Layne C. Price

Yulun Wu, Robert A. Barton, Zichen Wang et al. · amazon-science, harvard

Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's gene expressions under counterfactual perturbations (perturbations that this cell did not factually receive), leveraging information representing biological knowledge in the form of gene regulatory networks (GRNs) to aid individualized cellular response predictions. Aiming at a data-adaptive GRN, we also developed an adjacency matrix updating technique for graph convolutional networks and used it to refine GRNs during pre-training, which generated more insights on gene relations and enhanced model performance. Additionally, we propose a robust estimator within our framework for the asymptotically efficient estimation of marginal perturbation effect, which is yet to be carried out in previous works. With extensive experiments, we exhibited the advantage of our approach over state-of-the-art deep learning models for individual response prediction.

Yulun Wu, Layne C. Price, Zichen Wang et al.

Estimating an individual's potential outcomes under counterfactual treatments is a challenging task for traditional causal inference and supervised learning approaches when the outcome is high-dimensional (e.g. gene expressions, impulse responses, human faces) and covariates are relatively limited. In this case, to construct one's outcome under a counterfactual treatment, it is crucial to leverage individual information contained in its observed factual outcome on top of the covariates. We propose a deep variational Bayesian framework that rigorously integrates two main sources of information for outcome construction under a counterfactual treatment: one source is the individual features embedded in the high-dimensional factual outcome; the other source is the response distribution of similar subjects (subjects with the same covariates) that factually received this treatment of interest.

Chaitra Hedge, Gezheng Wen, Layne C. Price

Activity classification has become a vital feature of wearable health tracking devices. As innovation in this field grows, wearable devices worn on different parts of the body are emerging. To perform activity classification on a new body location, labeled data corresponding to the new locations are generally required, but this is expensive to acquire. In this work, we present an innovative method to leverage an existing activity classifier, trained on Inertial Measurement Unit (IMU) data from a reference body location (the source domain), in order to perform activity classification on a new body location (the target domain) in an unsupervised way, i.e. without the need for classification labels at the new location. Specifically, given an IMU embedding model trained to perform activity classification at the source domain, we train an embedding model to perform activity classification at the target domain by replicating the embeddings at the source domain. This is achieved using simultaneous IMU measurements at the source and target domains. The replicated embeddings at the target domain are used by a classification model that has previously been trained on the source domain to perform activity classification at the target domain. We have evaluated the proposed methods on three activity classification datasets PAMAP2, MHealth, and Opportunity, yielding high F1 scores of 67.19%, 70.40% and 68.34%, respectively when the source domain is the wrist and the target domain is the torso.

Raviteja Anantha, Nick Levato, Layne C. Price

Parameter-efficient fine-tuning (PEFT) methods face a tradeoff between adapter size and expressivity: ultra-low-parameter adapters are confined to fixed low-rank subspaces, capping performance even with extended training. We propose BoostLoRA, a gradient-boosting framework that overcomes this limit by iteratively training and merging minimal adapters on the examples the current model gets wrong. A ROTATE SVD basis strategy assigns each round to an orthogonal subspace, so cumulative effective rank grows linearly with the number of rounds while each adapter remains ultra-low-rank. After merging, adapters are discarded, leaving zero inference overhead. On Qwen2.5-3B, BoostLoRA reaches 89.1% on GSM8K and 68.8% on MATH-500, surpassing both the best single-shot ultra-low parameter adapter (TinyLoRA) and full fine-tuning; on code generation it reaches 57.2% on MBPP and 80.4% on HumanEval while full fine-tuning drops below the zero-shot baseline. We also demonstrate cross-architecture transfer on protein binding classification with ESM2-650M and cross-entropy training. BoostLoRA is, to our knowledge, the first PEFT method whose effective rank grows with training, separating per-round parameter cost from total representational capacity.

Raviteja Anantha, Soheil Hor, Teodor Nicola Antoniu et al.

We present NanoFlux, a novel adversarial framework for generating targeted training data to improve LLM reasoning, where adversarially-generated datasets containing fewer than 200 examples outperform conventional fine-tuning approaches. The framework employs a competitive dynamic between models alternating as Attacker and Defender, supervised by a tool-augmented Judge, synthesizing multi-step questions with explanatory annotations that target specific reasoning capabilities. Fine-tuning a 4B-parameter model on NanoFlux-generated data yields performance gains across diverse domains compared to full-benchmark fine-tuning: +5.9% on mathematical reasoning (GSMHard), +3.6% on scientific reasoning (GenomeBench), and +16.6% on medical reasoning (MultiMedQA), while reducing computational requirements by 3-14x. Ablation studies reveal a non-monotonic relationship between dataset characteristics and model performance, uncovering domain-specific optimal points for question complexity and reasoning quality. NanoFlux automates training data generation through embedding-based novelty filtering, tool-augmented evaluation, and multi-hop reasoning, suggesting that future model improvements may lie in the intelligent synthesis of small, precisely targeted training datasets.

Grigor Aslanyan, Richard Easther, Nathan Musoke et al.

Scientific analyses often rely on slow, but accurate forward models for observable data conditioned on known model parameters. While various emulation schemes exist to approximate these slow calculations, these approaches are only safe if the approximations are well understood and controlled. This workshop submission reviews and updates a previously published method, which has been used in cosmological simulations, to (1) train an emulator while simultaneously estimating posterior probabilities with MCMC and (2) explicitly propagate the emulation error into errors on the posterior probabilities for model parameters. We demonstrate how these techniques can be applied to quickly estimate posterior distributions for parameters of the $Λ$CDM cosmology model, while also gauging the robustness of the emulator approximation.

Mohammad Taha Bahadori, Layne C. Price

We study the invariance characteristics of pre-trained predictive models by empirically learning transformations on the input that leave the prediction function approximately unchanged. To learn invariant transformations, we minimize the Wasserstein distance between the predictive distribution conditioned on the data instances and the predictive distribution conditioned on the transformed data instances. To avoid finding degenerate or perturbative transformations, we add a similarity regularization to discourage similarity between the data and its transformed values. We theoretically analyze the correctness of the algorithm and the structure of the solutions. Applying the proposed technique to clinical time series data, we discover variables that commonly-used LSTM models do not rely on for their prediction, especially when the LSTM is trained to be adversarially robust. We also analyze the invariances of BioBERT on clinical notes and discover words that it is invariant to.

Siamak Ravanbakhsh, Junier Oliva, Sebastien Fromenteau et al.

A grand challenge of the 21st century cosmology is to accurately estimate the cosmological parameters of our Universe. A major approach to estimating the cosmological parameters is to use the large-scale matter distribution of the Universe. Galaxy surveys provide the means to map out cosmic large-scale structure in three dimensions. Information about galaxy locations is typically summarized in a "single" function of scale, such as the galaxy correlation function or power-spectrum. We show that it is possible to estimate these cosmological parameters directly from the distribution of matter. This paper presents the application of deep 3D convolutional networks to volumetric representation of dark-matter simulations as well as the results obtained using a recently proposed distribution regression framework, showing that machine learning techniques are comparable to, and can sometimes outperform, maximum-likelihood point estimates using "cosmological models". This opens the way to estimating the parameters of our Universe with higher accuracy.