OpenRaiser/Intern-Atlas huggingface dataset:
Residual Learning from Demonstration: Adapting DMPs for Contact-rich Manipulation
Venue: arXiv cs.RO 2022
Year: 2022

Manipulation skills involving contact and friction are inherent to many robotics tasks. Using the class of motor primitives for peg-in-hole like insertions, we study how robots can learn such skills. Dynamic Movement Primitives (DMP) are a popular way of extracting such policies through behaviour cloning (BC) but can struggle in the context of insertion. Policy adaptation strategies such as residual learning can help improve the overall performance of policies in the context of contact-rich manipulation. However, it is not clear how to best do this with DMPs. As a result, we consider several possible ways for adapting a DMP formulation and propose ``residual Learning from Demonstration`` (rLfD), a framework that combines DMPs with Reinforcement Learning (RL) to learn a residual correction policy. Our evaluations suggest that applying residual learning directly in task space and operating on the full pose of the robot can significantly improve the overall performance of DMPs. We show that rLfD offers a gentle to the joints solution that improves the task success and generalisation of DMPs \rb{and enables transfer to different geometries and frictions through few-shot task adaptation}. The proposed framework is evaluated on a set of tasks. A simulated robot and a physical robot have to successfully insert pegs, gears and plugs into their respective sockets. Other material and videos accompanying this paper are provided at https://sites.google.com/view/rlfd/.
Assigning function to protein-protein interactions: a weakly supervised BioBERT based approach using PubMed abstracts
Venue: arXiv cs.CL 2022
Year: 2022

Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is important for the construction of networks to analyse biological data. However, only a small percentage of PPIs captured in protein interaction databases have annotations of function available, e.g. only 4% of PPI are functionally annotated in the IntAct database. Here, we aim to label the function type of PPIs by extracting relationships described in PubMed abstracts. Method: We create a weakly supervised dataset from the IntAct PPI database containing interacting protein pairs with annotated function and associated abstracts from the PubMed database. We apply a state-of-the-art deep learning technique for biomedical natural language processing tasks, BioBERT, to build a model - dubbed PPI-BioBERT - for identifying the function of PPIs. In order to extract high quality PPI functions at large scale, we use an ensemble of PPI-BioBERT models to improve uncertainty estimation and apply an interaction type-specific threshold to counteract the effects of variations in the number of training samples per interaction type. Results: We scan 18 million PubMed abstracts to automatically identify 3253 new typed PPIs, including phosphorylation and acetylation interactions, with an overall precision of 46% (87% for acetylation) based on a human-reviewed sample. This work demonstrates that analysis of biomedical abstracts for PPI function extraction is a feasible approach to substantially increasing the number of interactions annotated with function captured in online databases.
Tuple-Independent Representations of Infinite Probabilistic Databases
Venue: arXiv cs.DB 2022
Year: 2022

Probabilistic databases (PDBs) are probability spaces over database instances. They provide a framework for handling uncertainty in databases, as occurs due to data integration, noisy data, data from unreliable sources or randomized processes. Most of the existing theory literature investigated finite, tuple-independent PDBs (TI-PDBs) where the occurrences of tuples are independent events. Only recently, Grohe and Lindner (PODS '19) introduced independence assumptions for PDBs beyond the finite domain assumption. In the finite, a major argument for discussing the theoretical properties of TI-PDBs is that they can be used to represent any finite PDB via views. This is no longer the case once the number of tuples is countably infinite. In this paper, we systematically study the representability of infinite PDBs in terms of TI-PDBs and the related block-independent disjoint PDBs. The central question is which infinite PDBs are representable as first-order views over tuple-independent PDBs. We give a necessary condition for the representability of PDBs and provide a sufficient criterion for representability in terms of the probability distribution of a PDB. With various examples, we explore the limits of our criteria. We show that conditioning on first order properties yields no additional power in terms of expressivity. Finally, we discuss the relation between purely logical and arithmetic reasons for (non-)representability.
Bits and Pieces: Understanding Information Decomposition from Part-whole Relationships and Formal Logic
Venue: arXiv cs.AI 2022
Year: 2022

Partial information decomposition (PID) seeks to decompose the multivariate mutual information that a set of source variables contains about a target variable into basic pieces, the so called "atoms of information". Each atom describes a distinct way in which the sources may contain information about the target. In this paper we show, first, that the entire theory of partial information decomposition can be derived from considerations of elementary parthood relationships between information contributions. This way of approaching the problem has the advantage of directly characterizing the atoms of information, instead of taking an indirect approach via the concept of redundancy. Secondly, we describe several intriguing links between PID and formal logic. In particular, we show how to define a measure of PID based on the information provided by certain statements about source realizations. Furthermore, we show how the mathematical lattice structure underlying PID theory can be translated into an isomorphic structure of logical statements with a particularly simple ordering relation: logical implication. The conclusion to be drawn from these considerations is that there are three isomorphic "worlds" of partial information decomposition, i.e. three equivalent ways to mathematically describe the decomposition of the information carried by a set of sources about a target: the world of parthood relationships, the world of logical statements, and the world of antichains that was utilized by Williams and Beer in their original exposition of PID theory. We additionally show how the parthood perspective provides a systematic way to answer a type of question that has been much discussed in the PID field: whether a partial information decomposition can be uniquely determined based on concepts other than redundant information.
From noisy point clouds to complete ear shapes: unsupervised pipeline
Venue: arXiv cs.CV 2022
Year: 2022

Ears are a particularly difficult region of the human face to model, not only due to the non-rigid deformations existing between shapes but also to the challenges in processing the retrieved data. The first step towards obtaining a good model is to have complete scans in correspondence, but these usually present a higher amount of occlusions, noise and outliers when compared to most face regions, thus requiring a specific procedure. Therefore, we propose a complete pipeline taking as input unordered 3D point clouds with the aforementioned problems, and producing as output a dataset in correspondence, with completion of the missing data. We provide a comparison of several state-of-the-art registration methods and propose a new approach for one of the steps of the pipeline, with better performance for our data.
Adaptive and Multiple Time-scale Eligibility Traces for Online Deep Reinforcement Learning
Venue: arXiv cs.RO 2022
Year: 2022

Deep reinforcement learning (DRL) is one promising approach to teaching robots to perform complex tasks. Because methods that directly reuse the stored experience data cannot follow the change of the environment in robotic problems with a time-varying environment, online DRL is required. The eligibility traces method is well known as an online learning technique for improving sample efficiency in traditional reinforcement learning with linear regressors rather than DRL. The dependency between parameters of deep neural networks would destroy the eligibility traces, which is why they are not integrated with DRL. Although replacing the gradient with the most influential one rather than accumulating the gradients as the eligibility traces can alleviate this problem, the replacing operation reduces the number of reuses of previous experiences. To address these issues, this study proposes a new eligibility traces method that can be used even in DRL while maintaining high sample efficiency. When the accumulated gradients differ from those computed using the latest parameters, the proposed method takes into account the divergence between the past and latest parameters to adaptively decay the eligibility traces. Bregman divergences between outputs computed by the past and latest parameters are exploited due to the infeasible computational cost of the divergence between the past and latest parameters. In addition, a generalized method with multiple time-scale traces is designed for the first time. This design allows for the replacement of the most influential adaptively accumulated (decayed) eligibility traces.
Bandit Data-Driven Optimization
Venue: arXiv cs.LG 2022
Year: 2022

Applications of machine learning in the non-profit and public sectors often feature an iterative workflow of data acquisition, prediction, and optimization of interventions. There are four major pain points that a machine learning pipeline must overcome in order to be actually useful in these settings: small data, data collected only under the default intervention, unmodeled objectives due to communication gap, and unforeseen consequences of the intervention. In this paper, we introduce bandit data-driven optimization, the first iterative prediction-prescription framework to address these pain points. Bandit data-driven optimization combines the advantages of online bandit learning and offline predictive analytics in an integrated framework. We propose PROOF, a novel algorithm for this framework and formally prove that it has no-regret. Using numerical simulations, we show that PROOF achieves superior performance than existing baseline. We also apply PROOF in a detailed case study of food rescue volunteer recommendation, and show that PROOF as a framework works well with the intricacies of ML models in real-world AI for non-profit and public sector applications.
On the Optimality of Vagueness: "Around", "Between", and the Gricean Maxims
Venue: arXiv cs.CL 2022
Year: 2022

Why is ordinary language vague? We argue that in contexts in which a cooperative speaker is not perfectly informed about the world, the use of vague expressions can offer an optimal tradeoff between truthfulness (Gricean Quality) and informativeness (Gricean Quantity). Focusing on expressions of approximation such as "around", which are semantically vague, we show that they allow the speaker to convey indirect probabilistic information, in a way that can give the listener a more accurate representation of the information available to the speaker than any more precise expression would (intervals of the form "between"). That is, vague sentences can be more informative than their precise counterparts. We give a probabilistic treatment of the interpretation of "around", and offer a model for the interpretation and use of "around"-statements within the Rational Speech Act (RSA) framework. In our account the shape of the speaker's distribution matters in ways not predicted by the Lexical Uncertainty model standardly used in the RSA framework for vague predicates. We use our approach to draw further lessons concerning the semantic flexibility of vague expressions and their irreducibility to more precise meanings.
The complexity of L(p,q)-Edge-Labelling
Venue: arXiv cs.DM 2022
Year: 2022

We consider the L(p,q)-Edge-Labelling problem, which is the edge variant of the well-known L(p,q)-Labelling problem. So far, the complexity of this problem was only partially classified. We complete this study for all nonnegative p and q, by showing that, whenever (p,q) is not (0,0), L(p,q)-Edge-Labelling problem is NP-complete. We do this by proving that for all nonnegative p and q, except p=q=0, there exists an integer k so that L(p,q)-Edge-k-Labelling is NP-complete.
On modularity in reactive control architectures, with an application to formal verification
Venue: arXiv cs.AI 2022
Year: 2022

Modularity is a central principle throughout the design process for cyber-physical systems. Modularity reduces complexity and increases reuse of behavior. In this paper we pose and answer the following question: how can we identify independent `modules' within the structure of reactive control architectures? To this end, we propose a graph-structured control architecture we call a decision structure, and show how it generalises some reactive control architectures which are popular in Artificial Intelligence (AI) and robotics, specifically Teleo-Reactive programs (TRs), Decision Trees (DTs), Behavior Trees (BTs) and Generalised Behavior Trees ($k$-BTs). Inspired by the definition of a module in graph theory, we define modules in decision structures and show how each decision structure possesses a canonical decomposition into its modules. We can naturally characterise each of the BTs, $k$-BTs, DTs and TRs by properties of their module decomposition. This allows us to recognise which decision structures are equivalent to each of these architectures in quadratic time. Our proposed concept of modules extends to formal verification, under any verification scheme capable of verifying a decision structure. Namely, we prove that a modification to a module within a decision structure has no greater flow-on effects than a modification to an individual action within that structure. This enables verification on modules to be done locally and hierarchically, where structures can be verified and then repeatedly locally modified, with modules replaced by modules while preserving correctness. To illustrate the findings, we present an example of a solar-powered drone controlled by a decision structure. We use a Linear Temporal Logic-based verification scheme to verify the correctness of this structure, and then show how one can modify modules while preserving its correctness.
Using Machine Learning for Particle Track Identification in the CLAS12 Detector
Venue: arXiv cs.CV 2022
Year: 2022

Particle track reconstruction is the most computationally intensive process in nuclear physics experiments. Traditional algorithms use a combinatorial approach that exhaustively tests track measurements ("hits") to identify those that form an actual particle trajectory. In this article, we describe the development of four machine learning (ML) models that assist the tracking algorithm by identifying valid track candidates from the measurements in drift chambers. Several types of machine learning models were tested, including: Convolutional Neural Networks (CNN), Multi-Layer Perceptrons (MLP), Extremely Randomized Trees (ERT) and Recurrent Neural Networks (RNN). As a result of this work, an MLP network classifier was implemented as part of the CLAS12 reconstruction software to provide the tracking code with recommended track candidates. The resulting software achieved accuracy of greater than 99\% and resulted in an end-to-end speedup of 35\% compared to existing algorithms.
Anomaly Detection by Recombining Gated Unsupervised Experts
Venue: arXiv cs.LG 2022
Year: 2022

Anomaly detection has been considered under several extents of prior knowledge. Unsupervised methods do not require any labelled data, whereas semi-supervised methods leverage some known anomalies. Inspired by mixture-of-experts models and the analysis of the hidden activations of neural networks, we introduce a novel data-driven anomaly detection method called ARGUE. Our method is not only applicable to unsupervised and semi-supervised environments, but also profits from prior knowledge of self-supervised settings. We designed ARGUE as a combination of dedicated expert networks, which specialise on parts of the input data. For its final decision, ARGUE fuses the distributed knowledge across the expert systems using a gated mixture-of-experts architecture. Our evaluation motivates that prior knowledge about the normal data distribution may be as valuable as known anomalies.
Lifelong Graph Learning
Venue: arXiv cs.LG 2022
Year: 2022

Graph neural networks (GNN) are powerful models for many graph-structured tasks. Existing models often assume that the complete structure of the graph is available during training. In practice, however, graph-structured data is usually formed in a streaming fashion so that learning a graph continuously is often necessary. In this paper, we bridge GNN and lifelong learning by converting a continual graph learning problem to a regular graph learning problem so GNN can inherit the lifelong learning techniques developed for convolutional neural networks (CNN). We propose a new topology, the feature graph, which takes features as new nodes and turns nodes into independent graphs. This successfully converts the original problem of node classification to graph classification. In the experiments, we demonstrate the efficiency and effectiveness of feature graph networks (FGN) by continuously learning a sequence of classical graph datasets. We also show that FGN achieves superior performance in two applications, i.e., lifelong human action recognition with wearable devices and feature matching. To the best of our knowledge, FGN is the first method to bridge graph learning and lifelong learning via a novel graph topology. Source code is available at https://github.com/wang-chen/LGL
Secure Encoded Instruction Graphs for End-to-End Data Validation in Autonomous Robots
Venue: arXiv cs.RO 2022
Year: 2022

As autonomous robots are becoming more widespread, more attention is being paid to the security of robotic operation. Autonomous robots can be seen as cyber-physical systems: they can operate in virtual, physical, and human realms. Therefore, securing the operations of autonomous robots requires not only securing their data (e.g., sensor inputs and mission instructions) but securing their interactions with their environment. There is currently a deficiency of methods that would allow robots to securely ensure their sensors and actuators are operating correctly without external feedback. This paper introduces an encoding method and end-to-end validation framework for the missions of autonomous robots. In particular, we present a proof of concept of a map encoding method, which allows robots to navigate realistic environments and validate operational instructions with almost zero {\it a priori} knowledge. We demonstrate our framework using two different encoded maps in experiments with simulated and real robots. Our encoded maps have the same advantages as typical landmark-based navigation, but with the added benefit of cryptographic hashes that enable end-to-end information validation. Our method is applicable to any aspect of robotic operation in which there is a predefined set of actions or instructions given to the robot.
Physarum-Inspired Multi-Commodity Flow Dynamics
Venue: arXiv cs.DS 2022
Year: 2022

In wet-lab experiments, the slime mold Physarum polycephalum has demonstrated its ability to solve shortest path problems and to design efficient networks. For the shortest path problem, a mathematical model for the evolution of the slime is available and it has been shown in computer experiments and through mathematical analysis that the dynamics solves the shortest path problem. In this paper, we introduce a dynamics for the network design problem. We formulate network design as the problem of constructing a network that efficiently supports a multi-commodity flow problem. We investigate the dynamics in computer simulations and analytically. The simulations show that the dynamics is able to construct efficient and elegant networks. In the theoretical part we show that the dynamics minimizes an objective combining the cost of the network and the cost of routing the demands through the network. We also give alternative characterization of the optimum solution.
Action and Perception as Divergence Minimization
Venue: arXiv cs.AI 2022
Year: 2022

To learn directed behaviors in complex environments, intelligent agents need to optimize objective functions. Various objectives are known for designing artificial agents, including task rewards and intrinsic motivation. However, it is unclear how the known objectives relate to each other, which objectives remain yet to be discovered, and which objectives better describe the behavior of humans. We introduce the Action Perception Divergence (APD), an approach for categorizing the space of possible objective functions for embodied agents. We show a spectrum that reaches from narrow to general objectives. While the narrow objectives correspond to domain-specific rewards as typical in reinforcement learning, the general objectives maximize information with the environment through latent variable models of input sequences. Intuitively, these agents use perception to align their beliefs with the world and use actions to align the world with their beliefs. They infer representations that are informative of past inputs, explore future inputs that are informative of their representations, and select actions or skills that maximally influence future inputs. This explains a wide range of unsupervised objectives from a single principle, including representation learning, information gain, empowerment, and skill discovery. Our findings suggest leveraging powerful world models for unsupervised exploration as a path toward highly adaptive agents that seek out large niches in their environments, rendering task rewards optional.
Don't miss the Mismatch: Investigating the Objective Function Mismatch for Unsupervised Representation Learning
Venue: arXiv cs.CV 2022
Year: 2022

Finding general evaluation metrics for unsupervised representation learning techniques is a challenging open research question, which recently has become more and more necessary due to the increasing interest in unsupervised methods. Even though these methods promise beneficial representation characteristics, most approaches currently suffer from the objective function mismatch. This mismatch states that the performance on a desired target task can decrease when the unsupervised pretext task is learned too long - especially when both tasks are ill-posed. In this work, we build upon the widely used linear evaluation protocol and define new general evaluation metrics to quantitatively capture the objective function mismatch and the more generic metrics mismatch. We discuss the usability and stability of our protocols on a variety of pretext and target tasks and study mismatches in a wide range of experiments. Thereby we disclose dependencies of the objective function mismatch across several pretext and target tasks with respect to the pretext model's representation size, target model complexity, pretext and target augmentations as well as pretext and target task types. In our experiments, we find that the objective function mismatch reduces performance by ~0.1-5.0% for Cifar10, Cifar100 and PCam in many setups, and up to ~25-59% in extreme cases for the 3dshapes dataset.