Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis and unfolds the full cause-effect structure of discrete dynamical systems of binary elements. The software allows users to easily study these structures, serves as an up-to-date reference implementation of the formalisms of integrated information theory, and has been applied in research on complexity, emergence, and certain biological questions. We first provide an overview of the main algorithm and demonstrate PyPhi's functionality in the course of analyzing an example system, and then describe details of the algorithm's design and implementation. PyPhi can be installed with Python's package manager via the command 'pip install pyphi' on Linux and macOS systems equipped with Python 3.4 or higher. PyPhi is open-source and licensed under the GPLv3; the source code is hosted on GitHub at https://github.com/wmayner/pyphi . Comprehensive and continually-updated documentation is available at https://pyphi.readthedocs.io/ . The pyphi-users mailing list can be joined at https://groups.google.com/forum/#!forum/pyphi-users . A web-based graphical interface to the software is available at http://integratedinformationtheory.org/calculate.html .
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially the lack of protein structure data, most of the existing computational methods rely heavily on the sequence data, with only a small portion of the methods utilizing the structural information. Recently, AlphaFold has revolutionized the entire protein and biology field. Foreseeably, the protein-RNA interaction prediction will also be promoted significantly in the upcoming years. In this work, we give a thorough review of this field, surveying both the binding site and binding preference prediction problems and covering the commonly used datasets, features, and models. We also point out the potential challenges and opportunities in this field. This survey summarizes the development of the RBP-RNA interaction field in the past and foresees its future development in the post-AlphaFold era.
In order to model the evolution of user preference, we should learn user/item embeddings based on time-ordered item purchasing sequences, which is defined as Sequential Recommendation (SR) problem. Existing methods leverage sequential patterns to model item transitions. However, most of them ignore crucial temporal collaborative signals, which are latent in evolving user-item interactions and coexist with sequential patterns. Therefore, we propose to unify sequential patterns and temporal collaborative signals to improve the quality of recommendation, which is rather challenging. Firstly, it is hard to simultaneously encode sequential patterns and collaborative signals. Secondly, it is non-trivial to express the temporal effects of collaborative signals. Hence, we design a new framework Temporal Graph Sequential Recommender (TGSRec) upon our defined continuous-time bi-partite graph. We propose a novel Temporal Collaborative Trans-former (TCT) layer in TGSRec, which advances the self-attention mechanism by adopting a novel collaborative attention. TCT layer can simultaneously capture collaborative signals from both users and items, as well as considering temporal dynamics inside sequential patterns. We propagate the information learned fromTCTlayerover the temporal graph to unify sequential patterns and temporal collaborative signals. Empirical results on five datasets show that TGSRec significantly outperforms other baselines, in average up to 22.5% and 22.1%absolute improvements in Recall@10and MRR, respectively.
Vibration patterns yield valuable information about the health state of a running machine, which is commonly exploited in predictive maintenance tasks for large industrial systems. However, the overhead, in terms of size, complexity and power budget, required by classical methods to exploit this information is often prohibitive for smaller-scale applications such as autonomous cars, drones or robotics. Here we propose a neuromorphic approach to perform vibration analysis using spiking neural networks that can be applied to a wide range of scenarios. We present a spike-based end-to-end pipeline able to detect system anomalies from vibration data, using building blocks that are compatible with analog-digital neuromorphic circuits. This pipeline operates in an online unsupervised fashion, and relies on a cochlea model, on feedback adaptation and on a balanced spiking neural network. We show that the proposed method achieves state-of-the-art performance or better against two publicly available data sets. Further, we demonstrate a working proof-of-concept implemented on an asynchronous neuromorphic processor device. This work represents a significant step towards the design and implementation of autonomous low-power edge-computing devices for online vibration monitoring.
Open Information Extraction (OIE) is the task of the unsupervised creation of structured information from text. OIE is often used as a starting point for a number of downstream tasks including knowledge base construction, relation extraction, and question answering. While OIE methods are targeted at being domain independent, they have been evaluated primarily on newspaper, encyclopedic or general web text. In this article, we evaluate the performance of OIE on scientific texts originating from 10 different disciplines. To do so, we use two state-of-the-art OIE systems applying a crowd-sourcing approach. We find that OIE systems perform significantly worse on scientific text than encyclopedic text. We also provide an error analysis and suggest areas of work to reduce errors. Our corpus of sentences and judgments are made available.
This study investigates robust speaker localization for con-tinuous speech separation and speaker diarization, where we use speaker directions to group non-contiguous segments of the same speaker. Assuming that speakers do not move and are located in different directions, the direction of arrival (DOA) information provides an informative cue for accurate sequential grouping and speaker diarization. Our system is block-online in the following sense. Given a block of frames with at most two speakers, we apply a two-speaker separa-tion model to separate (and enhance) the speakers, estimate the DOA of each separated speaker, and group the separation results across blocks based on the DOA estimates. Speaker diarization and speaker-attributed speech recognition results on the LibriCSS corpus demonstrate the effectiveness of the proposed algorithm.
Graph neural networks (GNNs) have received tremendous attention due to their power in learning effective representations for graphs. Most GNNs follow a message-passing scheme where the node representations are updated by aggregating and transforming the information from the neighborhood. Meanwhile, they adopt the same strategy in aggregating the information from different feature dimensions. However, suggested by social dimension theory and spectral embedding, there are potential benefits to treat the dimensions differently during the aggregation process. In this work, we investigate to enable heterogeneous contributions of feature dimensions in GNNs. In particular, we propose a general graph feature gating network (GFGN) based on the graph signal denoising problem and then correspondingly introduce three graph filters under GFGN to allow different levels of contributions from feature dimensions. Extensive experiments on various real-world datasets demonstrate the effectiveness and robustness of the proposed frameworks.
The field of deep learning has become increasingly important for particle physics experiments, yielding a multitude of advances, predominantly in event classification and reconstruction tasks. Many of these applications have been adopted from other domains. However, data in the field of physics are unique in the context of machine learning, insofar as their generation process and the laws and symmetries they abide by are usually well understood. Most commonly used deep learning architectures fail at utilizing this available information. In contrast, more traditional likelihood-based methods are capable of exploiting domain knowledge, but they are often limited by computational complexity. In this contribution, a hybrid approach is presented that utilizes generative neural networks to approximate the likelihood, which may then be used in a traditional maximum-likelihood setting. Domain knowledge, such as invariances and detector characteristics, can easily be incorporated in this approach. The hybrid approach is illustrated by the example of event reconstruction in IceCube.
Getting the distance to objects is crucial for autonomous vehicles. In instances where depth sensors cannot be used, this distance has to be estimated from RGB cameras. As opposed to cars, the task of estimating depth from on-board mounted cameras is made complex on drones because of the lack of constrains on motion during flights. %In the case of drones, this task is even more complex than for car-mounted cameras since the camera motion is unconstrained. In this paper, we present a method to estimate the distance of objects seen by an on-board mounted camera by using its RGB video stream and drone motion information. Our method is built upon a pyramidal convolutional neural network architecture and uses time recurrence in pair with geometric constraints imposed by motion to produce pixel-wise depth maps. %from a RGB video stream of a camera attached to the drone In our architecture, each level of the pyramid is designed to produce its own depth estimate based on past observations and information provided by the previous level in the pyramid. We introduce a spatial reprojection layer to maintain the spatio-temporal consistency of the data between the levels. We analyse the performance of our approach on Mid-Air, a public drone dataset featuring synthetic drone trajectories recorded in a wide variety of unstructured outdoor environments. Our experiments show that our network outperforms state-of-the-art depth estimation methods and that the use of motion information is the main contributing factor for this improvement. The code of our method is publicly available on GitHub; see $\href{https://github.com/michael-fonder/M4Depth}{\text{https://github.com/michael-fonder/M4Depth}}$
Graph structural information such as topologies or connectivities provides valuable guidance for graph convolutional networks (GCNs) to learn nodes' representations. Existing GCN models that capture nodes' structural information weight in- and out-neighbors equally or differentiate in- and out-neighbors globally without considering nodes' local topologies. We observe that in- and out-neighbors contribute differently for nodes with different local topologies. To explore the directional structural information for different nodes, we propose a GCN model with weighted structural features, named WGCN. WGCN first captures nodes' structural fingerprints via a direction and degree aware Random Walk with Restart algorithm, where the walk is guided by both edge direction and nodes' in- and out-degrees. Then, the interactions between nodes' structural fingerprints are used as the weighted node structural features. To further capture nodes' high-order dependencies and graph geometry, WGCN embeds graphs into a latent space to obtain nodes' latent neighbors and geometrical relationships. Based on nodes' geometrical relationships in the latent space, WGCN differentiates latent, in-, and out-neighbors with an attention-based geometrical aggregation. Experiments on transductive node classification tasks show that WGCN outperforms the baseline models consistently by up to 17.07% in terms of accuracy on five benchmark datasets.