arXiv subjects

Greg Ver Steeg

Publications and source records attributed to Greg Ver Steeg.

At least 37 records · Page 2Linked to original sources

arXiv2025

AbFlowNet: Optimizing Antibody-Antigen Binding Energy via Diffusion-GFlowNet Fusion

Complementarity Determining Regions (CDRs) are critical segments of an antibody that facilitate binding to specific antigens. Current computational methods for CDR design utilize reconstruction losses and do not jointly optimize binding energy, a crucial metric for antibody efficacy. Rather, binding energy optimization is done through computationally expensive Online Reinforcement Learning (RL) pipelines rely heavily on unreliable binding energy estimators. In this paper, we propose AbFlowNet, a novel generative framework that integrates GFlowNet with Diffusion models. By framing each diffusion step as a state in the GFlowNet framework, AbFlowNet jointly optimizes standard diffusion losses and binding energy by directly incorporating energy signals into the training process, thereby unifying diffusion and reward optimization in a single procedure. Experimental results show that AbFlowNet outperforms the base diffusion model by 3.06% in amino acid recovery, 20.40% in geometric reconstruction (RMSD), and 3.60% in binding energy improvement ratio. ABFlowNet also decreases Top-1 total energy and binding energy errors by 24.8% and 38.1% without pseudo-labeling the test dataset or using computationally expensive online RL regimes.

cs.LG↗

arXiv2025

Diffusion Bridge Models for 3D Medical Image Translation

Diffusion tensor imaging (DTI) provides crucial insights into the microstructure of the human brain, but it can be time-consuming to acquire compared to more readily available T1-weighted (T1w) magnetic resonance imaging (MRI). To address this challenge, we propose a diffusion bridge model for 3D brain image translation between T1w MRI and DTI modalities. Our model learns to generate high-quality DTI fractional anisotropy (FA) images from T1w images and vice versa, enabling cross-modality data augmentation and reducing the need for extensive DTI acquisition. We evaluate our approach using perceptual similarity, pixel-level agreement, and distributional consistency metrics, demonstrating strong performance in capturing anatomical structures and preserving information on white matter integrity. The practical utility of the synthetic data is validated through sex classification and Alzheimer's disease classification tasks, where the generated images achieve comparable performance to real data. Our diffusion bridge model offers a promising solution for improving neuroimaging datasets and supporting clinical decision-making, with the potential to significantly impact neuroimaging research and clinical practice.

cs.CV↗

arXiv2025

KG-LLM-Bench: A Scalable Benchmark for Evaluating LLM Reasoning on Textualized Knowledge Graphs

Knowledge graphs have emerged as a popular method for injecting up-to-date, factual knowledge into large language models (LLMs). This is typically achieved by converting the knowledge graph into text that the LLM can process in context. While multiple methods of encoding knowledge graphs have been proposed, the impact of this textualization process on LLM performance remains under-explored. We introduce KG-LLM-Bench, a comprehensive and extensible benchmark spanning five knowledge graph understanding tasks, and evaluate how different encoding strategies affect performance across various base models. Our extensive experiments with seven language models and five textualization strategies provide insights for optimizing LLM performance on KG reasoning tasks.

cs.CL↗

arXiv2025

Knowledge Enhanced Multi-Domain Recommendations in an AI Assistant Application

This work explores unifying knowledge enhanced recommendation with multi-domain recommendation systems in a conversational AI assistant application. Multi-domain recommendation leverages users' interactions in previous domains to improve recommendations in a new one. Knowledge graph enhancement seeks to use external knowledge graphs to improve recommendations within a single domain. Both research threads incorporate related information to improve the recommendation task. We propose to unify these approaches: using information from interactions in other domains as well as external knowledge graphs to make predictions in a new domain that would not be possible with either information source alone. We develop a new model and demonstrate the additive benefit of these approaches on a dataset derived from millions of users' queries for content across three domains (videos, music, and books) in a live virtual assistant application. We demonstrate significant improvement on overall recommendations as well as on recommendations for new users of a domain.

cs.IR↗

arXiv2025

Making Sense Of Distributed Representations With Activation Spectroscopy

In the study of neural network interpretability, there is growing evidence to suggest that relevant features are encoded across many neurons in a distributed fashion. Making sense of these distributed representations without knowledge of the network's encoding strategy is a combinatorial task that is not guaranteed to be tractable. This work explores one feasible path to both detecting and tracing the joint influence of neurons in a distributed representation. We term this approach Activation Spectroscopy (ActSpec), owing to its analysis of the pseudo-Boolean Fourier spectrum defined over the activation patterns of a network layer. The sub-network defined between a given layer and an output logit is cast as a special class of pseudo-Boolean function. The contributions of each subset of neurons in the specified layer can be quantified through the function's Fourier coefficients. We propose a combinatorial optimization procedure to search for Fourier coefficients that are simultaneously high-valued, and non-redundant. This procedure can be viewed as an extension of the Goldreich-Levin algorithm which incorporates additional problem-specific constraints. The resulting coefficients specify a collection of subsets, which are used to test the degree to which a representation is distributed. We verify our approach in a number of synthetic settings and compare against existing interpretability benchmarks. We conclude with a number of experimental evaluations on an MNIST classifier, and a transformer-based network for sentiment analysis.

cs.LG↗

arXiv2024

Learning Morphisms with Gauss-Newton Approximation for Growing Networks

A popular method for Neural Architecture Search (NAS) is based on growing networks via small local changes to the network's architecture called network morphisms. These methods start with a small seed network and progressively grow the network by adding new neurons in an automated way. However, it remains a challenge to efficiently determine which parts of the network are best to grow. Here we propose a NAS method for growing a network by using a Gauss-Newton approximation of the loss function to efficiently learn and evaluate candidate network morphisms. We compare our method with state of the art NAS methods for CIFAR-10 and CIFAR-100 classification tasks, and conclude our method learns similar quality or better architectures at a smaller computational cost.

cs.LG↗

arXiv2024

Your Diffusion Model is Secretly a Noise Classifier and Benefits from Contrastive Training

Diffusion models learn to denoise data and the trained denoiser is then used to generate new samples from the data distribution. In this paper, we revisit the diffusion sampling process and identify a fundamental cause of sample quality degradation: the denoiser is poorly estimated in regions that are far Outside Of the training Distribution (OOD), and the sampling process inevitably evaluates in these OOD regions. This can become problematic for all sampling methods, especially when we move to parallel sampling which requires us to initialize and update the entire sample trajectory of dynamics in parallel, leading to many OOD evaluations. To address this problem, we introduce a new self-supervised training objective that differentiates the levels of noise added to a sample, leading to improved OOD denoising performance. The approach is based on our observation that diffusion models implicitly define a log-likelihood ratio that distinguishes distributions with different amounts of noise, and this expression depends on denoiser performance outside the standard training distribution. We show by diverse experiments that the proposed contrastive diffusion training is effective for both sequential and parallel settings, and it improves the performance and speed of parallel samplers significantly.

cs.LG↗

arXiv2024

QuAILoRA: Quantization-Aware Initialization for LoRA

QLoRA reduces the memory-cost of fine-tuning a large language model (LLM) with LoRA by quantizing the base LLM. However, quantization introduces quantization errors that negatively impact model performance after fine-tuning. In this paper we introduce QuAILoRA, a quantization-aware initialization for LoRA that mitigates this negative impact by decreasing quantization errors at initialization. Our method spends a small amount of computational overhead to compute this quantization-aware initialization, without increasing the memory-cost of fine-tuning. We evaluate our method on several causal language modeling and downstream evaluation tasks using several different model sizes and families. We observe that almost all LLMs fined-tuned with QuAILoRA achieve better validation perplexity. When evaluated on downstream tasks, we find that QuAILoRA yields improvements proportional to the negative effect of quantization error. On average, applying QuAILoRA to 4-bit QLoRA models yields 75% of the validation perplexity decrease and 86% of the downstream task accuracy increase as doubling the quantization precision to 8-bit, without increasing GPU memory utilization during fine-tuning.

cs.LG↗

arXiv2024

Asymmetric Bias in Text-to-Image Generation with Adversarial Attacks

The widespread use of Text-to-Image (T2I) models in content generation requires careful examination of their safety, including their robustness to adversarial attacks. Despite extensive research on adversarial attacks, the reasons for their effectiveness remain underexplored. This paper presents an empirical study on adversarial attacks against T2I models, focusing on analyzing factors associated with attack success rates (ASR). We introduce a new attack objective - entity swapping using adversarial suffixes and two gradient-based attack algorithms. Human and automatic evaluations reveal the asymmetric nature of ASRs on entity swap: for example, it is easier to replace "human" with "robot" in the prompt "a human dancing in the rain." with an adversarial suffix, but the reverse replacement is significantly harder. We further propose probing metrics to establish indicative signals from the model's beliefs to the adversarial ASR. We identify conditions that result in a success probability of 60% for adversarial attacks and others where this likelihood drops below 5%.

cs.LG↗

arXiv2024

Interpretable Diffusion via Information Decomposition

Denoising diffusion models enable conditional generation and density modeling of complex relationships like images and text. However, the nature of the learned relationships is opaque making it difficult to understand precisely what relationships between words and parts of an image are captured, or to predict the effect of an intervention. We illuminate the fine-grained relationships learned by diffusion models by noticing a precise relationship between diffusion and information decomposition. Exact expressions for mutual information and conditional mutual information can be written in terms of the denoising model. Furthermore, pointwise estimates can be easily estimated as well, allowing us to ask questions about the relationships between specific images and captions. Decomposing information even further to understand which variables in a high-dimensional space carry information is a long-standing problem. For diffusion models, we show that a natural non-negative decomposition of mutual information emerges, allowing us to quantify informative relationships between words and pixels in an image. We exploit these new relations to measure the compositional understanding of diffusion models, to do unsupervised localization of objects in images, and to measure effects when selectively editing images through prompt interventions.

cs.LG↗

arXiv2024

Prompt Perturbation Consistency Learning for Robust Language Models

Large language models (LLMs) have demonstrated impressive performance on a number of natural language processing tasks, such as question answering and text summarization. However, their performance on sequence labeling tasks such as intent classification and slot filling (IC-SF), which is a central component in personal assistant systems, lags significantly behind discriminative models. Furthermore, there is a lack of substantive research on the robustness of LLMs to various perturbations in the input prompts. The contributions of this paper are three-fold. First, we show that fine-tuning sufficiently large LLMs can produce IC-SF performance comparable to discriminative models. Next, we systematically analyze the performance deterioration of those fine-tuned models due to three distinct yet relevant types of input perturbations - oronyms, synonyms, and paraphrasing. Finally, we propose an efficient mitigation approach, Prompt Perturbation Consistency Learning (PPCL), which works by regularizing the divergence between losses from clean and perturbed samples. Our experiments demonstrate that PPCL can recover on average 59% and 69% of the performance drop for IC and SF tasks, respectively. Furthermore, PPCL beats the data augmentation approach while using ten times fewer augmented data samples.

cs.CL↗

arXiv2024

Interpretable Measures of Conceptual Similarity by Complexity-Constrained Descriptive Auto-Encoding

Quantifying the degree of similarity between images is a key copyright issue for image-based machine learning. In legal doctrine however, determining the degree of similarity between works requires subjective analysis, and fact-finders (judges and juries) can demonstrate considerable variability in these subjective judgement calls. Images that are structurally similar can be deemed dissimilar, whereas images of completely different scenes can be deemed similar enough to support a claim of copying. We seek to define and compute a notion of "conceptual similarity" among images that captures high-level relations even among images that do not share repeated elements or visually similar components. The idea is to use a base multi-modal model to generate "explanations" (captions) of visual data at increasing levels of complexity. Then, similarity can be measured by the length of the caption needed to discriminate between the two images: Two highly dissimilar images can be discriminated early in their description, whereas conceptually dissimilar ones will need more detail to be distinguished. We operationalize this definition and show that it correlates with subjective (averaged human evaluation) assessment, and beats existing baselines on both image-to-image and text-to-text similarity benchmarks. Beyond just providing a number, our method also offers interpretability by pointing to the specific level of granularity of the description where the source data are differentiated.

cs.CV↗

arXiv2023

Functional Connectivity via Total Correlation: Analytical results in Visual Areas

Recent studies invoke the superiority of the multivariate Total Correlation concept over the conventional pairwise measures of functional connectivity in biological networks. Those seminal works certainly show that empirical measures of Total Correlation lead to connectivity patterns that differ from what is obtained using the most popular measure, linear correlation, or its higher order and nonlinear alternative Mutual Information. However, they do not provide analytical results that explain the differences beyond the obvious multivariate versus bivariate definitions. Moreover, the accuracy of the empirical estimators could not be addressed directly because no controlled scenario with known analytical result was provided either. This point is critical because empirical estimation of information theory measures is always challenging. As opposed to previous empirical approaches, in this work we present analytical results to prove the advantages of Total Correlation over Mutual Information to describe the functional connectivity. In particular, we do it in neural networks for early vision (retina-LGN-cortex) which are realistic but simple enough to get analytical results. The presented analytical setting is also useful to check empirical estimates of Total Correlation. Therefore, once certain estimate can be trusted, one can explore the behavior with natural signals where the analytical results (that assume Gaussian signals), may not be valid. In this regard, as applications (a) we explore the effect of connectivity and feedback in the analytical retina-LGN-cortex network with natural images, and (b) we assess the functional connectivity in visual areas V1-V2-V3-V4 from actual fMRI recordings.

q-bio.NC↗

arXiv2023

Ensembled Prediction Intervals for Causal Outcomes Under Hidden Confounding

Causal inference of exact individual treatment outcomes in the presence of hidden confounders is rarely possible. Recent work has extended prediction intervals with finite-sample guarantees to partially identifiable causal outcomes, by means of a sensitivity model for hidden confounding. In deep learning, predictors can exploit their inductive biases for better generalization out of sample. We argue that the structure inherent to a deep ensemble should inform a tighter partial identification of the causal outcomes that they predict. We therefore introduce an approach termed Caus-Modens, for characterizing causal outcome intervals by modulated ensembles. We present a simple approach to partial identification using existing causal sensitivity models and show empirically that Caus-Modens gives tighter outcome intervals, as measured by the necessary interval size to achieve sufficient coverage. The last of our three diverse benchmarks is a novel usage of GPT-4 for observational experiments with unknown but probeable ground truth.

cs.LG↗

arXiv2023

Secure & Private Federated Neuroimaging

The amount of biomedical data continues to grow rapidly. However, collecting data from multiple sites for joint analysis remains challenging due to security, privacy, and regulatory concerns. To overcome this challenge, we use Federated Learning, which enables distributed training of neural network models over multiple data sources without sharing data. Each site trains the neural network over its private data for some time, then shares the neural network parameters (i.e., weights, gradients) with a Federation Controller, which in turn aggregates the local models, sends the resulting community model back to each site, and the process repeats. Our Federated Learning architecture, MetisFL, provides strong security and privacy. First, sample data never leaves a site. Second, neural network parameters are encrypted before transmission and the global neural model is computed under fully-homomorphic encryption. Finally, we use information-theoretic methods to limit information leakage from the neural model to prevent a curious site from performing model inversion or membership attacks. We present a thorough evaluation of the performance of secure, private federated learning in neuroimaging tasks, including for predicting Alzheimer's disease and estimating BrainAGE from magnetic resonance imaging (MRI) studies, in challenging, heterogeneous federated environments where sites have different amounts of data and statistical distributions.

cs.LG↗

arXiv2023

Partial Identification of Dose Responses with Hidden Confounders

Inferring causal effects of continuous-valued treatments from observational data is a crucial task promising to better inform policy- and decision-makers. A critical assumption needed to identify these effects is that all confounding variables -- causal parents of both the treatment and the outcome -- are included as covariates. Unfortunately, given observational data alone, we cannot know with certainty that this criterion is satisfied. Sensitivity analyses provide principled ways to give bounds on causal estimates when confounding variables are hidden. While much attention is focused on sensitivity analyses for discrete-valued treatments, much less is paid to continuous-valued treatments. We present novel methodology to bound both average and conditional average continuous-valued treatment-effect estimates when they cannot be point identified due to hidden confounding. A semi-synthetic benchmark on multiple datasets shows our method giving tighter coverage of the true dose-response curve than a recently proposed continuous sensitivity model and baselines. Finally, we apply our method to a real-world observational case study to demonstrate the value of identifying dose-dependent causal effects.

stat.ME↗

arXiv2023

Jointly Reparametrized Multi-Layer Adaptation for Efficient and Private Tuning

Efficient finetuning of pretrained language transformers is becoming increasingly prevalent for solving natural language processing tasks. While effective, it can still require a large number of tunable parameters. This can be a drawback for low-resource applications and training with differential-privacy constraints, where excessive noise may be introduced during finetuning. To this end, we propose a novel language transformer finetuning strategy that introduces task-specific parameters in multiple transformer layers. These parameters are derived from fixed random projections of a single trainable vector, enabling finetuning with significantly fewer parameters while maintaining performance. We achieve within 5% of full finetuning performance on GLUE tasks with as few as 4,100 parameters per task, outperforming other parameter-efficient finetuning approaches that use a similar number of per-task parameters. Besides, the random projections can be precomputed at inference, avoiding additional computational latency. All these make our method particularly appealing for low-resource applications. Finally, our method achieves the best or comparable utility compared to several recent finetuning methods when training with the same privacy constraints, underscoring its effectiveness and potential real-world impact.

cs.CL↗

arXiv2023

Neural Architecture Search for Parameter-Efficient Fine-tuning of Large Pre-trained Language Models

Parameter-efficient tuning (PET) methods fit pre-trained language models (PLMs) to downstream tasks by either computing a small compressed update for a subset of model parameters, or appending and fine-tuning a small number of new model parameters to the pre-trained network. Hand-designed PET architectures from the literature perform well in practice, but have the potential to be improved via automated neural architecture search (NAS). We propose an efficient NAS method for learning PET architectures via structured and unstructured pruning. We present experiments on GLUE demonstrating the effectiveness of our algorithm and discuss how PET architectural design choices affect performance in practice.

cs.CL↗