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Publications
DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images
The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for… (voir plus) biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods.
MiRGraph: A hybrid deep learning approach to identify microRNA-target interactions by integrating heterogeneous regulatory network and genomic sequences
MicroRNAs (miRNAs) mediates gene expression regulation by targeting specific messenger RNAs (mRNAs) in the cytoplasm. They can function as b… (voir plus)oth tumor suppressors and oncogenes depending on the specific miRNA and its target genes. Detecting miRNA-target interactions (MTIs) is critical for unraveling the complex mechanisms of gene regulation and promising towards RNA therapy for cancer. There is currently a lack of MTIs prediction methods that simultaneously perform feature learning from heterogeneous gene regulatory network (GRN) and genomic sequences. To improve the prediction performance of MTIs, we present a novel transformer-based multiview feature learning method – MiRGraph, which consists of two main modules for learning the sequence-based and GRN-based feature embedding. For the former, we utilize the mature miRNA sequences and the complete 3’UTR sequence of the target mRNAs to encode sequence features using a hybrid transformer and convolutional neural network (CNN) (TransCNN) architecture. For the latter, we utilize a heterogeneous graph transformer (HGT) module to extract the relational and structural information from the GRN consisting of miRNA-miRNA, gene-gene and miRNA-target interactions. The TransCNN and HGT modules can be learned end-to-end to predict experimentally validated MTIs from MiRTarBase. MiRGraph outperforms existing methods in not only recapitulating the true MTIs but also in predicting strength of the MTIs based on the in-vitro measurements of miRNA transfections. In a case study on breast cancer, we identified plausible target genes of an oncomir.
Large language models (LLMs) are increasingly applied to complex reasoning tasks that require executing several complex steps before receivi… (voir plus)ng any reward. Properly assigning credit to these steps is essential for enhancing model performance. Proximal Policy Optimization (PPO), a state-of-the-art reinforcement learning (RL) algorithm used for LLM finetuning, employs value networks to tackle credit assignment. However, value networks face challenges in predicting the expected cumulative rewards accurately in complex reasoning tasks, often leading to high-variance updates and suboptimal performance. In this work, we systematically evaluate the efficacy of value networks and reveal their significant shortcomings in reasoning-heavy LLM tasks, showing that they barely outperform a random baseline when comparing alternative steps. To address this, we propose VinePPO, a straightforward approach that leverages the flexibility of language environments to compute unbiased Monte Carlo-based estimates, bypassing the need for large value networks. Our method consistently outperforms PPO and other RL-free baselines across MATH and GSM8K datasets with fewer gradient updates (up to 9x), less wall-clock time (up to 3.0x). These results emphasize the importance of accurate credit assignment in RL finetuning of LLM and demonstrate VinePPO's potential as a superior alternative.
Correlation does not imply causation, but patterns of statistical association between variables can be exploited to infer a causal structure… (voir plus) (even with purely observational data) with the burgeoning field of causal discovery. As a purely observational science, astrophysics has much to gain by exploiting these new methods. The supermassive black hole (SMBH)–galaxy interaction has long been constrained by observed scaling relations, which is low-scatter correlations between variables such as SMBH mass and the central velocity dispersion of stars in a host galaxy's bulge. This study, using advanced causal discovery techniques and an up-to-date data set, reveals a causal link between galaxy properties and dynamically measured SMBH masses. We apply a score-based Bayesian framework to compute the exact conditional probabilities of every causal structure that could possibly describe our galaxy sample. With the exact posterior distribution, we determine the most likely causal structures and notice a probable causal reversal when separating galaxies by morphology. In elliptical galaxies, bulge properties (built from major mergers) tend to influence SMBH growth, while, in spiral galaxies, SMBHs are seen to affect host galaxy properties, potentially through feedback in gas-rich environments. For spiral galaxies, SMBHs progressively quench star formation, whereas, in elliptical galaxies, quenching is complete, and the causal connection has reversed. Our findings support theoretical models of hierarchical assembly of galaxies and active galactic nuclei feedback regulating galaxy evolution. Our study suggests the potentiality for further exploration of causal links in astrophysical and cosmological scaling relations, as well as any other observational science.
Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational cha… (voir plus)llenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the question of conditioning the process to reach a given endpoint or desired rare event is definitively answered by Doob's h-transform. However, the naive estimation of this transform is infeasible, as it requires simulating sufficiently many forward trajectories to estimate rare event probabilities. In this work, we propose a variational formulation of Doob's h-transform as an optimization problem over trajectories between a given initial point and the desired ending point. To solve this optimization, we propose a simulation-free training objective with a model parameterization that imposes the desired boundary conditions by design. Our approach significantly reduces the search space over trajectories and avoids expensive trajectory simulation and inefficient importance sampling estimators which are required in existing methods. We demonstrate the ability of our method to find feasible transition paths on real-world molecular simulation and protein folding tasks.
Receiver Operating Characteristic (ROC) curves are useful for evaluation in binary classification and changepoint detection, but difficult t… (voir plus)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… (voir plus)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… (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 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 … (voir plus)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).
