Xin Liu

Ziwei Yang, Zheng Chen, Xin Liu et al.

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail to effectively integrate gene interaction knowledge from databases or explicitly learn subtype-specific interactions. To address this mismatch, we propose GeSubNet, which learns a unified representation capable of predicting gene interactions while distinguishing between different disease subtypes. Graphs generated by such representations can be considered subtype-specific networks. GeSubNet is a multi-step representation learning framework with three modules: First, a deep generative model learns distinct disease subtypes from patient gene expression profiles. Second, a graph neural network captures representations of prior gene networks from knowledge databases, ensuring accurate physical gene interactions. Finally, we integrate these two representations using an inference loss that leverages graph generation capabilities, conditioned on the patient separation loss, to refine subtype-specific information in the learned representation. GeSubNet consistently outperforms traditional methods, with average improvements of 30.6%, 21.0%, 20.1%, and 56.6% across four graph evaluation metrics, averaged over four cancer datasets. Particularly, we conduct a biological simulation experiment to assess how the behavior of selected genes from over 11,000 candidates affects subtypes or patient distributions. The results show that the generated network has the potential to identify subtype-specific genes with an 83% likelihood of impacting patient distribution shifts.

Albara Ah Ramli, Xin Liu, Kelly Berndt et al.

Differences in gait patterns of children with Duchenne muscular dystrophy (DMD) and typically-developing (TD) peers are visible to the eye, but quantifications of those differences outside of the gait laboratory have been elusive. In this work, we measured vertical, mediolateral, and anteroposterior acceleration using a waist-worn iPhone accelerometer during ambulation across a typical range of velocities. Fifteen TD and fifteen DMD children from 3-16 years of age underwent eight walking/running activities, including five 25 meters walk/run speed-calibration tests at a slow walk to running speeds (SC-L1 to SC-L5), a 6-minute walk test (6MWT), a 100 meters fast-walk/jog/run (100MRW), and a free walk (FW). For clinical anchoring purposes, participants completed a Northstar Ambulatory Assessment (NSAA). We extracted temporospatial gait clinical features (CFs) and applied multiple machine learning (ML) approaches to differentiate between DMD and TD children using extracted temporospatial gait CFs and raw data. Extracted temporospatial gait CFs showed reduced step length and a greater mediolateral component of total power (TP) consistent with shorter strides and Trendelenberg-like gait commonly observed in DMD. ML approaches using temporospatial gait CFs and raw data varied in effectiveness at differentiating between DMD and TD controls at different speeds, with an accuracy of up to 100%. We demonstrate that by using ML with accelerometer data from a consumer-grade smartphone, we can capture DMD-associated gait characteristics in toddlers to teens.

Sergei Alyamkin, Matthew Ardi, Achille Brighton et al.

The Low-Power Image Recognition Challenge (LPIRC, https://rebootingcomputing.ieee.org/lpirc) is an annual competition started in 2015. The competition identifies the best technologies that can classify and detect objects in images efficiently (short execution time and low energy consumption) and accurately (high precision). Over the four years, the winners' scores have improved more than 24 times. As computer vision is widely used in many battery-powered systems (such as drones and mobile phones), the need for low-power computer vision will become increasingly important. This paper summarizes LPIRC 2018 by describing the three different tracks and the winners' solutions.