Causal Inference in Gene Regulatory Networks with GFlowNet: Towards Scalability in Large Systems

Understanding causal relationships within Gene Regulatory Networks (GRNs) is essential for unraveling the gene interactions in cellular processes. However, causal discovery in GRNs is a challenging problem for multiple reasons including the existence of cyclic feedback loops and uncertainty that yields diverse possible causal structures. Previous works in this area either ignore cyclic dynamics (assume acyclic structure) or struggle with scalability. We introduce Swift-DynGFN as a novel framework that enhances causal structure learning in GRNs while addressing scalability concerns. Specifically, Swift-DynGFN exploits gene-wise independence to boost parallelization and to lower computational cost. Experiments on real single-cell RNA velocity and synthetic GRN datasets showcase the advancement in learning causal structure in GRNs and scalability in larger systems.

Attention Schema in Neural Agents

Attention has become a common ingredient in deep learning architectures. It adds a dynamical selection of information on top of the static selection of information supported by weights. In the same way, we can imagine a higher-order informational filter built on top of attention: an Attention Schema (AS), namely, a descriptive and predictive model of attention. In cognitive neuroscience, Attention Schema Theory (AST) supports this idea of distinguishing attention from AS. A strong prediction of this theory is that an agent can use its own AS to also infer the states of other agents' attention and consequently enhance coordination with other agents. As such, multi-agent reinforcement learning would be an ideal setting to experimentally test the validity of AST. We explore different ways in which attention and AS interact with each other. Our preliminary results indicate that agents that implement the AS as a recurrent internal control achieve the best performance. In general, these exploratory experiments suggest that equipping artificial agents with a model of attention can enhance their social intelligence.

Enhancing Human Capabilities through Symbiotic Artificial Intelligence with Shared Sensory Experiences

The merging of human intelligence and artificial intelligence has long been a subject of interest in both science fiction and academia. In this paper, we introduce a novel concept in Human-AI interaction called Symbiotic Artificial Intelligence with Shared Sensory Experiences (SAISSE), which aims to establish a mutually beneficial relationship between AI systems and human users through shared sensory experiences. By integrating multiple sensory input channels and processing human experiences, SAISSE fosters a strong human-AI bond, enabling AI systems to learn from and adapt to individual users, providing personalized support, assistance, and enhancement. Furthermore, we discuss the incorporation of memory storage units for long-term growth and development of both the AI system and its human user. As we address user privacy and ethical guidelines for responsible AI-human symbiosis, we also explore potential biases and inequalities in AI-human symbiosis and propose strategies to mitigate these challenges. Our research aims to provide a comprehensive understanding of the SAISSE concept and its potential to effectively support and enhance individual human users through symbiotic AI systems. This position article aims at discussing poteintial AI-human interaction related topics within the scientific community, rather than providing experimental or theoretical results.

Reusable Slotwise Mechanisms

Agents that can understand and reason over the dynamics of objects can have a better capability to act robustly and generalize to novel scenarios. Such an ability, however, requires a suitable representation of the scene as well as an understanding of the mechanisms that govern the interactions of different subsets of objects. To address this problem, we propose RSM, or Reusable Slotwise Mechanisms, that jointly learns a slotwise representation of the scene and a modular architecture that dynamically chooses one mechanism among a set of reusable mechanisms to predict the next state of each slot. RSM crucially takes advantage of a \textit{Central Contextual Information (CCI)}, which lets each selected reusable mechanism access the rest of the slots through a bottleneck, effectively allowing for modeling higher order and complex interactions that might require a sparse subset of objects. We show how this model outperforms state-of-the-art methods in a variety of next-step prediction tasks ranging from grid-world environments to Atari 2600 games. Particularly, we challenge methods that model the dynamics with Graph Neural Networks (GNNs) on top of slotwise representations, and modular architectures that restrict the interactions to be only pairwise. Finally, we show that RSM is able to generalize to scenes with objects varying in number and shape, highlighting its out-of-distribution generalization capabilities. Our implementation is available online\footnote{\hyperlink{https://github.com/trangnnp/RSM}{github.com/trangnnp/RSM}}.

A Transformer-based Deep Learning Algorithm to Auto-record Undocumented Clinical One-Lung Ventilation Events

As a team studying the predictors of complications after lung surgery, we have encountered high missingness of data on one-lung ventilation (OLV) start and end times due to high clinical workload and cognitive overload during surgery. Such missing data limit the precision and clinical applicability of our findings. We hypothesized that available intraoperative mechanical ventilation and physiological time-series data combined with other clinical events could be used to accurately predict missing start and end times of OLV. Such a predictive model can recover existing miss-documented records and relieves the documentation burden by deploying it in clinical settings. To this end, we develop a deep learning model to predict the occurrence and timing of OLV based on routinely collected intraoperative data. Our approach combines the variables' spatial and frequency domain features, using Transformer encoders to model the temporal evolution and convolutional neural network to abstract frequency-of-interest from wavelet spectrum images. The performance of the proposed method is evaluated on a benchmark dataset curated from Massachusetts General Hospital (MGH) and Brigham and Women's Hospital (BWH). Experiments show our approach outperforms baseline methods significantly and produces a satisfactory accuracy for clinical use.

Construction of extra-large scale screening tools for risks of severe mental illnesses using real world healthcare data

Importance: The prevalence of severe mental illnesses (SMIs) in the United States is approximately 3% of the whole population. The ability to conduct risk screening of SMIs at large scale could inform early prevention and treatment. Objective: A scalable machine learning based tool was developed to conduct population-level risk screening for SMIs, including schizophrenia, schizoaffective disorders, psychosis, and bipolar disorders,using 1) healthcare insurance claims and 2) electronic health records (EHRs). Design, setting and participants: Data from beneficiaries from a nationwide commercial healthcare insurer with 77.4 million members and data from patients from EHRs from eight academic hospitals based in the U.S. were used. First, the predictive models were constructed and tested using data in case-control cohorts from insurance claims or EHR data. Second, performance of the predictive models across data sources were analyzed. Third, as an illustrative application, the models were further trained to predict risks of SMIs among 18-year old young adults and individuals with substance associated conditions. Main outcomes and measures: Machine learning-based predictive models for SMIs in the general population were built based on insurance claims and EHR.

GFlowOut: Dropout with Generative Flow Networks

Bayesian Inference offers principled tools to tackle many critical problems with modern neural networks such as poor calibration and generalization, and data inefficiency. However, scaling Bayesian inference to large architectures is challenging and requires restrictive approximations. Monte Carlo Dropout has been widely used as a relatively cheap way for approximate Inference and to estimate uncertainty with deep neural networks. Traditionally, the dropout mask is sampled independently from a fixed distribution. Recent works show that the dropout mask can be viewed as a latent variable, which can be inferred with variational inference. These methods face two important challenges: (a) the posterior distribution over masks can be highly multi-modal which can be difficult to approximate with standard variational inference and (b) it is not trivial to fully utilize sample-dependent information and correlation among dropout masks to improve posterior estimation. In this work, we propose GFlowOut to address these issues. GFlowOut leverages the recently proposed probabilistic framework of Generative Flow Networks (GFlowNets) to learn the posterior distribution over dropout masks. We empirically demonstrate that GFlowOut results in predictive distributions that generalize better to out-of-distribution data, and provide uncertainty estimates which lead to better performance in downstream tasks.

Stateful active facilitator: Coordination and Environmental Heterogeneity in Cooperative Multi-Agent Reinforcement Learning

In cooperative multi-agent reinforcement learning, a team of agents works together to achieve a common goal. Different environments or tasks may require varying degrees of coordination among agents in order to achieve the goal in an optimal way. The nature of coordination will depend on properties of the environment -- its spatial layout, distribution of obstacles, dynamics, etc. We term this variation of properties within an environment as heterogeneity. Existing literature has not sufficiently addressed the fact that different environments may have different levels of heterogeneity. We formalize the notions of coordination level and heterogeneity level of an environment and present HECOGrid, a suite of multi-agent RL environments that facilitates empirical evaluation of different MARL approaches across different levels of coordination and environmental heterogeneity by providing a quantitative control over coordination and heterogeneity levels of the environment. Further, we propose a Centralized Training Decentralized Execution learning approach called Stateful Active Facilitator (SAF) that enables agents to work efficiently in high-coordination and high-heterogeneity environments through a differentiable and shared knowledge source used during training and dynamic selection from a shared pool of policies. We evaluate SAF and compare its performance against baselines IPPO and MAPPO on HECOGrid. Our results show that SAF consistently outperforms the baselines across different tasks and different heterogeneity and coordination levels.

Graph-Based Active Machine Learning Method for Diverse and Novel Antimicrobial Peptides Generation and Selection

As antibiotic-resistant bacterial strains are rapidly spreading worldwide, infections caused by these strains are emerging as a global crisis causing the death of millions of people every year. Antimicrobial Peptides (AMPs) are one of the candidates to tackle this problem because of their potential diversity, and ability to favorably modulate the host immune response. However, large-scale screening of new AMP candidates is expensive, time-consuming, and now affordable in developing countries, which need the treatments the most. In this work, we propose a novel active machine learning-based framework that statistically minimizes the number of wet-lab experiments needed to design new AMPs, while ensuring a high diversity and novelty of generated AMPs sequences, in multi-rounds of wet-lab AMP screening settings. Combining recurrent neural network models and a graph-based filter (GraphCC), our proposed approach delivers novel and diverse candidates and demonstrates better performances according to our defined metrics.

Coordinating Policies Among Multiple Agents via an Intelligent Communication Channel

In Multi-Agent Reinforcement Learning (MARL), specialized channels are often introduced that allow agents to communicate directly with one another. In this paper, we propose an alternative approach whereby agents communicate through an intelligent facilitator that learns to sift through and interpret signals provided by all agents to improve the agents' collective performance. To ensure that this facilitator does not become a centralized controller, agents are incentivized to reduce their dependence on the messages it conveys, and the messages can only influence the selection of a policy from a fixed set, not instantaneous actions given the policy. We demonstrate the strength of this architecture over existing baselines on several cooperative MARL environments.