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Publications
Trajectory Flow Matching with Applications to Clinical Time Series Modeling
Modeling stochastic and irregularly sampled time series is a challenging problem found in a wide range of applications, especially in medici… (voir plus)ne. Neural stochastic differential equations (Neural SDEs) are an attractive modeling technique for this problem, which parameterize the drift and diffusion terms of an SDE with neural networks. However, current algorithms for training Neural SDEs require backpropagation through the SDE dynamics, greatly limiting their scalability and stability. To address this, we propose Trajectory Flow Matching (TFM), which trains a Neural SDE in a simulation-free manner, bypassing backpropagation through the dynamics. TFM leverages the flow matching technique from generative modeling to model time series. In this work we first establish necessary conditions for TFM to learn time series data. Next, we present a reparameterization trick which improves training stability. Finally, we adapt TFM to the clinical time series setting, demonstrating improved performance on three clinical time series datasets both in terms of absolute performance and uncertainty prediction.
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress… (voir plus) has been made in predicting static folded structures, modeling protein motions on microsecond to millisecond scales remains challenging. To address these challenges, we introduce a novel deep learning architecture, Protein Transformer with Scattering, Attention, and Positional Embedding (ProtSCAPE), which leverages the geometric scattering transform alongside transformer-based attention mechanisms to capture protein dynamics from molecular dynamics (MD) simulations. ProtSCAPE utilizes the multi-scale nature of the geometric scattering transform to extract features from protein structures conceptualized as graphs and integrates these features with dual attention structures that focus on residues and amino acid signals, generating latent representations of protein trajectories. Furthermore, ProtSCAPE incorporates a regression head to enforce temporally coherent latent representations.
In drug discovery, highly automated high-throughput laboratories are used to screen a large number of compounds in search of effective drugs… (voir plus). These experiments are expensive, so one might hope to reduce their cost by only experimenting on a subset of the compounds, and predicting the outcomes of the remaining experiments. In this work, we model this scenario as a sequential subset selection problem: we aim to select the smallest set of candidates in order to achieve some desired level of accuracy for the system as a whole. Our key observation is that, if there is heterogeneity in the difficulty of the prediction problem across the input space, selectively obtaining the labels for the hardest examples in the acquisition pool will leave only the relatively easy examples to remain in the inference set, leading to better overall system performance. We call this mechanism inference set design, and propose the use of a confidence-based active learning solution to prune out these challenging examples. Our algorithm includes an explicit stopping criterion that interrupts the acquisition loop when it is sufficiently confident that the system has reached the target performance. Our empirical studies on image and molecular datasets, as well as a real-world large-scale biological assay, show that active learning for inference set design leads to significant reduction in experimental cost while retaining high system performance.
In drug discovery, highly automated high-throughput laboratories are used to screen a large number of compounds in search of effective drugs… (voir plus). These experiments are expensive, so one might hope to reduce their cost by only experimenting on a subset of the compounds, and predicting the outcomes of the remaining experiments. In this work, we model this scenario as a sequential subset selection problem: we aim to select the smallest set of candidates in order to achieve some desired level of accuracy for the system as a whole. Our key observation is that, if there is heterogeneity in the difficulty of the prediction problem across the input space, selectively obtaining the labels for the hardest examples in the acquisition pool will leave only the relatively easy examples to remain in the inference set, leading to better overall system performance. We call this mechanism inference set design, and propose the use of a confidence-based active learning solution to prune out these challenging examples. Our algorithm includes an explicit stopping criterion that interrupts the acquisition loop when it is sufficiently confident that the system has reached the target performance. Our empirical studies on image and molecular datasets, as well as a real-world large-scale biological assay, show that active learning for inference set design leads to significant reduction in experimental cost while retaining high system performance.
scMoE: single-cell mixture of experts for learning hierarchical, cell-type-specific, and interpretable representations from heterogeneous scRNA-seq data
Advancements in single-cell transcriptomics methods have resulted in a wealth of single-cell RNA sequencing (scRNA-seq) data. Methods to lea… (voir plus)rn cell representation from atlas-level scRNA-seq data across diverse tissues can shed light into cell functions implicated in diseases such as cancer. However, integrating large-scale and heterogeneous scRNA-seq data is challenging due to the disparity of cell-types and batch effects. We present single-cell Mixture of Expert (scMoE), a hierarchical mixture of experts single-cell topic model. Our key contributions are the cell-type specific experts, which explicitly aligns topics with cell-types, and the integration of hierarchical cell-type lineages and domain knowledge. scMoE is both transferable and highly interpretable. We benchmarked our scMoE’s performance on 9 single-cell RNA-seq datasets for clustering and 3 simulated spatial datasets for spatial deconvolution. We additionally show that our model, using single-cell references, yields meaningful biological results by deconvolving 3 cancer bulk RNA-seq datasets and 2 spatial transcriptomics datasets. scMoE is able to identify cell-types of survival importance, find cancer subtype specific deconvolutional patterns, and capture meaningful spatially distinct cell-type distributions.
Despite its widespread adoption, Adam's advantage over Stochastic Gradient Descent (SGD) lacks a comprehensive theoretical explanation. This… (voir plus) paper investigates Adam's sensitivity to rotations of the parameter space. We demonstrate that Adam's performance in training transformers degrades under random rotations of the parameter space, indicating a crucial sensitivity to the choice of basis. This reveals that conventional rotation-invariant assumptions are insufficient to capture Adam's advantages theoretically. To better understand the rotation-dependent properties that benefit Adam, we also identify structured rotations that preserve or even enhance its empirical performance. We then examine the rotation-dependent assumptions in the literature, evaluating their adequacy in explaining Adam's behavior across various rotation types. This work highlights the need for new, rotation-dependent theoretical frameworks to fully understand Adam's empirical success in modern machine learning tasks.
Forecasting is a critical task in decision making across various domains. While numerical data provides a foundation, it often lacks crucial… (voir plus) context necessary for accurate predictions. Human forecasters frequently rely on additional information, such as background knowledge or constraints, which can be efficiently communicated through natural language. However, the ability of existing forecasting models to effectively integrate this textual information remains an open question. To address this, we introduce"Context is Key"(CiK), a time series forecasting benchmark that pairs numerical data with diverse types of carefully crafted textual context, requiring models to integrate both modalities. We evaluate a range of approaches, including statistical models, time series foundation models, and LLM-based forecasters, and propose a simple yet effective LLM prompting method that outperforms all other tested methods on our benchmark. Our experiments highlight the importance of incorporating contextual information, demonstrate surprising performance when using LLM-based forecasting models, and also reveal some of their critical shortcomings. By presenting this benchmark, we aim to advance multimodal forecasting, promoting models that are both accurate and accessible to decision-makers with varied technical expertise. The benchmark can be visualized at https://servicenow.github.io/context-is-key-forecasting/v0/ .
Forecasting is a critical task in decision making across various domains. While numerical data provides a foundation, it often lacks crucial… (voir plus) context necessary for accurate predictions. Human forecasters frequently rely on additional information, such as background knowledge or constraints, which can be efficiently communicated through natural language. However, the ability of existing forecasting models to effectively integrate this textual information remains an open question. To address this, we introduce"Context is Key"(CiK), a time series forecasting benchmark that pairs numerical data with diverse types of carefully crafted textual context, requiring models to integrate both modalities. We evaluate a range of approaches, including statistical models, time series foundation models, and LLM-based forecasters, and propose a simple yet effective LLM prompting method that outperforms all other tested methods on our benchmark. Our experiments highlight the importance of incorporating contextual information, demonstrate surprising performance when using LLM-based forecasting models, and also reveal some of their critical shortcomings. By presenting this benchmark, we aim to advance multimodal forecasting, promoting models that are both accurate and accessible to decision-makers with varied technical expertise. The benchmark can be visualized at https://servicenow.github.io/context-is-key-forecasting/v0/ .
