Pharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD models are known to possess significant uncertainty with respect to constituent parameter data, leading to uncertainty in the model predictions. Furthermore, experimental data to calibrate these models is often limited or unavailable for novel pathways. In this study, we present a Bayesian optimal experimental design approach for improving PD model prediction accuracy. We then apply our method using simulated experimental data to account for uncertainty in hypothetical laboratory measurements. This leads to a probabilistic prediction of drug performance and a quantitative measure of which prospective laboratory experiment will optimally reduce prediction uncertainty in the PD model. The methods proposed here provide a way forward for uncertainty quantification and guided experimental design for models of novel biological pathways.
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ACM/IEEE第23屆模型驅動工程語言和系統國際會議，是模型驅動軟件和系統工程的首要會議系列，由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來，模型涵蓋了建模的各個方面，從語言和方法到工具和應用程序。模特的參加者來自不同的背景，包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇，參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會，并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。
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Learning from demonstration (LfD) is a popular technique that uses expert demonstrations to learn robot control policies. However, the difficulty in acquiring expert-quality demonstrations limits the applicability of LfD methods: real-world data collection is often costly, and the quality of the demonstrations depends greatly on the demonstrator's abilities and safety concerns. A number of works have leveraged data augmentation (DA) to inexpensively generate additional demonstration data, but most DA works generate augmented data in a random fashion and ultimately produce highly suboptimal data. In this work, we propose Guided Data Augmentation (GuDA), a human-guided DA framework that generates expert-quality augmented data. The key insight of GuDA is that while it may be difficult to demonstrate the sequence of actions required to produce expert data, a user can often easily identify when an augmented trajectory segment represents task progress. Thus, the user can impose a series of simple rules on the DA process to automatically generate augmented samples that approximate expert behavior. To extract a policy from GuDA, we use off-the-shelf offline reinforcement learning and behavior cloning algorithms. We evaluate GuDA on a physical robot soccer task as well as simulated D4RL navigation tasks, a simulated autonomous driving task, and a simulated soccer task. Empirically, we find that GuDA enables learning from a small set of potentially suboptimal demonstrations and substantially outperforms a DA strategy that samples augmented data randomly.
We consider the problem of learning a function respecting a symmetry from among a class of symmetries. We develop a unified framework that enables symmetry discovery across a broad range of subgroups including locally symmetric, dihedral and cyclic subgroups. At the core of the framework is a novel architecture composed of linear, matrix-valued and non-linear functions that expresses functions invariant to these subgroups in a principled manner. The structure of the architecture enables us to leverage multi-armed bandit algorithms and gradient descent to efficiently optimize over the linear and the non-linear functions, respectively, and to infer the symmetry that is ultimately learnt. We also discuss the necessity of the matrix-valued functions in the architecture. Experiments on image-digit sum and polynomial regression tasks demonstrate the effectiveness of our approach.
Neural additive models (NAMs) can improve the interpretability of deep neural networks by handling input features in separate additive sub-networks. However, they lack inherent mechanisms that provide calibrated uncertainties and enable selection of relevant features and interactions. Approaching NAMs from a Bayesian perspective, we enhance them in three primary ways, namely by a) providing credible intervals for the individual additive sub-networks; b) estimating the marginal likelihood to perform an implicit selection of features via an empirical Bayes procedure; and c) enabling a ranking of feature pairs as candidates for second-order interaction in fine-tuned models. In particular, we develop Laplace-approximated NAMs (LA-NAMs), which show improved empirical performance on tabular datasets and challenging real-world medical tasks.
Diffusion models (DMs) are generative models that learn to synthesize images from Gaussian noise. DMs can be trained to do a variety of tasks such as image generation and image super-resolution. Researchers have made significant improvement in the capability of synthesizing photorealistic images in the past few years. These successes also hasten the need to address the potential misuse of synthesized images. In this paper, we highlight the effectiveness of computing local statistics, as opposed to global statistics, in distinguishing digital camera images from DM-generated images. We hypothesized that local statistics should be used to address the spatial non-stationarity problem in images. We show that our approach produced promising results and it is also robust to various perturbations such as image resizing and JPEG compression.
Within the multimodal field, the key to integrating vision and language lies in establishing a good alignment strategy. Recently, benefiting from the success of self-supervised learning, significant progress has been made in multimodal semantic representation based on pre-trained models for vision and language. However, there is still room for improvement in visual semantic representation. The lack of spatial semantic coherence and vulnerability to noise makes it challenging for current pixel or patch-based methods to accurately extract complex scene boundaries. To this end, this paper develops superpixel as a comprehensive compact representation of learnable image data, which effectively reduces the number of visual primitives for subsequent processing by clustering perceptually similar pixels. To mine more precise topological relations, we propose a Multiscale Difference Graph Convolutional Network (MDGCN). It parses the entire image as a fine-to-coarse hierarchical structure of constituent visual patterns, and captures multiscale features by progressively merging adjacent superpixels as graph nodes. Moreover, we predict the differences between adjacent nodes through the graph structure, facilitating key information aggregation of graph nodes to reason actual semantic relations. Afterward, we design a multi-level fusion rule in a bottom-up manner to avoid understanding deviation by learning complementary spatial information at different regional scales. Our proposed method can be well applied to multiple downstream task learning. Extensive experiments demonstrate that our method is competitive with other state-of-the-art methods in visual reasoning. Our code will be released upon publication.
Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word ambiguity, (2) word synonymity, and (3) dynamic contextual dependency. To address these challenges, we propose a novel GNN-based sparse structure learning model for inductive document classification. Specifically, a document-level graph is initially generated by a disjoint union of sentence-level word co-occurrence graphs. Our model collects a set of trainable edges connecting disjoint words between sentences and employs structure learning to sparsely select edges with dynamic contextual dependencies. Graphs with sparse structures can jointly exploit local and global contextual information in documents through GNNs. For inductive learning, the refined document graph is further fed into a general readout function for graph-level classification and optimization in an end-to-end manner. Extensive experiments on several real-world datasets demonstrate that the proposed model outperforms most state-of-the-art results, and reveal the necessity to learn sparse structures for each document.
Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.
Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust 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.
Embedding models for deterministic Knowledge Graphs (KG) have been extensively studied, with the purpose of capturing latent semantic relations between entities and incorporating the structured knowledge into machine learning. However, there are many KGs that model uncertain knowledge, which typically model the inherent uncertainty of relations facts with a confidence score, and embedding such uncertain knowledge represents an unresolved challenge. The capturing of uncertain knowledge will benefit many knowledge-driven applications such as question answering and semantic search by providing more natural characterization of the knowledge. In this paper, we propose a novel uncertain KG embedding model UKGE, which aims to preserve both structural and uncertainty information of relation facts in the embedding space. Unlike previous models that characterize relation facts with binary classification techniques, UKGE learns embeddings according to the confidence scores of uncertain relation facts. To further enhance the precision of UKGE, we also introduce probabilistic soft logic to infer confidence scores for unseen relation facts during training. We propose and evaluate two variants of UKGE based on different learning objectives. Experiments are conducted on three real-world uncertain KGs via three tasks, i.e. confidence prediction, relation fact ranking, and relation fact classification. UKGE shows effectiveness in capturing uncertain knowledge by achieving promising results on these tasks, and consistently outperforms baselines on these tasks.
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