Electronic health records (EHR) offer unprecedented opportunities for in-depth clinical phenotyping and prediction of clinical outcomes. Combining multiple data sources is crucial to generate a complete picture of disease prevalence, incidence and trajectories. The standard approach to combining clinical data involves collating clinical terms across different terminology systems using curated maps, which are often inaccurate and/or incomplete. Here, we propose sEHR-CE, a novel framework based on transformers to enable integrated phenotyping and analyses of heterogeneous clinical datasets without relying on these mappings. We unify clinical terminologies using textual descriptors of concepts, and represent individuals' EHR as sections of text. We then fine-tune pre-trained language models to predict disease phenotypes more accurately than non-text and single terminology approaches. We validate our approach using primary and secondary care data from the UK Biobank, a large-scale research study. Finally, we illustrate in a type 2 diabetes use case how sEHR-CE identifies individuals without diagnosis that share clinical characteristics with patients.

Choosing which properties of the data to use as input to multivariate decision algorithms -- a.k.a. feature selection -- is an important step in solving any problem with machine learning. While there is a clear trend towards training sophisticated deep networks on large numbers of relatively unprocessed inputs (so-called automated feature engineering), for many tasks in physics, sets of theoretically well-motivated and well-understood features already exist. Working with such features can bring many benefits, including greater interpretability, reduced training and run time, and enhanced stability and robustness. We develop a new feature selection method based on Distance Correlation (DisCo), and demonstrate its effectiveness on the tasks of boosted top- and $W$-tagging. Using our method to select features from a set of over 7,000 energy flow polynomials, we show that we can match the performance of much deeper architectures, by using only ten features and two orders-of-magnitude fewer model parameters.

Recent advances in operator learning theory have improved our knowledge about learning maps between infinite dimensional spaces. However, for large-scale engineering problems such as concurrent multiscale simulation for mechanical properties, the training cost for the current operator learning methods is very high. The article presents a thorough analysis on the mathematical underpinnings of the operator learning paradigm and proposes a kernel learning method that maps between function spaces. We first provide a survey of modern kernel and operator learning theory, as well as discuss recent results and open problems. From there, the article presents an algorithm to how we can analytically approximate the piecewise constant functions on R for operator learning. This implies the potential feasibility of success of neural operators on clustered functions. Finally, a k-means clustered domain on the basis of a mechanistic response is considered and the Lippmann-Schwinger equation for micro-mechanical homogenization is solved. The article briefly discusses the mathematics of previous kernel learning methods and some preliminary results with those methods. The proposed kernel operator learning method uses graph kernel networks to come up with a mechanistic reduced order method for multiscale homogenization.

Pretrained transformer models have achieved state-of-the-art results in many tasks and benchmarks recently. Many state-of-the-art Language Models (LMs), however, do not scale well above the threshold of 512 input tokens. In specialized domains though (such as legal, scientific or biomedical), models often need to process very long text (sometimes well above 10000 tokens). Even though many efficient transformers have been proposed (such as Longformer, BigBird or FNet), so far, only very few such efficient models are available for specialized domains. Additionally, since the pretraining process is extremely costly in general - but even more so as the sequence length increases - it is often only in reach of large research labs. One way of making pretraining cheaper is the Replaced Token Detection (RTD) task, by providing more signal during training, since the loss can be computed over all tokens. In this work, we train Longformer models with the efficient RTD task on legal data to showcase that pretraining efficient LMs is possible using much less compute. We evaluate the trained models on challenging summarization tasks requiring the model to summarize long texts to show to what extent the models can achieve good performance on downstream tasks. We find that both the small and base models outperform their baselines on the in-domain BillSum and out-of-domain PubMed tasks in their respective parameter range. We publish our code and models for research purposes.

In contrast to the rapid digitalization of several industries, agriculture suffers from low adoption of smart farming tools. While AI-driven digital agriculture tools can offer high-performing predictive functionalities, they lack tangible quantitative evidence on their benefits to the farmers. Field experiments can derive such evidence, but are often costly, time consuming and hence limited in scope and scale of application. To this end, we propose an observational causal inference framework for the empirical evaluation of the impact of digital tools on target farm performance indicators (e.g., yield in this case). This way, we can increase farmers' trust via enhancing the transparency of the digital agriculture market and accelerate the adoption of technologies that aim to secure farmer income resilience and global agricultural sustainability. As a case study, we designed and implemented a recommendation system for the optimal sowing time of cotton based on numerical weather predictions, which was used by a farmers' cooperative during the growing season of 2021. We then leverage agricultural knowledge, collected yield data, and environmental information to develop a causal graph of the farm system. Using the back-door criterion, we identify the impact of sowing recommendations on the yield and subsequently estimate it using linear regression, matching, inverse propensity score weighting and meta-learners. The results reveal that a field sown according to our recommendations exhibited a statistically significant yield increase that ranged from 12% to 17%, depending on the method. The effect estimates were robust, as indicated by the agreement among the estimation methods and four successful refutation tests. We argue that this approach can be implemented for decision support systems of other fields, extending their evaluation beyond a performance assessment of internal functionalities.

A normalizing flow (NF) is a mapping that transforms a chosen probability distribution to a normal distribution. Such flows are a common technique used for data generation and density estimation in machine learning and data science. The density estimate obtained with a NF requires a change of variables formula that involves the computation of the Jacobian determinant of the NF transformation. In order to tractably compute this determinant, continuous normalizing flows (CNF) estimate the mapping and its Jacobian determinant using a neural ODE. Optimal transport (OT) theory has been successfully used to assist in finding CNFs by formulating them as OT problems with a soft penalty for enforcing the standard normal distribution as a target measure. A drawback of OT-based CNFs is the addition of a hyperparameter, $\alpha$, that controls the strength of the soft penalty and requires significant tuning. We present JKO-Flow, an algorithm to solve OT-based CNF without the need of tuning $\alpha$. This is achieved by integrating the OT CNF framework into a Wasserstein gradient flow framework, also known as the JKO scheme. Instead of tuning $\alpha$, we repeatedly solve the optimization problem for a fixed $\alpha$ effectively performing a JKO update with a time-step $\alpha$. Hence we obtain a "divide and conquer" algorithm by repeatedly solving simpler problems instead of solving a potentially harder problem with large $\alpha$.

One of the most successful paradigms for reward learning uses human feedback in the form of comparisons. Although these methods hold promise, human comparison labeling is expensive and time consuming, constituting a major bottleneck to their broader applicability. Our insight is that we can greatly improve how effectively human time is used in these approaches by batching comparisons together, rather than having the human label each comparison individually. To do so, we leverage data dimensionality-reduction and visualization techniques to provide the human with a interactive GUI displaying the state space, in which the user can label subportions of the state space. Across some simple Mujoco tasks, we show that this high-level approach holds promise and is able to greatly increase the performance of the resulting agents, provided the same amount of human labeling time.

Graph neural networks (GNNs) are popular weapons for modeling relational data. Existing GNNs are not specified for attribute-incomplete graphs, making missing attribute imputation a burning issue. Until recently, many works notice that GNNs are coupled with spectral concentration, which means the spectrum obtained by GNNs concentrates on a local part in spectral domain, e.g., low-frequency due to oversmoothing issue. As a consequence, GNNs may be seriously flawed for reconstructing graph attributes as graph spectral concentration tends to cause a low imputation precision. In this work, we present a regularized graph autoencoder for graph attribute imputation, named MEGAE, which aims at mitigating spectral concentration problem by maximizing the graph spectral entropy. Notably, we first present the method for estimating graph spectral entropy without the eigen-decomposition of Laplacian matrix and provide the theoretical upper error bound. A maximum entropy regularization then acts in the latent space, which directly increases the graph spectral entropy. Extensive experiments show that MEGAE outperforms all the other state-of-the-art imputation methods on a variety of benchmark datasets.

The target of image-text clustering (ITC) is to find correct clusters by integrating complementary and consistent information of multi-modalities for these heterogeneous samples. However, the majority of current studies analyse ITC on the ideal premise that the samples in every modality are complete. This presumption, however, is not always valid in real-world situations. The missing data issue degenerates the image-text feature learning performance and will finally affect the generalization abilities in ITC tasks. Although a series of methods have been proposed to address this incomplete image text clustering issue (IITC), the following problems still exist: 1) most existing methods hardly consider the distinct gap between heterogeneous feature domains. 2) For missing data, the representations generated by existing methods are rarely guaranteed to suit clustering tasks. 3) Existing methods do not tap into the latent connections both inter and intra modalities. In this paper, we propose a Clustering-Induced Generative Incomplete Image-Text Clustering(CIGIT-C) network to address the challenges above. More specifically, we first use modality-specific encoders to map original features to more distinctive subspaces. The latent connections between intra and inter-modalities are thoroughly explored by using the adversarial generating network to produce one modality conditional on the other modality. Finally, we update the corresponding modalityspecific encoders using two KL divergence losses. Experiment results on public image-text datasets demonstrated that the suggested method outperforms and is more effective in the IITC job.

Since higher-order tensors are naturally suitable for representing multi-dimensional data in real-world, e.g., color images and videos, low-rank tensor representation has become one of the emerging areas in machine learning and computer vision. However, classical low-rank tensor representations can only represent data on finite meshgrid due to their intrinsical discrete nature, which hinders their potential applicability in many scenarios beyond meshgrid. To break this barrier, we propose a low-rank tensor function representation (LRTFR), which can continuously represent data beyond meshgrid with infinite resolution. Specifically, the suggested tensor function, which maps an arbitrary coordinate to the corresponding value, can continuously represent data in an infinite real space. Parallel to discrete tensors, we develop two fundamental concepts for tensor functions, i.e., the tensor function rank and low-rank tensor function factorization. We theoretically justify that both low-rank and smooth regularizations are harmoniously unified in the LRTFR, which leads to high effectiveness and efficiency for data continuous representation. Extensive multi-dimensional data recovery applications arising from image processing (image inpainting and denoising), machine learning (hyperparameter optimization), and computer graphics (point cloud upsampling) substantiate the superiority and versatility of our method as compared with state-of-the-art methods. Especially, the experiments beyond the original meshgrid resolution (hyperparameter optimization) or even beyond meshgrid (point cloud upsampling) validate the favorable performances of our method for continuous representation.