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We propose a continuous optimization framework for discovering a latent directed acyclic graph (DAG) from observational data. Our approach optimizes over the polytope of permutation vectors, the so-called Permutahedron, to learn a topological ordering. Edges can be optimized jointly, or learned conditional on the ordering via a non-differentiable subroutine. Compared to existing continuous optimization approaches our formulation has a number of advantages including: 1. validity: optimizes over exact DAGs as opposed to other relaxations optimizing approximate DAGs; 2. modularity: accommodates any edge-optimization procedure, edge structural parameterization, and optimization loss; 3. end-to-end: either alternately iterates between node-ordering and edge-optimization, or optimizes them jointly. We demonstrate, on real-world data problems in protein-signaling and transcriptional network discovery, that our approach lies on the Pareto frontier of two key metrics, the SID and SHD.

We study the interplay between the data distribution and Q-learning-based algorithms with function approximation. We provide a unified theoretical and empirical analysis as to how different properties of the data distribution influence the performance of Q-learning-based algorithms. We connect different lines of research, as well as validate and extend previous results. We start by reviewing theoretical bounds on the performance of approximate dynamic programming algorithms. We then introduce a novel four-state MDP specifically tailored to highlight the impact of the data distribution in the performance of Q-learning-based algorithms with function approximation, both online and offline. Finally, we experimentally assess the impact of the data distribution properties on the performance of two offline Q-learning-based algorithms under different environments. According to our results: (i) high entropy data distributions are well-suited for learning in an offline manner; and (ii) a certain degree of data diversity (data coverage) and data quality (closeness to optimal policy) are jointly desirable for offline learning.

Labeling data is one of the most costly processes in machine learning pipelines. Active learning is a standard approach to alleviating this problem. Pool-based active learning first builds a pool of unlabelled data and iteratively selects data to be labeled so that the total number of required labels is minimized, keeping the model performance high. Many effective criteria for choosing data from the pool have been proposed in the literature. However, how to build the pool is less explored. Specifically, most of the methods assume that a task-specific pool is given for free. In this paper, we advocate that such a task-specific pool is not always available and propose the use of a myriad of unlabelled data on the Web for the pool for which active learning is applied. As the pool is extremely large, it is likely that relevant data exist in the pool for many tasks, and we do not need to explicitly design and build the pool for each task. The challenge is that we cannot compute the acquisition scores of all data exhaustively due to the size of the pool. We propose an efficient method, Seafaring, to retrieve informative data in terms of active learning from the Web using a user-side information retrieval algorithm. In the experiments, we use the online Flickr environment as the pool for active learning. This pool contains more than ten billion images and is several orders of magnitude larger than the existing pools in the literature for active learning. We confirm that our method performs better than existing approaches of using a small unlabelled pool.

Artificial intelligence (AI) systems utilizing deep neural networks (DNNs) and machine learning (ML) algorithms are widely used for solving important problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNNs or ML models, which are often perceived as opaque and black-box, can make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. Additionally, in sensitive areas like healthcare, explainability and accountability are not only desirable but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable artificial intelligence (XAI) aims to overcome the opaqueness of black-box models and provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and the factors that influence their outcomes. However, most state-of-the-art interpretable ML methods are domain-agnostic and evolved from fields like computer vision, automated reasoning, or statistics, making direct application to bioinformatics problems challenging without customization and domain-specific adaptation. In this paper, we discuss the importance of explainability in the context of bioinformatics, provide an overview of model-specific and model-agnostic interpretable ML methods and tools, and outline their potential caveats and drawbacks. Besides, we discuss how to customize existing interpretable ML methods for bioinformatics problems. Nevertheless, we demonstrate how XAI methods can improve transparency through case studies in bioimaging, cancer genomics, and text mining.

This work introduces a highly-scalable spectral graph densification framework (SGL) for learning resistor networks with linear measurements, such as node voltages and currents. We show that the proposed graph learning approach is equivalent to solving the classical graphical Lasso problems with Laplacian-like precision matrices. We prove that given $O(\log N)$ pairs of voltage and current measurements, it is possible to recover sparse $N$-node resistor networks that can well preserve the effective resistance distances on the original graph. In addition, the learned graphs also preserve the structural (spectral) properties of the original graph, which can potentially be leveraged in many circuit design and optimization tasks. To achieve more scalable performance, we also introduce a solver-free method (SF-SGL) that exploits multilevel spectral approximation of the graphs and allows for a scalable and flexible decomposition of the entire graph spectrum (to be learned) into multiple different eigenvalue clusters (frequency bands). Such a solver-free approach allows us to more efficiently identify the most spectrally-critical edges for reducing various ranges of spectral embedding distortions. Through extensive experiments for a variety of real-world test cases, we show that the proposed approach is highly scalable for learning sparse resistor networks without sacrificing solution quality. We also introduce a data-driven EDA algorithm for vectorless power/thermal integrity verifications to allow estimating worst-case voltage/temperature (gradient) distributions across the entire chip by leveraging a few voltage/temperature measurements.

Advances in artificial intelligence often stem from the development of new environments that abstract real-world situations into a form where research can be done conveniently. This paper contributes such an environment based on ideas inspired by elementary Microeconomics. Agents learn to produce resources in a spatially complex world, trade them with one another, and consume those that they prefer. We show that the emergent production, consumption, and pricing behaviors respond to environmental conditions in the directions predicted by supply and demand shifts in Microeconomics. We also demonstrate settings where the agents' emergent prices for goods vary over space, reflecting the local abundance of goods. After the price disparities emerge, some agents then discover a niche of transporting goods between regions with different prevailing prices -- a profitable strategy because they can buy goods where they are cheap and sell them where they are expensive. Finally, in a series of ablation experiments, we investigate how choices in the environmental rewards, bartering actions, agent architecture, and ability to consume tradable goods can either aid or inhibit the emergence of this economic behavior. This work is part of the environment development branch of a research program that aims to build human-like artificial general intelligence through multi-agent interactions in simulated societies. By exploring which environment features are needed for the basic phenomena of elementary microeconomics to emerge automatically from learning, we arrive at an environment that differs from those studied in prior multi-agent reinforcement learning work along several dimensions. For example, the model incorporates heterogeneous tastes and physical abilities, and agents negotiate with one another as a grounded form of communication.

In the past decade, we have witnessed the rise of deep learning to dominate the field of artificial intelligence. Advances in artificial neural networks alongside corresponding advances in hardware accelerators with large memory capacity, together with the availability of large datasets enabled researchers and practitioners alike to train and deploy sophisticated neural network models that achieve state-of-the-art performance on tasks across several fields spanning computer vision, natural language processing, and reinforcement learning. However, as these neural networks become bigger, more complex, and more widely used, fundamental problems with current deep learning models become more apparent. State-of-the-art deep learning models are known to suffer from issues that range from poor robustness, inability to adapt to novel task settings, to requiring rigid and inflexible configuration assumptions. Ideas from collective intelligence, in particular concepts from complex systems such as self-organization, emergent behavior, swarm optimization, and cellular systems tend to produce solutions that are robust, adaptable, and have less rigid assumptions about the environment configuration. It is therefore natural to see these ideas incorporated into newer deep learning methods. In this review, we will provide a historical context of neural network research's involvement with complex systems, and highlight several active areas in modern deep learning research that incorporate the principles of collective intelligence to advance its current capabilities. To facilitate a bi-directional flow of ideas, we also discuss work that utilize modern deep learning models to help advance complex systems research. We hope this review can serve as a bridge between complex systems and deep learning communities to facilitate the cross pollination of ideas and foster new collaborations across disciplines.

The last decade has witnessed an experimental revolution in data science and machine learning, epitomised by deep learning methods. Indeed, many high-dimensional learning tasks previously thought to be beyond reach -- such as computer vision, playing Go, or protein folding -- are in fact feasible with appropriate computational scale. Remarkably, the essence of deep learning is built from two simple algorithmic principles: first, the notion of representation or feature learning, whereby adapted, often hierarchical, features capture the appropriate notion of regularity for each task, and second, learning by local gradient-descent type methods, typically implemented as backpropagation. While learning generic functions in high dimensions is a cursed estimation problem, most tasks of interest are not generic, and come with essential pre-defined regularities arising from the underlying low-dimensionality and structure of the physical world. This text is concerned with exposing these regularities through unified geometric principles that can be applied throughout a wide spectrum of applications. Such a 'geometric unification' endeavour, in the spirit of Felix Klein's Erlangen Program, serves a dual purpose: on one hand, it provides a common mathematical framework to study the most successful neural network architectures, such as CNNs, RNNs, GNNs, and Transformers. On the other hand, it gives a constructive procedure to incorporate prior physical knowledge into neural architectures and provide principled way to build future architectures yet to be invented.

The Q-learning algorithm is known to be affected by the maximization bias, i.e. the systematic overestimation of action values, an important issue that has recently received renewed attention. Double Q-learning has been proposed as an efficient algorithm to mitigate this bias. However, this comes at the price of an underestimation of action values, in addition to increased memory requirements and a slower convergence. In this paper, we introduce a new way to address the maximization bias in the form of a "self-correcting algorithm" for approximating the maximum of an expected value. Our method balances the overestimation of the single estimator used in conventional Q-learning and the underestimation of the double estimator used in Double Q-learning. Applying this strategy to Q-learning results in Self-correcting Q-learning. We show theoretically that this new algorithm enjoys the same convergence guarantees as Q-learning while being more accurate. Empirically, it performs better than Double Q-learning in domains with rewards of high variance, and it even attains faster convergence than Q-learning in domains with rewards of zero or low variance. These advantages transfer to a Deep Q Network implementation that we call Self-correcting DQN and which outperforms regular DQN and Double DQN on several tasks in the Atari 2600 domain.

Deep learning has yielded state-of-the-art performance on many natural language processing tasks including named entity recognition (NER). However, this typically requires large amounts of labeled data. In this work, we demonstrate that the amount of labeled training data can be drastically reduced when deep learning is combined with active learning. While active learning is sample-efficient, it can be computationally expensive since it requires iterative retraining. To speed this up, we introduce a lightweight architecture for NER, viz., the CNN-CNN-LSTM model consisting of convolutional character and word encoders and a long short term memory (LSTM) tag decoder. The model achieves nearly state-of-the-art performance on standard datasets for the task while being computationally much more efficient than best performing models. We carry out incremental active learning, during the training process, and are able to nearly match state-of-the-art performance with just 25\% of the original training data.