Kevin Chen

Fabrizio Angaroni, Kevin Chen, Chiara Damiani et al.

Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive models of cancer evolution. Yet, available methods cannot infer logical formulas connecting events to represent alternative evolutionary routes or convergent evolution. Results: We introduce PMCE, an expressive framework that leverages mutational profiles from cross-sectional sequencing data to infer probabilistic graphical models of cancer evolution including arbitrary logical formulas, and which outperforms the state-of-the-art in terms of accuracy and robustness to noise, on simulations. The application of PMCE to 7866 samples from the TCGA database allows us to identify a highly significant correlation between the predicted evolutionary paths and the overall survival in 7 tumor types, proving that our approach can effectively stratify cancer patients in reliable risk groups. Availability: PMCE is freely available at https://github.com/BIMIB-DISCo/PMCE, in addition to the code to replicate all the analyses presented in the manuscript. Contacts: daniele.ramazzotti@unimib.it, alex.graudenzi@ibfm.cnr.it.

Howard S. Cohl, Moritz Schubotz, Abdou Youssef et al.

Document preparation systems like LaTeX offer the ability to render mathematical expressions as one would write these on paper. Using LaTeX, LaTeXML, and tools generated for use in the National Institute of Standards (NIST) Digital Library of Mathematical Functions, semantically enhanced mathematical LaTeX markup (semantic LaTeX) is achieved by using a semantic macro set. Computer algebra systems (CAS) such as Maple and Mathematica use alternative markup to represent mathematical expressions. By taking advantage of Youssef's Part-of-Math tagger and CAS internal representations, we develop algorithms to translate mathematical expressions represented in semantic LaTeX to corresponding CAS representations and vice versa. We have also developed tools for translating the entire Wolfram Encoding Continued Fraction Knowledge and University of Antwerp Continued Fractions for Special Functions datasets, for use in the NIST Digital Repository of Mathematical Formulae. The overall goal of these efforts is to provide semantically enriched standard conforming MathML representations to the public for formulae in digital mathematics libraries. These representations include presentation MathML, content MathML, generic LaTeX, semantic LaTeX, and now CAS representations as well.

Suraj Nair, Eric Mitchell, Kevin Chen et al.

We study the problem of learning a range of vision-based manipulation tasks from a large offline dataset of robot interaction. In order to accomplish this, humans need easy and effective ways of specifying tasks to the robot. Goal images are one popular form of task specification, as they are already grounded in the robot's observation space. However, goal images also have a number of drawbacks: they are inconvenient for humans to provide, they can over-specify the desired behavior leading to a sparse reward signal, or under-specify task information in the case of non-goal reaching tasks. Natural language provides a convenient and flexible alternative for task specification, but comes with the challenge of grounding language in the robot's observation space. To scalably learn this grounding we propose to leverage offline robot datasets (including highly sub-optimal, autonomously collected data) with crowd-sourced natural language labels. With this data, we learn a simple classifier which predicts if a change in state completes a language instruction. This provides a language-conditioned reward function that can then be used for offline multi-task RL. In our experiments, we find that on language-conditioned manipulation tasks our approach outperforms both goal-image specifications and language conditioned imitation techniques by more than 25%, and is able to perform visuomotor tasks from natural language, such as "open the right drawer" and "move the stapler", on a Franka Emika Panda robot.

Kevin Chen, Junshen K. Chen, Jo Chuang et al.

Conventional approaches to vision-and-language navigation (VLN) are trained end-to-end but struggle to perform well in freely traversable environments. Inspired by the robotics community, we propose a modular approach to VLN using topological maps. Given a natural language instruction and topological map, our approach leverages attention mechanisms to predict a navigation plan in the map. The plan is then executed with low-level actions (e.g. forward, rotate) using a robust controller. Experiments show that our method outperforms previous end-to-end approaches, generates interpretable navigation plans, and exhibits intelligent behaviors such as backtracking.

Ayzaan Wahid, Austin Stone, Kevin Chen et al.

Object navigation is defined as navigating to an object of a given label in a complex, unexplored environment. In its general form, this problem poses several challenges for Robotics: semantic exploration of unknown environments in search of an object and low-level control. In this work we study object-guided exploration and low-level control, and present an end-to-end trained navigation policy achieving a success rate of 0.68 and SPL of 0.58 on unseen, visually complex scans of real homes. We propose a highly scalable implementation of an off-policy Reinforcement Learning algorithm, distributed Soft Actor Critic, which allows the system to utilize 98M experience steps in 24 hours on 8 GPUs. Our system learns to control a differential drive mobile base in simulation from a stack of high dimensional observations commonly used on robotic platforms. The learned policy is capable of object-guided exploratory behaviors and low-level control learned from pure experiences in realistic environments.

Kevin Chen, Juan Pablo de Vicente, Gabriel Sepulveda et al.

Inspired by research in psychology, we introduce a behavioral approach for visual navigation using topological maps. Our goal is to enable a robot to navigate from one location to another, relying only on its visual input and the topological map of the environment. We propose using graph neural networks for localizing the agent in the map, and decompose the action space into primitive behaviors implemented as convolutional or recurrent neural networks. Using the Gibson simulator, we verify that our approach outperforms relevant baselines and is able to navigate in both seen and unseen environments.

Xiaoxue Zang, Ashwini Pokle, Marynel Vázquez et al.

We propose an end-to-end deep learning model for translating free-form natural language instructions to a high-level plan for behavioral robot navigation. We use attention models to connect information from both the user instructions and a topological representation of the environment. We evaluate our model's performance on a new dataset containing 10,050 pairs of navigation instructions. Our model significantly outperforms baseline approaches. Furthermore, our results suggest that it is possible to leverage the environment map as a relevant knowledge base to facilitate the translation of free-form navigational instruction.

Lin Sun, Kui Jia, Kevin Chen et al.

Human actions captured in video sequences are three-dimensional signals characterizing visual appearance and motion dynamics. To learn action patterns, existing methods adopt Convolutional and/or Recurrent Neural Networks (CNNs and RNNs). CNN based methods are effective in learning spatial appearances, but are limited in modeling long-term motion dynamics. RNNs, especially Long Short-Term Memory (LSTM), are able to learn temporal motion dynamics. However, naively applying RNNs to video sequences in a convolutional manner implicitly assumes that motions in videos are stationary across different spatial locations. This assumption is valid for short-term motions but invalid when the duration of the motion is long. In this work, we propose Lattice-LSTM (L2STM), which extends LSTM by learning independent hidden state transitions of memory cells for individual spatial locations. This method effectively enhances the ability to model dynamics across time and addresses the non-stationary issue of long-term motion dynamics without significantly increasing the model complexity. Additionally, we introduce a novel multi-modal training procedure for training our network. Unlike traditional two-stream architectures which use RGB and optical flow information as input, our two-stream model leverages both modalities to jointly train both input gates and both forget gates in the network rather than treating the two streams as separate entities with no information about the other. We apply this end-to-end system to benchmark datasets (UCF-101 and HMDB-51) of human action recognition. Experiments show that on both datasets, our proposed method outperforms all existing ones that are based on LSTM and/or CNNs of similar model complexities.