DEs provide relationships between some, but not all, factors relevant to AD. We assume that the missing relationships must satisfy general criteria about the working of the brain, for e.g., maximizing cognition while minimizing the cost of supporting cognition. This allows us to extract the missing relationships by using RL to optimize an objective (reward) function that captures the above criteria. We use our model consisting of DEs (as a simulator) and the trained RL agent to predict individualized 10-year AD progression using baseline (year 0) features on synthetic and real data. The model was comparable or better at predicting 10-year cognition trajectories than state-of-the-art learning-based models. Our interpretable model demonstrated, and provided insights into, recovery/compensatory processes that mitigate the effect of AD, even though those processes were not explicitly encoded in the model. Our framework combines DEs with RL for modelling AD progression and has broad applicability for understanding other neurological disorders.

Large Language Models (LLMs) have demonstrated remarkable capabilities across various domains and are moving towards more specialized areas. Recent advanced proprietary models such as GPT-4 and Gemini have achieved significant advancements in biomedicine, which have also raised privacy and security challenges. The construction of specialized generalists hinges largely on high-quality datasets, enhanced by techniques like supervised fine-tuning and reinforcement learning from human or AI feedback, and direct preference optimization. However, these leading technologies (e.g., preference learning) are still significantly limited in the open source community due to the scarcity of specialized data. In this paper, we present the UltraMedical collections, which consist of high-quality manual and synthetic datasets in the biomedicine domain, featuring preference annotations across multiple advanced LLMs. By utilizing these datasets, we fine-tune a suite of specialized medical models based on Llama-3 series, demonstrating breathtaking capabilities across various medical benchmarks. Moreover, we develop powerful reward models skilled in biomedical and general reward benchmark, enhancing further online preference learning within the biomedical LLM community.

A central mechanism in machine learning is to identify, store, and recognize patterns. How to learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent transformer architectures. We show that the attention mechanism of transformer architectures is actually the update rule of modern Hopfield networks that can store exponentially many patterns. We exploit this high storage capacity of modern Hopfield networks to solve a challenging multiple instance learning (MIL) problem in computational biology: immune repertoire classification. In immune repertoire classification, a vast number of immune receptors are used to predict the immune status of an individual. This constitutes a MIL problem with an unprecedentedly massive number of instances, two orders of magnitude larger than currently considered problems, and with an extremely low witness rate. Accurate and interpretable machine learning methods solving this problem could pave the way towards new vaccines and therapies, which is currently a very relevant research topic intensified by the COVID-19 crisis.

We propose a novel approach that integrates machine learning into compartmental disease modeling (e.g., SEIR) to predict the progression of COVID-19. Our model is explainable by design as it explicitly shows how different compartments evolve and it uses interpretable encoders to incorporate covariates and improve performance. Explainability is valuable to ensure that the model's forecasts are credible to epidemiologists and to instill confidence in end-users such as policy makers and healthcare institutions. Our model can be applied at different geographic resolutions, and we demonstrate it for states and counties in the United States. We show that our model provides more accurate forecasts compared to the alternatives, and that it provides qualitatively meaningful explanatory insights.

Image restoration techniques, spanning from the convolution to the transformer paradigm, have demonstrated robust spatial representation capabilities to deliver high-quality performance.Yet, many of these methods, such as convolution and the Feed Forward Network (FFN) structure of transformers, primarily leverage the basic first-order channel interactions and have not maximized the potential benefits of higher-order modeling. To address this limitation, our research dives into understanding relationships within the channel dimension and introduces a simple yet efficient, high-order channel-wise operator tailored for image restoration. Instead of merely mimicking high-order spatial interaction, our approach offers several added benefits: Efficiency: It adheres to the zero-FLOP and zero-parameter principle, using a spatial-shifting mechanism across channel-wise groups. Simplicity: It turns the favorable channel interaction and aggregation capabilities into element-wise multiplications and convolution units with $1 \times 1$ kernel. Our new formulation expands the first-order channel-wise interactions seen in previous works to arbitrary high orders, generating a hierarchical receptive field akin to a Rubik's cube through the combined action of shifting and interactions. Furthermore, our proposed Rubik's cube convolution is a flexible operator that can be incorporated into existing image restoration networks, serving as a drop-in replacement for the standard convolution unit with fewer parameters overhead. We conducted experiments across various low-level vision tasks, including image denoising, low-light image enhancement, guided image super-resolution, and image de-blurring. The results consistently demonstrate that our Rubik's cube operator enhances performance across all tasks.

Many experts argue that the future of artificial intelligence is limited by the field's ability to integrate symbolic logical reasoning into deep learning architectures. The recently proposed differentiable MAXSAT solver, SATNet, was a breakthrough in its capacity to integrate with a traditional neural network and solve visual reasoning problems. For instance, it can learn the rules of Sudoku purely from image examples. Despite its success, SATNet was shown to succumb to a key challenge in neurosymbolic systems known as the Symbol Grounding Problem: the inability to map visual inputs to symbolic variables without explicit supervision (label leakage). In this work, we present a self-supervised pre-training pipeline that enables SATNet to overcome this limitation, thus broadening the class of problems that SATNet architectures can solve to include datasets where no intermediary labels are available at all. We demonstrate that our method allows SATNet to attain full accuracy even with a harder problem setup that prevents any label leakage. We additionally introduce a proofreading method that further improves the performance of SATNet architectures, beating the state-of-the-art on Visual Sudoku.

The COVID-19 pandemic continues to bring up various topics discussed or debated on social media. In order to explore the impact of pandemics on people's lives, it is crucial to understand the public's concerns and attitudes towards pandemic-related entities (e.g., drugs, vaccines) on social media. However, models trained on existing named entity recognition (NER) or targeted sentiment analysis (TSA) datasets have limited ability to understand COVID-19-related social media texts because these datasets are not designed or annotated from a medical perspective. In this paper, we release METS-CoV, a dataset containing medical entities and targeted sentiments from COVID-19 related tweets. METS-CoV contains 10,000 tweets with 7 types of entities, including 4 medical entity types (Disease, Drug, Symptom, and Vaccine) and 3 general entity types (Person, Location, and Organization). To further investigate tweet users' attitudes toward specific entities, 4 types of entities (Person, Organization, Drug, and Vaccine) are selected and annotated with user sentiments, resulting in a targeted sentiment dataset with 9,101 entities (in 5,278 tweets). To the best of our knowledge, METS-CoV is the first dataset to collect medical entities and corresponding sentiments of COVID-19 related tweets.

Team sports is a new application domain for agent modeling with high real-world impact. A fundamental challenge for modeling professional players is their large number (over 1K), which includes many bench players with sparse participation in a game season. The diversity and sparsity of player observations make it difficult to extend previous agent representation models to the sports domain. This paper develops a new approach for agent representations, based on a Markov game model, that is tailored towards applications in professional ice hockey. We introduce a novel player representation via player generation framework where a variational encoder embeds player information with latent variables. The encoder learns a context-specific shared prior to induce a shrinkage effect for the posterior player representations, allowing it to share statistical information across players with different participations. To model the play dynamics in sequential sports data, we design a Variational Recurrent Ladder Agent Encoder (VaRLAE). It learns a contextualized player representation with a hierarchy of latent variables that effectively prevents latent posterior collapse.

In this paper, we focus on auditing black-box prediction models for compliance with the GDPR's data minimization principle. This principle restricts prediction models to use the minimal information that is necessary for performing the task at hand. Given the challenge of the black-box setting, our key idea is to check if each of the prediction model's input features is individually necessary by assigning it some constant value (i.e., applying a simple imputation) across all prediction instances, and measuring the extent to which the model outcomes would change. We introduce a metric for data minimization that is based on model instability under simple imputations. We extend the applicability of this metric from a finite sample model to a distributional setting by introducing a probabilistic data minimization guarantee, which we derive using a Bayesian approach. Furthermore, we address the auditing problem under a constraint on the number of queries to the prediction system.

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