induces a generalized beta prime prior distribution on the global variance of the linear predictor in the model. This method can also be thought of as shrinking the fit towards the intercept-only (null) model. We derive an efficient Gibbs sampler for the majority of the parameters and use Metropolis-Hasting updates for the others. Finally, the method is applied to a marine protection area data set. We estimate the effect of marine policies on biodiversity and conclude that no-take restrictions lead to a slight increase in biodiversity and that the majority of the variance in the linear predictor comes from the spatial effect.\vspace{12pt}

Modeling longitudinal and survival data jointly offers many advantages such as addressing measurement error and missing data in the longitudinal processes, understanding and quantifying the association between the longitudinal markers and the survival events and predicting the risk of events based on the longitudinal markers. A joint model involves multiple submodels (one for each longitudinal/survival outcome) usually linked together through correlated or shared random effects. Their estimation is computationally expensive (particularly due to a multidimensional integration of the likelihood over the random effects distribution) so that inference methods become rapidly intractable, and restricts applications of joint models to a small number of longitudinal markers and/or random effects. We introduce a Bayesian approximation based on the Integrated Nested Laplace Approximation algorithm implemented in the R package R-INLA to alleviate the computational burden and allow the estimation of multivariate joint models with fewer restrictions. Our simulation studies show that R-INLA substantially reduces the computation time and the variability of the parameter estimates compared to alternative estimation strategies. We further apply the methodology to analyze 5 longitudinal markers (3 continuous, 1 count, 1 binary, and 16 random effects) and competing risks of death and transplantation in a clinical trial on primary biliary cholangitis. R-INLA provides a fast and reliable inference technique for applying joint models to the complex multivariate data encountered in health research.

Automated logging statement generation techniques facilitate developers in writing appropriate logging statements that document software behaviors. Current retrieval-based and learning-based logging methods fail to provide accurate logging statements in complex software. Although existing large language models (LLMs) might be a good fit for the task due to their great success in natural language generation and programming language comprehension, their effectiveness and generalization capabilities have not been explored. To this end, this paper performs the first extensive study on applying LLMs for logging statement generation. We build LogBench, the first logging statement generation dataset. On LogBench, we evaluate the effectiveness and generalization capabilities of eight state-of-the-art LLMs, which include general-purpose and code-specific models ranging from 60M to 175B in size. Specifically, we evaluate LLM's logging effectiveness by studying 1) their ability to decide logging ingredients, 2) the impact of the internal characteristics of LLMs, and 3) the influence of external factors. We further evaluate LLM's logging generalization capabilities using unseen data derived from code transformation techniques. Our study demonstrates that existing LLMs fall short of practical requirements for generating proper logging statement texts. We also disclose the impact of internal characteristics and external factors for LLMs in automated logging. In addition, we observe that existing LLMs cannot generalize to logging unseen code, revealing their unsatisfactory generalization capabilities. Based on our findings, we further discuss three implications that can enhance logging statement generation in the future, such as developing a unified metric for logging quality, incorporating shareable code knowledge into LLMs, and devising suitable prompts.

Large language models(LLMS) have shown excellent text generation capabilities,capable of generating fluent responses for many downstream tasks. However,applying large language models to real-world critical tasks remains challenging due to their susceptibility to hallucinations and inability to directly use external knowledge. To address the above challenges,this paper proposes PatternGPT, a pattern-driven text generation framework for large language models. First,the framework utilizes the extraction capabilities of large language models to generate rich and diverse patterns and later draws on the idea of federated learning. Using multiple agents to achieve sharing to obtain more diverse patterns. Finally, it searches for high-quality patterns using judgment criteria and optimization algorithms and uses the searched patterns to guide the model for generation. This framework has the advantages of generating diversified patterns, protecting data privacy,combining external knowledge, and improving the quality of generation, which provides an effective method to optimize the text generation capability of large language models,and make it better applied to the field of intelligent dialogue and content generation.

Data valuation is critical in machine learning, as it helps enhance model transparency and protect data properties. Existing data valuation methods have primarily focused on discriminative models, neglecting deep generative models that have recently gained considerable attention. Similar to discriminative models, there is an urgent need to assess data contributions in deep generative models as well. However, previous data valuation approaches mainly relied on discriminative model performance metrics and required model retraining. Consequently, they cannot be applied directly and efficiently to recent deep generative models, such as generative adversarial networks and diffusion models, in practice. To bridge this gap, we formulate the data valuation problem in generative models from a similarity-matching perspective. Specifically, we introduce Generative Model Valuator (GMValuator), the first model-agnostic approach for any generative models, designed to provide data valuation for generation tasks. We have conducted extensive experiments to demonstrate the effectiveness of the proposed method. To the best of their knowledge, GMValuator is the first work that offers a training-free, post-hoc data valuation strategy for deep generative models.

Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning induces expressive methods that can learn the underlying representation and properties of data. Such capability provides new opportunities in figuring out the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationship to generate structural data given the desired properties. This article provides a systematic review of this promising research area, commonly known as controllable deep data generation. Firstly, the potential challenges are raised and preliminaries are provided. Then the controllable deep data generation is formally defined, a taxonomy on various techniques is proposed and the evaluation metrics in this specific domain are summarized. After that, exciting applications of controllable deep data generation are introduced and existing works are experimentally analyzed and compared. Finally, the promising future directions of controllable deep data generation are highlighted and five potential challenges are identified.

Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.

Automatic KB completion for commonsense knowledge graphs (e.g., ATOMIC and ConceptNet) poses unique challenges compared to the much studied conventional knowledge bases (e.g., Freebase). Commonsense knowledge graphs use free-form text to represent nodes, resulting in orders of magnitude more nodes compared to conventional KBs (18x more nodes in ATOMIC compared to Freebase (FB15K-237)). Importantly, this implies significantly sparser graph structures - a major challenge for existing KB completion methods that assume densely connected graphs over a relatively smaller set of nodes. In this paper, we present novel KB completion models that can address these challenges by exploiting the structural and semantic context of nodes. Specifically, we investigate two key ideas: (1) learning from local graph structure, using graph convolutional networks and automatic graph densification and (2) transfer learning from pre-trained language models to knowledge graphs for enhanced contextual representation of knowledge. We describe our method to incorporate information from both these sources in a joint model and provide the first empirical results for KB completion on ATOMIC and evaluation with ranking metrics on ConceptNet. Our results demonstrate the effectiveness of language model representations in boosting link prediction performance and the advantages of learning from local graph structure (+1.5 points in MRR for ConceptNet) when training on subgraphs for computational efficiency. Further analysis on model predictions shines light on the types of commonsense knowledge that language models capture well.

Generating texts which express complex ideas spanning multiple sentences requires a structured representation of their content (document plan), but these representations are prohibitively expensive to manually produce. In this work, we address the problem of generating coherent multi-sentence texts from the output of an information extraction system, and in particular a knowledge graph. Graphical knowledge representations are ubiquitous in computing, but pose a significant challenge for text generation techniques due to their non-hierarchical nature, collapsing of long-distance dependencies, and structural variety. We introduce a novel graph transforming encoder which can leverage the relational structure of such knowledge graphs without imposing linearization or hierarchical constraints. Incorporated into an encoder-decoder setup, we provide an end-to-end trainable system for graph-to-text generation that we apply to the domain of scientific text. Automatic and human evaluations show that our technique produces more informative texts which exhibit better document structure than competitive encoder-decoder methods.