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Publications
Efficient line search for optimizing Area Under the ROC Curve in gradient descent
Receiver Operating Characteristic (ROC) curves are useful for evaluation in binary classification and changepoint detection, but difficult t… (see more)o use for learning since the Area Under the Curve (AUC) is piecewise constant (gradient zero almost everywhere). Recently the Area Under Min (AUM) of false positive and false negative rates has been proposed as a differentiable surrogate for AUC. In this paper we study the piecewise linear/constant nature of the AUM/AUC, and propose new efficient path-following algorithms for choosing the learning rate which is optimal for each step of gradient descent (line search), when optimizing a linear model. Remarkably, our proposed line search algorithm has the same log-linear asymptotic time complexity as gradient descent with constant step size, but it computes a complete representation of the AUM/AUC as a function of step size. In our empirical study of binary classification problems, we verify that our proposed algorithm is fast and exact; in changepoint detection problems we show that the proposed algorithm is just as accurate as grid search, but faster.
Binary segmentation is the classic greedy algorithm which recursively splits a sequential data set by optimizing some loss or likelihood fun… (see more)ction. Binary segmentation is widely used for changepoint detection in data sets measured over space or time, and as a sub-routine for decision tree learning. In theory it should be extremely fast for
Long-term outcomes of critically ill patients with hematological malignancies: what is the impact of the coronavirus disease 2019 pandemic? Author's reply
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress… (see more) 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.
Offline black-box optimization aims to maximize a black-box function using an offline dataset of designs and their measured properties. Two … (see more)main approaches have emerged: the forward approach, which learns a mapping from input to its value, thereby acting as a proxy to guide optimization, and the inverse approach, which learns a mapping from value to input for conditional generation. (a) Although proxy-free~(classifier-free) diffusion shows promise in robustly modeling the inverse mapping, it lacks explicit guidance from proxies, essential for generating high-performance samples beyond the training distribution. Therefore, we propose \textit{proxy-enhanced sampling} which utilizes the explicit guidance from a trained proxy to bolster proxy-free diffusion with enhanced sampling control. (b) Yet, the trained proxy is susceptible to out-of-distribution issues. To address this, we devise the module \textit{diffusion-based proxy refinement}, which seamlessly integrates insights from proxy-free diffusion back into the proxy for refinement. To sum up, we propose \textit{\textbf{R}obust \textbf{G}uided \textbf{D}iffusion for Offline Black-box Optimization}~(\textbf{RGD}), combining the advantages of proxy~(explicit guidance) and proxy-free diffusion~(robustness) for effective conditional generation. RGD achieves state-of-the-art results on various design-bench tasks, underscoring its efficacy. Our code is at https://github.com/GGchen1997/RGD.
Mastering complex sequential tasks continues to pose a significant challenge in robotics. While there has been progress in learning long-hor… (see more)izon manipulation tasks, most existing approaches lack rigorous mathematical guarantees for ensuring reliable and successful execution. In this paper, we extend previous work on learning long-horizon tasks and stable policies, focusing on improving task success rates while reducing the amount of training data needed. Our approach introduces a novel method that (1) segments long-horizon demonstrations into discrete steps defined by waypoints and subgoals, and (2) learns globally stable dynamical system policies to guide the robot to each subgoal, even in the face of sensory noise and random disturbances. We validate our approach through both simulation and real-world experiments, demonstrating effective transfer from simulation to physical robotic platforms. Code is available at https://github.com/Alestaubin/stable-imitation-policy-with-waypoints
In many real-world applications of machine learning, we are interested to know if it is possible to train on the data that we have gathered … (see more)so far, and obtain accurate predictions on a new test data subset that is qualitatively different in some respect (time period, geographic region, etc). Another question is whether data subsets are similar enough so that it is beneficial to combine subsets during model training. We propose SOAK, Same/Other/All K-fold cross-validation, a new method which can be used to answer both questions. SOAK systematically compares models which are trained on different subsets of data, and then used for prediction on a fixed test subset, to estimate the similarity of learnable/predictable patterns in data subsets. We show results of using SOAK on six new real data sets (with geographic/temporal subsets, to check if predictions are accurate on new subsets), 3 image pair data sets (subsets are different image types, to check that we get smaller prediction error on similar images), and 11 benchmark data sets with predefined train/test splits (to check similarity of predefined splits).
