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Estimating causal effects from observational data is a central problem in many domains. A general approach is to balance covariates with weights such that the distribution of the data mimics randomization. We present generalized balancing weights, Neural Balancing Weights (NBW), to estimate the causal effects of an arbitrary mixture of discrete and continuous interventions. The weights were obtained through direct estimation of the density ratio between the source and balanced distributions by optimizing the variational representation of $f$-divergence. For this, we selected $\alpha$-divergence as it presents efficient optimization because it has an estimator whose sample complexity is independent of its ground truth value and unbiased mini-batch gradients; moreover, it is advantageous for the vanishing-gradient problem. In addition, we provide the following two methods for estimating the balancing weights: improving the generalization performance of the balancing weights and checking the balance of the distribution changed by the weights. Finally, we discuss the sample size requirements for the weights as a general problem of a curse of dimensionality when balancing multidimensional data. Our study provides a basic approach for estimating the balancing weights of multidimensional data using variational $f$-divergences.

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Causal inference in networks should account for interference, which occurs when a unit's outcome is influenced by treatments or outcomes of peers. Heterogeneous peer influence (HPI) occurs when a unit's outcome is influenced differently by different peers based on their attributes and relationships, or when each unit has a different susceptibility to peer influence. Existing solutions to estimating direct causal effects under interference consider either homogeneous influence from peers or specific heterogeneous influence mechanisms (e.g., based on local neighborhood structure). This paper presents a methodology for estimating individual direct causal effects in the presence of HPI where the mechanism of influence is not known a priori. We propose a structural causal model for networks that can capture different possible assumptions about network structure, interference conditions, and causal dependence and enables reasoning about identifiability in the presence of HPI. We find potential heterogeneous contexts using the causal model and propose a novel graph neural network-based estimator to estimate individual direct causal effects. We show that state-of-the-art methods for individual direct effect estimation produce biased results in the presence of HPI, and that our proposed estimator is robust.

With the increasing amount of data available to scientists in disciplines as diverse as bioinformatics, physics, and remote sensing, scientific workflow systems are becoming increasingly important for composing and executing scalable data analysis pipelines. When writing such workflows, users need to specify the resources to be reserved for tasks so that sufficient resources are allocated on the target cluster infrastructure. Crucially, underestimating a task's memory requirements can result in task failures. Therefore, users often resort to overprovisioning, resulting in significant resource wastage and decreased throughput. In this paper, we propose a novel online method that uses monitoring time series data to predict task memory usage in order to reduce the memory wastage of scientific workflow tasks. Our method predicts a task's runtime, divides it into k equally-sized segments, and learns the peak memory value for each segment depending on the total file input size. We evaluate the prototype implementation of our method using workflows from the publicly available nf-core repository, showing an average memory wastage reduction of 29.48% compared to the best state-of-the-art approach

The notion of variation is introduced for the Boolean set and based on which Boolean logic backpropagation principle is developed. Using this concept, deep models can be built with weights and activations being Boolean numbers and operated with Boolean logic instead of real arithmetic. In particular, Boolean deep models can be trained directly in the Boolean domain without latent weights. No gradient but logic is synthesized and backpropagated through layers.

We present the framework of slowly varying regression under sparsity, allowing sparse regression models to exhibit slow and sparse variations. The problem of parameter estimation is formulated as a mixed-integer optimization problem. We demonstrate that it can be precisely reformulated as a binary convex optimization problem through a novel relaxation technique. This relaxation involves a new equality on Moore-Penrose inverses, convexifying the non-convex objective function while matching the original objective on all feasible binary points. This enables us to efficiently solve the problem to provable optimality using a cutting plane-type algorithm. We develop a highly optimized implementation of this algorithm, substantially improving upon the asymptotic computational complexity of a straightforward implementation. Additionally, we propose a fast heuristic method that guarantees a feasible solution and, as empirically illustrated, produces high-quality warm-start solutions for the binary optimization problem. To tune the framework's hyperparameters, we suggest a practical procedure relying on binary search that, under certain assumptions, is guaranteed to recover the true model parameters. On both synthetic and real-world datasets, we demonstrate that the resulting algorithm outperforms competing formulations in comparable times across various metrics, including estimation accuracy, predictive power, and computational time. The algorithm is highly scalable, allowing us to train models with thousands of parameters. Our implementation is available open-source at //github.com/vvdigalakis/SSVRegression.git.

Significant scientific discoveries have driven the progress of human civilisation. The explosion of scientific literature and data has created information barriers across disciplines that have slowed the pace of scientific discovery. Large Language Models (LLMs) hold a wealth of global and interdisciplinary knowledge that promises to break down these information barriers and foster a new wave of scientific discovery. However, the potential of LLMs for scientific discovery has not been formally explored. In this paper, we start from investigating whether LLMs can propose scientific hypotheses. To this end, we construct a dataset consist of background knowledge and hypothesis pairs from biomedical literature. The dataset is divided into training, seen, and unseen test sets based on the publication date to control visibility. We subsequently evaluate the hypothesis generation capabilities of various top-tier instructed models in zero-shot, few-shot, and fine-tuning settings, including both closed and open-source LLMs. Additionally, we introduce an LLM-based multi-agent cooperative framework with different role designs and external tools to enhance the capabilities related to generating hypotheses. We also design four metrics through a comprehensive review to evaluate the generated hypotheses for both ChatGPT-based and human evaluations. Through experiments and analyses, we arrive at the following findings: 1) LLMs surprisingly generate untrained yet validated hypotheses from testing literature. 2) Increasing uncertainty facilitates candidate generation, potentially enhancing zero-shot hypothesis generation capabilities. These findings strongly support the potential of LLMs as catalysts for new scientific discoveries and guide further exploration.

We propose a general method to break down a main complex task into a set of intermediary easier sub-tasks, which are formulated in natural language as binary questions related to the final target task. Our method allows for representing each example by a vector consisting of the answers to these questions. We call this representation Natural Language Learned Features (NLLF). NLLF is generated by a small transformer language model (e.g., BERT) that has been trained in a Natural Language Inference (NLI) fashion, using weak labels automatically obtained from a Large Language Model (LLM). We show that the LLM normally struggles for the main task using in-context learning, but can handle these easiest subtasks and produce useful weak labels to train a BERT. The NLI-like training of the BERT allows for tackling zero-shot inference with any binary question, and not necessarily the ones seen during the training. We show that this NLLF vector not only helps to reach better performances by enhancing any classifier, but that it can be used as input of an easy-to-interpret machine learning model like a decision tree. This decision tree is interpretable but also reaches high performances, surpassing those of a pre-trained transformer in some cases.We have successfully applied this method to two completely different tasks: detecting incoherence in students' answers to open-ended mathematics exam questions, and screening abstracts for a systematic literature review of scientific papers on climate change and agroecology.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

This manuscript portrays optimization as a process. In many practical applications the environment is so complex that it is infeasible to lay out a comprehensive theoretical model and use classical algorithmic theory and mathematical optimization. It is necessary as well as beneficial to take a robust approach, by applying an optimization method that learns as one goes along, learning from experience as more aspects of the problem are observed. This view of optimization as a process has become prominent in varied fields and has led to some spectacular success in modeling and systems that are now part of our daily lives.

Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.

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