Family history is considered a risk factor for many diseases because it implicitly captures shared genetic, environmental and lifestyle factors. Finland's nationwide electronic health record (EHR) system spanning multiple generations presents new opportunities for studying a connected network of medical histories for entire families. In this work we present a graph-based deep learning approach for learning explainable, supervised representations of how each family member's longitudinal medical history influences a patient's disease risk. We demonstrate that this approach is beneficial for predicting 10-year disease onset for 5 complex disease phenotypes, compared to clinically-inspired and deep learning baselines for Finland's nationwide EHR system comprising 7 million individuals with up to third-degree relatives. Through the use of graph explainability techniques, we illustrate that a graph-based approach enables more personalized modeling of family information and disease risk by identifying important relatives and features for prediction.
相關內容
Auxiliary data sources have become increasingly important in epidemiological surveillance, as they are often available at a finer spatial and temporal resolution, larger coverage, and lower latency than traditional surveillance signals. We describe the problem of spatial and temporal heterogeneity in these signals derived from these data sources, where spatial and/or temporal biases are present. We present a method to use a ``guiding'' signal to correct for these biases and produce a more reliable signal that can be used for modeling and forecasting. The method assumes that the heterogeneity can be approximated by a low-rank matrix and that the temporal heterogeneity is smooth over time. We also present a hyperparameter selection algorithm to choose the parameters representing the matrix rank and degree of temporal smoothness of the corrections. In the absence of ground truth, we use maps and plots to argue that this method does indeed reduce heterogeneity. Reducing heterogeneity from auxiliary data sources greatly increases their utility in modeling and forecasting epidemics.
The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.
Flexible estimation of the mean outcome under a treatment regimen (i.e., value function) is the key step toward personalized medicine. We define our target parameter as a conditional value function given a set of baseline covariates which we refer to as a stratum based value function. We focus on semiparametric class of decision rules and propose a sieve based nonparametric covariate adjusted regimen-response curve estimator within that class. Our work contributes in several ways. First, we propose an inverse probability weighted nonparametrically efficient estimator of the smoothed regimen-response curve function. We show that asymptotic linearity is achieved when the nuisance functions are undersmoothed sufficiently. Asymptotic and finite sample criteria for undersmoothing are proposed. Second, using Gaussian process theory, we propose simultaneous confidence intervals for the smoothed regimen-response curve function. Third, we provide consistency and convergence rate for the optimizer of the regimen-response curve estimator; this enables us to estimate an optimal semiparametric rule. The latter is important as the optimizer corresponds with the optimal dynamic treatment regimen. Some finite-sample properties are explored with simulations.
Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how weakly supervised and self-supervised deep learning approaches scale when training larger models on larger datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised models. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 95-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised models at inferring known biological relationships curated from public databases.
Understanding the interactions of a solute with its environment is of fundamental importance in chemistry and biology. In this work, we propose a deep neural network architecture for atom type embeddings in its molecular context and interatomic potential that follows fundamental physical laws. The architecture is applied to predict physicochemical properties in heterogeneous systems including solvation in diverse solvents, 1-octanol-water partitioning, and PAMPA with a single set of network weights. We show that our architecture is generalized well to the physicochemical properties and outperforms state-of-the-art approaches based on quantum mechanics and neural networks in the task of solvation free energy prediction. The interatomic potentials at each atom in a solute obtained from the model allow quantitative analysis of the physicochemical properties at atomic resolution consistent with chemical and physical reasoning. The software is available at //github.com/SehanLee/C3Net.
Multilingual self-supervised learning (SSL) has often lagged behind state-of-the-art (SOTA) methods due to the expenses and complexity required to handle many languages. This further harms the reproducibility of SSL, which is already limited to few research groups due to its resource usage. We show that more powerful techniques can actually lead to more efficient pre-training, opening SSL to more research groups. We propose WavLabLM, which extends WavLM's joint prediction and denoising to 40k hours of data across 136 languages. To build WavLabLM, we devise a novel multi-stage pre-training method, designed to address the language imbalance of multilingual data. WavLabLM achieves comparable performance to XLS-R on ML-SUPERB with less than 10% of the training data, making SSL realizable with academic compute. We show that further efficiency can be achieved with a vanilla HuBERT Base model, which can maintain 94% of XLS-R's performance with only 3% of the data, 4 GPUs, and limited trials. We open-source all code and models in ESPnet.
This study focuses on how different modalities of human communication can be used to distinguish between healthy controls and subjects with schizophrenia who exhibit strong positive symptoms. We developed a multi-modal schizophrenia classification system using audio, video, and text. Facial action units and vocal tract variables were extracted as low-level features from video and audio respectively, which were then used to compute high-level coordination features that served as the inputs to the audio and video modalities. Context-independent text embeddings extracted from transcriptions of speech were used as the input for the text modality. The multi-modal system is developed by fusing a segment-to-session-level classifier for video and audio modalities with a text model based on a Hierarchical Attention Network (HAN) with cross-modal attention. The proposed multi-modal system outperforms the previous state-of-the-art multi-modal system by 8.53% in the weighted average F1 score.
In causal inference studies, interest often lies in understanding the mechanisms through which a treatment affects an outcome. One approach is principal stratification (PS), which introduces well-defined causal effects in the presence of confounded post-treatment variables, or mediators, and clearly defines the assumptions for identification and estimation of those effects. The goal of this paper is to extend the PS framework to studies with continuous treatments and continuous post-treatment variables, which introduces a number of unique challenges both in terms of defining causal effects and performing inference. This manuscript provides three key methodological contributions: 1) we introduce novel principal estimands for continuous treatments that provide valuable insights into different causal mechanisms, 2) we utilize Bayesian nonparametric approaches to model the joint distribution of the potential mediating variables based on both Gaussian processes and Dirichlet process mixtures to ensure our approach is robust to model misspecification, and 3) we provide theoretical and numerical justification for utilizing a model for the potential outcomes to identify the joint distribution of the potential mediating variables. Lastly, we apply our methodology to a novel study of the relationship between the economy and arrest rates, and how this is potentially mediated by police capacity.
In large-scale systems there are fundamental challenges when centralised techniques are used for task allocation. The number of interactions is limited by resource constraints such as on computation, storage, and network communication. We can increase scalability by implementing the system as a distributed task-allocation system, sharing tasks across many agents. However, this also increases the resource cost of communications and synchronisation, and is difficult to scale. In this paper we present four algorithms to solve these problems. The combination of these algorithms enable each agent to improve their task allocation strategy through reinforcement learning, while changing how much they explore the system in response to how optimal they believe their current strategy is, given their past experience. We focus on distributed agent systems where the agents' behaviours are constrained by resource usage limits, limiting agents to local rather than system-wide knowledge. We evaluate these algorithms in a simulated environment where agents are given a task composed of multiple subtasks that must be allocated to other agents with differing capabilities, to then carry out those tasks. We also simulate real-life system effects such as networking instability. Our solution is shown to solve the task allocation problem to 6.7% of the theoretical optimal within the system configurations considered. It provides 5x better performance recovery over no-knowledge retention approaches when system connectivity is impacted, and is tested against systems up to 100 agents with less than a 9% impact on the algorithms' performance.
Knowledge graphs (KGs) of real-world facts about entities and their relationships are useful resources for a variety of natural language processing tasks. However, because knowledge graphs are typically incomplete, it is useful to perform knowledge graph completion or link prediction, i.e. predict whether a relationship not in the knowledge graph is likely to be true. This paper serves as a comprehensive survey of embedding models of entities and relationships for knowledge graph completion, summarizing up-to-date experimental results on standard benchmark datasets and pointing out potential future research directions.
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191