搜索结果：Proceedings of machine learning research

The tropics hold most of the planet's biodiversity but face significant knowledge gaps. This is particularly concerning in the Brazilian Amazon, where anthropogenic disturbances are driving species loss. Our study focused on sarcosaprophagous flies, a group with key roles in public health and ecosystem functioning. Using 8244 occurrence records of flies and machine learning, we mapped knowledge distribution at three levels: families, the best-sampled species and a null model simulating chance knowledge probability. Analyses revealed substantial biases. Sampling was uneven, with approximately 40% of forested areas showing <10% probability of occurrence for families and species, while 80% of the region aligned with null expectations. Knowledge probability increased with accessibility, and species were better documented in degraded areas, exceeding chance expectations, whereas remote areas of high conservation value, including Quilombola territories, were neglected. These patterns were consistent across taxonomic levels, highlighting that addressing knowledge biases requires more than increasing research effort. Our findings underscore the importance of studying less-charismatic groups, such as sarcosaprophagous flies. We bring new insights into the value of targeted surveys in remote areas and collaborative engagement with local traditional communities, essential for building a comprehensive understanding of biodiversity and promoting effective conservation in the Amazon.

Deep learning-based electrocardiogram (ECG) classification has shown impressive performance but clinical adoption has been slowed by the lack of transparent and faithful explanations. Post hoc methods such as saliency maps may fail to reflect a model's true decision process. Prototype-based reasoning offers a more transparent alternative by grounding decisions in similarity to learned representations of real ECG segments-enabling faithful, case-based explanations. We introduce ProtoECGNet, a prototype-based deep learning model for interpretable, multi-label ECG classification. ProtoECGNet employs a structured, multi-branch architecture that reflects clinical interpretation workflows: it integrates a 1D CNN with global prototypes for rhythm classification, a 2D CNN with time-localized prototypes for morphology-based reasoning, and a 2D CNN with global prototypes for diffuse abnormalities. Each branch is trained with a prototype loss designed for multi-label learning, combining clustering, separation, diversity, and a novel contrastive loss that encourages appropriate separation between prototypes of unrelated classes while allowing clustering for frequently co-occurring diagnoses. We evaluate ProtoECGNet on all 71 labels from the PTB-XL dataset, demonstrating competitive performance relative to state-of-the-art black-box models while providing structured, case-based explanations. To assess prototype quality, we conduct a structured clinician review of the final model's projected prototypes, finding that they are rated as representative and clear. ProtoECGNet shows that prototype learning can be effectively scaled to complex, multi-label time-series classification, offering a practical path toward transparent and trustworthy deep learning models for clinical decision support.

Reliable prediction of pediatric obesity can offer a valuable resource to providers, helping them engage in timely preventive interventions before the disease is established. Many efforts have been made to develop ML-based predictive models of obesity, and some studies have reported high predictive performances. However, no commonly used clinical decision support tool based on existing ML models currently exists. This study presents a novel end-to-end pipeline specifically designed for pediatric obesity prediction, which supports the entire process of data extraction, inference, and communication via an API or a user interface. While focusing only on routinely recorded data in pediatric electronic health records (EHRs), our pipeline uses a diverse expert-curated list of medical concepts to predict the 1-3 years risk of developing obesity. Furthermore, by using the Fast Healthcare Interoperability Resources (FHIR) standard in our design procedure, we specifically target facilitating low-effort integration of our pipeline with different EHR systems. In our experiments, we report the effectiveness of the predictive model as well as its alignment with the feedback from various stakeholders, including ML scientists, providers, health IT personnel, health administration representatives, and patient group representatives.

Large language models (LLMs) have demonstrated remarkable capabilities for medical question answering and programming, but their potential for generating interpretable computable phenotypes (CPs) is under-explored. In this work, we investigate whether LLMs can generate accurate and concise CPs for six clinical phenotypes of varying complexity, which could be leveraged to enable scalable clinical decision support to improve care for patients with hypertension. In addition to evaluating zero-short performance, we propose and test a synthesize, execute, debug, instruct strategy that uses LLMs to generate and iteratively refine CPs using data-driven feedback. Our results show that LLMs, coupled with iterative learning, can generate interpretable and reasonably accurate programs that approach the performance of state-of-the-art ML methods while requiring significantly fewer training examples.

Probabilistic survival analysis models seek to estimate the distribution of the future occurrence (time) of an event given a set of covariates. In recent years, these models have preferred nonparametric specifications that avoid directly estimating survival distributions via discretization. Specifically, they estimate the probability of an individual event at fixed times or the time of an event at fixed probabilities (quantiles), using supervised learning. Borrowing ideas from the quantile regression literature, we propose a parametric survival analysis method based on the Asymmetric Laplace Distribution (ALD). This distribution allows for closed-form calculation of popular event summaries such as mean, median, mode, variation, and quantiles. The model is optimized by maximum likelihood to learn, at the individual level, the parameters (location, scale, and asymmetry) of the ALD distribution. Extensive results on synthetic and real-world data demonstrate that the proposed method outperforms parametric and nonparametric approaches in terms of accuracy, discrimination and calibration.

Computational design of T cell receptors (TCRs) that bind to epitopes holds the potential to revolutionize targeted immunotherapy. However, computational design of TCRs for novel epitopes is challenging due to the scarcity of training data, and the absence of known cognate TCRs for novel epitopes. In this study, we aim to generate high-quality cognate TCRs particularly for novel epitopes with no known cognate TCRs, a problem that remains under-explored in the field. We propose to incorporate in-context learning, successfully used with large language models to perform new generative tasks, to the task of TCR generation for novel epitopes. By providing cognate TCRs as additional context, we enhance the model's ability to generate high-quality TCRs for novel epitopes. We first unlock the power of in-context learning by training a model to generate new TCRs based on both a target epitope and a small set of its cognate TCRs, so-called in-context training (ICT). We then self-generate its own TCR contexts based on a target epitope, as novel epitopes lack known binding TCRs, and use it as an inference prompt, referred to as self-contemplation prompting (SCP). Our experiments first demonstrate that aligning training and inference distribution by ICT is critical for effectively leveraging context TCRs. Subsequently, we show that providing context TCRs significantly improves TCR generation for novel epitopes. Furthermore, we show TCR generation using SCP-synthesized context TCRs achieves performance comparable to, and sometimes surpassing, ground-truth context TCRs, especially when combined with refined prompt selection based on binding affinity and authenticity metrics. We assess the designed sequences' binding probability and sequence authenticity using seven diverse computational models.

Confounders are extraneous variables that affect both the input and the target, resulting in spurious correlations and biased predictions. There are recent advances in dealing with or removing confounders in traditional models, such as metadata normalization (MDN), where the distribution of the learned features is adjusted based on the study confounders. However, in the context of continual learning, where a model learns continuously from new data over time without forgetting, learning feature representations that are invariant to confounders remains a significant challenge. To remove their influence from intermediate feature representations, we introduce the Recursive MDN (R-MDN) layer, which can be integrated into any deep learning architecture, including vision transformers, and at any model stage. R-MDN performs statistical regression via the recursive least squares algorithm to maintain and continually update an internal model state with respect to changing distributions of data and confounding variables. Our experiments demonstrate that R-MDN promotes equitable predictions across population groups, both within static learning and across different stages of continual learning, by reducing catastrophic forgetting caused by confounder effects changing over time.

Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL is the new frontier for relational learning. TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.

Neural recording technologies now enable simultaneous recording of population activity across many brain regions, motivating the development of data-driven models of communication between brain regions. However, existing models can struggle to disentangle the sources that influence recorded neural populations, leading to inaccurate portraits of inter-regional communication. Here, we introduce Multi-Region Latent Factor Analysis via Dynamical Systems (MR-LFADS), a sequential variational autoencoder designed to disentangle inter-regional communication, inputs from unobserved regions, and local neural population dynamics. We show that MR-LFADS outperforms existing approaches at identifying communication across dozens of simulations of task-trained multi-region networks. When applied to large-scale electrophysiology, MR-LFADS predicts brain-wide effects of circuit perturbations that were held out during model fitting. These validations on synthetic and real neural data position MR-LFADS as a promising tool for discovering principles of brain-wide information processing.

Modality fusion is a cornerstone of multimodal learning, enabling information integration from diverse data sources. However, vanilla fusion methods are limited by (1) inability to account for heterogeneous interactions between modalities and (2) lack of interpretability in uncovering the multimodal interactions inherent in the data. To this end, we propose I2MoE (Interpretable Multimodal Interaction-aware Mixture of Experts), an end-to-end MoE framework designed to enhance modality fusion by explicitly modeling diverse multimodal interactions, as well as providing interpretation on a local and global level. First, I2MoE utilizes different interaction experts with weakly supervised interaction losses to learn multimodal interactions in a data-driven way. Second, I2MoE deploys a reweighting model that assigns importance scores for the output of each interaction expert, which offers sample-level and dataset-level interpretation. Extensive evaluation of medical and general multimodal datasets shows that I2MoE is flexible enough to be combined with different fusion techniques, consistently improves task performance, and provides interpretation across various real-world scenarios. Code is available at https://github.com/Raina-Xin/I2MoE.

Self-supervised learning of multi-modal, high-frequency physiological signals is largely unexplored, despite its potential for critical care applications. We present PhysioJEPA, a Joint Embedding Predictive Architecture (JEPA) designed for multi-modal physiological signals from critical care bedside monitoring devices. PhysioJEPA learns representations from 30-minute segments of physiological signals from three channels: arterial blood pressure, electrocardiography lead II, and photoplethysmography. Trained on over 10.7 million minutes of data from 4,282 intensive care unit stays (N=2,631 patients) in the Medical Information Mart for Intensive Care-III (MIMIC-III) Waveform Database, the learned, frozen representations of PhysioJEPA can be used to estimate 5-minute risk of hypotension (AUROC = 0.83 [Confidence Interval or CI 0.83-0.84]) and shock index (AUROC = 0.95 [0.95-0.96]), with comparable performance to a self-supervised Patch Time Series Transformer framework (AUROC = 0.87 [0.86-0.87] and 0.96 [0.96-0.96]), better performance compared to another JEPA physiological signal model, ECG-JEPA (AUROC = 0.73 [0.72-74] and 0.92 [0.92-0.93]), and better performance compared to a supervised convolutional model (AUROC = 0.78 [0.78-0.78] and 0.95 [0.95-0.95]). Notably, it can generalize to an independent healthcare system (AUROC = 0.78 [0.78-0.78] and 0.92 [0.92-0.93]) better than all comparison models. These results suggest that self-supervised JEPA representation learning is a promising approach for multi-modal bedside monitoring signal data.

Medical research faces well-documented challenges in translating novel treatments into clinical practice. Publishing incentives encourage researchers to present "positive" findings, even when empirical results are equivocal. Consequently, it is well-documented that authors often spin study results, especially in article abstracts. Such spin can influence clinician interpretation of evidence and may affect patient care decisions. In this study, we ask whether the interpretation of trial results offered by Large Language Models (LLMs) is similarly affected by spin. This is important since LLMs are increasingly being used to trawl through and synthesize published medical evidence. We evaluated 22 LLMs and found that they are across the board more susceptible to spin than humans. They might also propagate spin into their outputs: We find evidence, e.g., that LLMs implicitly incorporate spin into plain language summaries that they generate. We also find, however, that LLMs are generally capable of recognizing spin, and can be prompted in a way to mitigate spin's impact on LLM outputs.

Personalized federated learning (PFL) based on Bayesian approach tackle the challenges from statistical heterogeneity of client data by computing a personalized posterior distribution over the parameters of each client's local model and constructing a global distribution by aggregating the parameters of these personalized posteriors. However, the heuristic aggregation methods introduce strong biases and result in global models with poor generalization. We thus propose a novel hierarchical Bayesian inference framework for PFL by specifying a conjugate hyper-prior over the parameters of the personalized posteriors. This allows us to jointly compute a global posterior distribution for aggregation and the personalized ones at local level. This hierarchical Bayesian inference framework achieves elegant balance between local personalization and global model robustness. Extensive empirical study shows that by effectively sharing the heterogeneous statistical strength across the local models while retaining their distinctive characteristics, our framework yields state-of-the-art performance. We also show that existing Bayesian PFLs are special cases of our framework.

Use of machine learning to perform database operations, such as indexing, cardinality estimation, and sorting, is shown to provide substantial performance benefits. However, when datasets change and data distribution shifts, empirical results also show performance degradation for learned models, possibly to worse than non-learned alternatives. This, together with a lack of theoretical understanding of learned methods undermines their practical applicability, since there are no guarantees on how well the models will perform after deployment. In this paper, we present the first known theoretical characterization of the performance of learned models in dynamic datasets, for the aforementioned operations. Our results show novel theoretical characteristics achievable by learned models and provide bounds on the performance of the models that characterize their advantages over non-learned methods, showing why and when learned models can outperform the alternatives. Our analysis develops the distribution learnability framework and novel theoretical tools which build the foundation for the analysis of learned database operations in the future.

Encoding geospatial objects is fundamental for geospatial artificial intelligence (GeoAI) applications, which leverage machine learning (ML) models to analyze spatial information. Common approaches transform each object into known formats, like image and text, for compatibility with ML models. However, this process often discards crucial spatial information, such as the object's position relative to the entire space, reducing downstream task effectiveness. Alternative encoding methods that preserve some spatial properties are often devised for specific data objects (e.g., point encoders), making them unsuitable for tasks that involve different data types (i.e., points, polylines, and polygons). To this end, we propose Poly2Vec, a polymorphic Fourier-based encoding approach that unifies the representation of geospatial objects, while preserving the essential spatial properties. Poly2Vec incorporates a learned fusion module that adaptively integrates the magnitude and phase of the Fourier transform for different tasks and geometries. We evaluate Poly2Vec on five diverse tasks, organized into two categories. The first empirically demonstrates that Poly2Vec consistently outperforms object-specific baselines in preserving three key spatial relationships: topology, direction, and distance. The second shows that integrating Poly2Vec into a state-of-the-art GeoAI workflow improves the performance in two popular tasks: population prediction and land use inference.

Persistence diagrams are one of the most popular types of data summaries used in Topological Data Analysis. The prevailing statistical approach to analyzing persistence diagrams is concerned with filtering out topological noise. In this paper, we adopt a different viewpoint and aim at estimating the actual distribution of a random persistence diagram, which captures both topological signal and noise. To that effect, Chazal and Divol (2019) proved that, under general conditions, the expected value of a random persistence diagram is a measure admitting a Lebesgue density, called the persistence intensity function. In this paper, we are concerned with estimating the persistence intensity function and a novel, normalized version of it - called the persistence density function. We present a class of kernel-based estimators based on an i.i.d. sample of persistence diagrams and derive estimation rates in the supremum norm. As a direct corollary, we obtain uniform consistency rates for estimating linear representations of persistence diagrams, including Betti numbers and persistence surfaces. Interestingly, the persistence density function delivers stronger statistical guarantees.

We consider reinforcement learning (RL) for a class of problems with bagged decision times. A bag contains a finite sequence of consecutive decision times. The transition dynamics are non-Markovian and non-stationary within a bag. All actions within a bag jointly impact a single reward, observed at the end of the bag. For example, in mobile health, multiple activity suggestions in a day collectively affect a user's daily commitment to being active. Our goal is to develop an online RL algorithm to maximize the discounted sum of the bag-specific rewards. To handle non-Markovian transitions within a bag, we utilize an expert-provided causal directed acyclic graph (DAG). Based on the DAG, we construct states as a dynamical Bayesian sufficient statistic of the observed history, which results in Markov state transitions within and across bags. We then formulate this problem as a periodic Markov decision process (MDP) that allows non-stationarity within a period. An online RL algorithm based on Bellman equations for stationary MDPs is generalized to handle periodic MDPs. We show that our constructed state achieves the maximal optimal value function among all state constructions for a periodic MDP. Finally, we evaluate the proposed method on testbed variants built from real data in a mobile health clinical trial.

Ensemble learning is a powerful approach for improving generalization under distribution shifts, but its effectiveness heavily depends on how individual models are combined. Existing methods often optimize ensemble weights based on validation data, which may not represent unseen test distributions, leading to suboptimal performance in out-of-distribution (OoD) settings. Inspired by Distributionally Robust Optimization (DRO), we propose Structure-informed Risk Minimization (SRM), a principled framework that learns robust ensemble weights without access to test data. Unlike standard DRO, which defines uncertainty sets based on divergence metrics alone, SRM incorporates structural information of training distributions, ensuring that the uncertainty set aligns with plausible real-world shifts. This approach mitigates the over-pessimism of traditional worst-case optimization while maintaining robustness. We introduce a computationally efficient optimization algorithm with theoretical guarantees and demonstrate that SRM achieves superior OoD generalization compared to existing ensemble combination strategies across diverse benchmarks. Code is available at: https://github.com/deep-real/SRM.

Selective labels occur when label observations are subject to a decision-making process; e.g., diagnoses that depend on the administration of laboratory tests. We study a clinically-inspired selective label problem called disparate censorship, where labeling biases vary across subgroups and unlabeled individuals are imputed as "negative" (i.e., no diagnostic test = no illness). Machine learning models na&#xef;vely trained on such labels could amplify labeling bias. Inspired by causal models of selective labels, we propose Disparate Censorship Expectation-Maximization (DCEM), an algorithm for learning in the presence of disparate censorship. We theoretically analyze how DCEM mitigates the effects of disparate censorship on model performance. We validate DCEM on synthetic data, showing that it improves bias mitigation (area between ROC curves) without sacrificing discriminative performance (AUC) compared to baselines. We achieve similar results in a sepsis classification task using clinical data.