Mobile health studies often collect multiple within-day self-reported assessments of participants' behavior and well-being on different scales such as physical activity (continuous), pain levels (truncated), mood states (ordinal), and life events (binary). These assessments, when indexed by time of day, can be treated as functional data of different types - continuous, truncated, ordinal, and binary. We develop a functional principal component analysis that deals with all four types of functional data in a unified manner. It employs a semiparametric Gaussian copula model, assuming a generalized latent non-paranormal process as the underlying mechanism for these four types of functional data. We specify latent temporal dependence using a covariance estimated through Kendall's tau bridging method, incorporating smoothness during the bridging process. Simulation studies demonstrate the method's competitive performance under both dense and sparse sampling conditions. We then apply this approach to data from 497 participants in the National Institute of Mental Health Family Study of the Mood Disorder Spectrum to characterize within-day temporal patterns of mood differences among individuals with major mood disorder subtypes, including Major Depressive Disorder, Type 1, and Type 2 Bipolar Disorder.
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A remarkable ability of human beings resides in compositional reasoning, i.e., the capacity to make "infinite use of finite means". However, current large vision-language foundation models (VLMs) fall short of such compositional abilities due to their "bag-of-words" behaviors and inability to construct words that correctly represent visual entities and the relations among the entities. To this end, we propose CoVLM, which can guide the LLM to explicitly compose visual entities and relationships among the text and dynamically communicate with the vision encoder and detection network to achieve vision-language communicative decoding. Specifically, we first devise a set of novel communication tokens for the LLM, for dynamic communication between the visual detection system and the language system. A communication token is generated by the LLM following a visual entity or a relation, to inform the detection network to propose regions that are relevant to the sentence generated so far. The proposed regions-of-interests (ROIs) are then fed back into the LLM for better language generation contingent on the relevant regions. The LLM is thus able to compose the visual entities and relationships through the communication tokens. The vision-to-language and language-to-vision communication are iteratively performed until the entire sentence is generated. Our framework seamlessly bridges the gap between visual perception and LLMs and outperforms previous VLMs by a large margin on compositional reasoning benchmarks (e.g., ~20% in HICO-DET mAP, ~14% in Cola top-1 accuracy, and ~3% on ARO top-1 accuracy). We also achieve state-of-the-art performances on traditional vision-language tasks such as referring expression comprehension and visual question answering.
The rapid digitization of real-world data offers an unprecedented opportunity for optimizing healthcare delivery and accelerating biomedical discovery. In practice, however, such data is most abundantly available in unstructured forms, such as clinical notes in electronic medical records (EMRs), and it is generally plagued by confounders. In this paper, we present TRIALSCOPE, a unifying framework for distilling real-world evidence from population-level observational data. TRIALSCOPE leverages biomedical language models to structure clinical text at scale, employs advanced probabilistic modeling for denoising and imputation, and incorporates state-of-the-art causal inference techniques to combat common confounders. Using clinical trial specification as generic representation, TRIALSCOPE provides a turn-key solution to generate and reason with clinical hypotheses using observational data. In extensive experiments and analyses on a large-scale real-world dataset with over one million cancer patients from a large US healthcare network, we show that TRIALSCOPE can produce high-quality structuring of real-world data and generates comparable results to marquee cancer trials. In addition to facilitating in-silicon clinical trial design and optimization, TRIALSCOPE may be used to empower synthetic controls, pragmatic trials, post-market surveillance, as well as support fine-grained patient-like-me reasoning in precision diagnosis and treatment.
The acuity state of patients in the intensive care unit (ICU) can quickly change from stable to unstable, sometimes leading to life-threatening conditions. Early detection of deteriorating conditions can result in providing more timely interventions and improved survival rates. Current approaches rely on manual daily assessments. Some data-driven approaches have been developed, that use mortality as a proxy of acuity in the ICU. However, these methods do not integrate acuity states to determine the stability of a patient or the need for life-sustaining therapies. In this study, we propose APRICOT (Acuity Prediction in Intensive Care Unit), a Transformer-based neural network to predict acuity state in real-time in ICU patients. We develop and extensively validate externally, temporally, and prospectively the APRICOT model on three large datasets: University of Florida Health (UFH), eICU Collaborative Research Database (eICU), and Medical Information Mart for Intensive Care (MIMIC)-IV. The performance of APRICOT shows comparable results to state-of-the-art mortality prediction models (external AUROC 0.93-0.93, temporal AUROC 0.96-0.98, and prospective AUROC 0.98) as well as acuity prediction models (external AUROC 0.80-0.81, temporal AUROC 0.77-0.78, and prospective AUROC 0.87). Furthermore, APRICOT can make predictions for the need for life-sustaining therapies, showing comparable results to state-of-the-art ventilation prediction models (external AUROC 0.80-0.81, temporal AUROC 0.87-0.88, and prospective AUROC 0.85), and vasopressor prediction models (external AUROC 0.82-0.83, temporal AUROC 0.73-0.75, prospective AUROC 0.87). This tool allows for real-time acuity monitoring of a patient and can provide helpful information to clinicians to make timely interventions. Furthermore, the model can suggest life-sustaining therapies that the patient might need in the next hours in the ICU.
In many applications, e.g. in healthcare and e-commerce, the goal of a contextual bandit may be to learn an optimal treatment assignment policy at the end of the experiment. That is, to minimize simple regret. However, this objective remains understudied. We propose a new family of computationally efficient bandit algorithms for the stochastic contextual bandit setting, where a tuning parameter determines the weight placed on cumulative regret minimization (where we establish near-optimal minimax guarantees) versus simple regret minimization (where we establish state-of-the-art guarantees). Our algorithms work with any function class, are robust to model misspecification, and can be used in continuous arm settings. This flexibility comes from constructing and relying on "conformal arm sets" (CASs). CASs provide a set of arms for every context, encompassing the context-specific optimal arm with a certain probability across the context distribution. Our positive results on simple and cumulative regret guarantees are contrasted with a negative result, which shows that no algorithm can achieve instance-dependent simple regret guarantees while simultaneously achieving minimax optimal cumulative regret guarantees.
This paper studies inference in randomized controlled trials with multiple treatments, where treatment status is determined according to a "matched tuples" design. Here, by a matched tuples design, we mean an experimental design where units are sampled i.i.d. from the population of interest, grouped into "homogeneous" blocks with cardinality equal to the number of treatments, and finally, within each block, each treatment is assigned exactly once uniformly at random. We first study estimation and inference for matched tuples designs in the general setting where the parameter of interest is a vector of linear contrasts over the collection of average potential outcomes for each treatment. Parameters of this form include standard average treatment effects used to compare one treatment relative to another, but also include parameters which may be of interest in the analysis of factorial designs. We first establish conditions under which a sample analogue estimator is asymptotically normal and construct a consistent estimator of its corresponding asymptotic variance. Combining these results establishes the asymptotic exactness of tests based on these estimators. In contrast, we show that, for two common testing procedures based on t-tests constructed from linear regressions, one test is generally conservative while the other generally invalid. We go on to apply our results to study the asymptotic properties of what we call "fully-blocked" 2^K factorial designs, which are simply matched tuples designs applied to a full factorial experiment. Leveraging our previous results, we establish that our estimator achieves a lower asymptotic variance under the fully-blocked design than that under any stratified factorial design which stratifies the experimental sample into a finite number of "large" strata. A simulation study and empirical application illustrate the practical relevance of our results.
The rapid digitization of real-world data offers an unprecedented opportunity for optimizing healthcare delivery and accelerating biomedical discovery. In practice, however, such data is most abundantly available in unstructured forms, such as clinical notes in electronic medical records (EMRs), and it is generally plagued by confounders. In this paper, we present TRIALSCOPE, a unifying framework for distilling real-world evidence from population-level observational data. TRIALSCOPE leverages biomedical language models to structure clinical text at scale, employs advanced probabilistic modeling for denoising and imputation, and incorporates state-of-the-art causal inference techniques to combat common confounders. Using clinical trial specification as generic representation, TRIALSCOPE provides a turn-key solution to generate and reason with clinical hypotheses using observational data. In extensive experiments and analyses on a large-scale real-world dataset with over one million cancer patients from a large US healthcare network, we show that TRIALSCOPE can produce high-quality structuring of real-world data and generates comparable results to marquee cancer trials. In addition to facilitating in-silicon clinical trial design and optimization, TRIALSCOPE may be used to empower synthetic controls, pragmatic trials, post-market surveillance, as well as support fine-grained patient-like-me reasoning in precision diagnosis and treatment.
Empathy is a social skill that indicates an individual's ability to understand others. Over the past few years, empathy has drawn attention from various disciplines, including but not limited to Affective Computing, Cognitive Science and Psychology. Empathy is a context-dependent term; thus, detecting or recognising empathy has potential applications in society, healthcare and education. Despite being a broad and overlapping topic, the avenue of empathy detection studies leveraging Machine Learning remains underexplored from a holistic literature perspective. To this end, we systematically collect and screen 801 papers from 10 well-known databases and analyse the selected 54 papers. We group the papers based on input modalities of empathy detection systems, i.e., text, audiovisual, audio and physiological signals. We examine modality-specific pre-processing and network architecture design protocols, popular dataset descriptions and availability details, and evaluation protocols. We further discuss the potential applications, deployment challenges and research gaps in the Affective Computing-based empathy domain, which can facilitate new avenues of exploration. We believe that our work is a stepping stone to developing a privacy-preserving and unbiased empathic system inclusive of culture, diversity and multilingualism that can be deployed in practice to enhance the overall well-being of human life.
The presence of detailed clinical information in electronic health record (EHR) systems presents promising prospects for enhancing patient care through automated retrieval techniques. Nevertheless, it is widely acknowledged that accessing data within EHRs is hindered by various methodological challenges. Specifically, the clinical notes stored in EHRs are composed in a narrative form, making them prone to ambiguous formulations and highly unstructured data presentations, while structured reports commonly suffer from missing and/or erroneous data entries. This inherent complexity poses significant challenges when attempting automated large-scale medical knowledge extraction tasks, necessitating the application of advanced tools, such as natural language processing (NLP), as well as data audit techniques. This work aims to address these obstacles by creating and validating a novel pipeline designed to extract relevant data pertaining to prostate cancer patients. The objective is to exploit the inherent redundancies available within the integrated structured and unstructured data entries within EHRs in order to generate comprehensive and reliable medical databases, ready to be used in advanced research studies. Additionally, the study explores potential opportunities arising from these data, offering valuable prospects for advancing research in prostate cancer.
Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.
Ensembles over neural network weights trained from different random initialization, known as deep ensembles, achieve state-of-the-art accuracy and calibration. The recently introduced batch ensembles provide a drop-in replacement that is more parameter efficient. In this paper, we design ensembles not only over weights, but over hyperparameters to improve the state of the art in both settings. For best performance independent of budget, we propose hyper-deep ensembles, a simple procedure that involves a random search over different hyperparameters, themselves stratified across multiple random initializations. Its strong performance highlights the benefit of combining models with both weight and hyperparameter diversity. We further propose a parameter efficient version, hyper-batch ensembles, which builds on the layer structure of batch ensembles and self-tuning networks. The computational and memory costs of our method are notably lower than typical ensembles. On image classification tasks, with MLP, LeNet, and Wide ResNet 28-10 architectures, our methodology improves upon both deep and batch ensembles.
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