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Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p&lt;0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

AAAI 2021

PANTHER: Pathway Augmented Nonnegative Tensor Factorization for HighER-Order Feature Learning

The purpose of the AAAI conference is to promote research in artificial intelligence (AI) and scientific exchange among AI researchers, practitioners, scientists, and engineers in affiliated disciplines. 

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

technical paper

Humans constantly restructure knowledge to use it more efficiently. Our goal is to give a machine learning system similar abilities so that it can learn more efficiently. We introduce the knowledge refactoring problem, where the goal is to restructure a learner's knowledge base to reduce its size and to minimise redundancy in it. We focus on inductive logic programming, where the knowledge base is a logic program. We introduce Knorf, a system which solves the refactoring problem using constraint optimisation. A key feature of Knorf is that, rather than simply removing knowledge, it also introduces new knowledge through predicate invention. We evaluate our approach on two domains: building Lego structures and real-world string transformations. Our experiments show that learning from refactored knowledge can improve predictive accuracies fourfold and reduce learning times by half.

Knowledge Refactoring for Inductive Program Synthesis

We present LCollision, a learning-based method that synthesizes collision-free 3D human poses. At the crux of our approach is a novel deep architecture that simultaneously decodes new human poses from the latent space and predicts colliding body parts. These two components of our architecture are used as the objective function and surrogate hard constraints in a constrained optimization for collision-free human pose generation. A novel aspect of our approach is the use of a bilevel autoencoder that decomposes whole-body collisions into groups of collisions between localized body parts. By solving the constrained optimizations, we show that a significant amount of collision artifacts can be resolved. Furthermore, in a large test set of 2.5 Ã— 10 6 randomized poses from SCAPE, our architecture achieves a collision-prediction accuracy of 94.1% with 80Ã— speedup over exact collision detection algorithms. To the best of our knowledge, LCollision is the ï¬rst approach that accelerates collision detection and resolves penetrations using a neural network.

LCollision: Fast Generation of Collision-Free Human Poses Using Learned Non-Penetration Constraints

Modern deep learning methods have achieved great success in machine learning and computer vision fields by learning a set of pre-defined datasets. Howerver, these methods perform unsatisfactorily when applied into real-world situations. The reason of this phenomenon is that learning new tasks leads the trained model quickly forget the knowledge of old tasks, which is referred to as catastrophic forgetting. Current state-of-the-art incremental learning methods tackle catastrophic forgetting problem in traditional classification networks and ignore the problem existing in embedding networks, which are the basic networks for image retrieval, face recognition, zero-shot learning, etc. Different from traditional incremental classification networks, the semantic gap between the embedding spaces of two adjacent tasks is the main challenge for embedding networks under incremental learning setting. Thus, we propose a novel class-incremental method for embedding network, named as zero-shot translation class-incremental method (ZSTCI), which leverages zero-shot translation to estimate and compensate the semantic gap without any exemplars. Then, we try to learn a unified representation for two adjacent tasks in sequential learning process, which captures the relationships of previous classes and current classes precisely. In addition, ZSTCI can easily be combined with existing regularization-based incremental learning methods to further improve performance of embedding networks. We conduct extensive experiments on CUB-200-2011 and CIFAR100, and the experiment results prove the effectiveness of our method. The code of our method has been released in https://github.com/Drkun/ZSTCI.

Incremental Embedding Learning via Zero-Shot Translation

Weakly-supervised temporal action localization aims to learn detecting temporal intervals of action classes with only video-level labels. To this end, it is crucial to separate frames of action classes from the background frames (i.e., frames not belonging to any action classes). In this paper, we present a new perspective on background frames where they are modeled as out-of-distribution samples regarding their inconsistency. Then, background frames can be detected by estimating the probability of each frame being out-of-distribution, known as uncertainty, but it is infeasible to directly learn uncertainty without frame-level labels. To realize the uncertainty learning in the weakly-supervised setting, we leverage the multiple instance learning formulation. Moreover, we further introduce a background entropy loss to better discriminate background frames by encouraging their in-distribution (action) probabilities to be uniformly distributed over all action classes. Experimental results show that our uncertainty modeling is effective at alleviating the interference of background frames and brings a large performance gain without bells and whistles. We demonstrate that our model significantly outperforms state-of-the-art methods on the benchmarks, THUMOS'14 and ActivityNet (1.2 & 1.3). Our code is available at https://github.com/Pilhyeon/WTAL-Uncertainty-Modeling.

Weakly-Supervised Temporal Action Localization by Uncertainty Modeling

3D Convolution Neural Networks (CNNs) have been widely applied to 3D scene understanding, such as video analysis and volumetric image recognition. However, 3D networks can easily lead to over-parameterization which incurs expensive computation cost. In this paper, we propose Channel-wise Automatic KErnel Shrinking (CAKES), to enable efficient 3D learning by shrinking standard 3D convolutions into a set of economic operations (e.g., 1D, 2D convolutions). Unlike previous methods, CAKES performs channel-wise kernel shrinkage, which enjoys the following benefits: 1) enabling operations deployed in every layer to be heterogeneous, so that they can extract diverse and complementary information to benefit the learning process; and 2) allowing for an efficient and flexible replacement design, which can be generalized to both spatial-temporal and volumetric data. Further, we propose a new search space based on CAKES, so that the configuration can be determined automatically for simplifying 3D networks. CAKES shows superior performance to other methods with similar model size, and it also achieves comparable performance to state-of-the-art methods with much fewer parameters and computational costs on tasks including 3D medical imaging segmentation and video action recognition. Codes and models are available at https://github.com/yucornetto/CAKES

CAKES: Channel-Wise Automatic Kernel Shrinking for Efficient 3D Networks

Landmarks (LMs) are state features that need to be made true or tasks that need to be contained in every solution of a planning problem. They are a valuable source of information in planning and can be exploited in various ways. LMs have been used both in classical and hierarchical planning, but while there is much work in classical planning, the techniques in hierarchical planning are less evolved. We introduce a novel LM generation method for Hierarchical Task Network (HTN) planning and show that it is sound and incomplete. We show that every complete approach is as hard as the co-class of the underlying HTN problem, i.e. coNP-hard for our setting (while our approach is in P). On a widely used benchmark set, our approach finds more than twice the number of landmarks than the approach from the literature. Though our focus is on LM generation, we show that the newly discovered landmarks bear information beneficial for solvers.

Landmark Generation in HTN Planning

The regret bound of dynamic online learning algorithms is often expressed in terms of the variation in the function sequence (V_T) and/or the path-length of the minimizer sequence after T rounds. For strongly convex and smooth functions, Zhang et al. (2017) establish the squared path-length of the minimizer sequence (C*_{2,T}) as a lower bound on regret. They also show that online gradient descent (OGD) achieves this lower bound using multiple gradient queries per round. In this paper, we focus on unconstrained online optimization. We first show that a preconditioned variant of OGD achieves O(min{C*_T,C*_{2,T}}) with one gradient query per round (C*_T refers to the normal path-length). We then propose online optimistic Newton (OON) method for the case when the first and second order information of the function sequence is predictable. The regret bound of OON is captured via the quartic path-length of the minimizer sequence (C*_{4,T}), which can be much smaller than C*_{2,T}. We finally show that by using multiple gradients for OGD, we can achieve an upper bound of O(min{C*_{2,T},V_T}) on regret.

On Online Optimization: Dynamic Regret Analysis of Strongly Convex and Smooth Problems

An agent, or a coalition of agents, faces an ethical dilemma between several statements if she is forced to make a conscious choice between which of these statements will be true. This paper proposes to capture ethical dilemmas as a modality in strategic game settings with and without limit on sacrifice and for perfect and imperfect information games. The authors show that the dilemma modality cannot be defined through the earlier proposed blameworthiness modality. The main technical result is a sound and complete axiomatization of the properties of this modality with sacrifice in games with perfect information.

Ethical Dilemmas in Strategic Games

The ability of an agent to comprehend a sentence is tightly connected to the agent's prior experiences and background knowledge. The paper suggests to interpret comprehension as a modality and proposes a complete bimodal logical system that describes an interplay between comprehension and knowledge modalities.

Comprehension and Knowledge

The paper suggests a definition of "know who" as a modality using Grove-Halpern semantics of names. It also introduces a logical system that describes the interplay between modalities "knows who", "knows", and "for all agents". The main technical result is a completeness theorem for the proposed system.

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