arXiv subjects

Jeffrey Willette

Publications and source records attributed to Jeffrey Willette.

9 recordsLinked to original sources

arXiv2025

Robust Molecular Property Prediction via Densifying Scarce Labeled Data

A widely recognized limitation of molecular prediction models is their reliance on structures observed in the training data, resulting in poor generalization to out-of-distribution compounds. Yet in drug discovery, the compounds most critical for advancing research often lie beyond the training set, making the bias toward the training data particularly problematic. This mismatch introduces substantial covariate shift, under which standard deep learning models produce unstable and inaccurate predictions. Furthermore, the scarcity of labeled data-stemming from the onerous and costly nature of experimental validation-further exacerbates the difficulty of achieving reliable generalization. To address these limitations, we propose a novel bilevel optimization approach that leverages unlabeled data to interpolate between in-distribution (ID) and out-of-distribution (OOD) data, enabling the model to learn how to generalize beyond the training distribution. We demonstrate significant performance gains on challenging real-world datasets with substantial covariate shift, supported by t-SNE visualizations highlighting our interpolation method.

cs.LG↗

arXiv2025

Delta Attention: Fast and Accurate Sparse Attention Inference by Delta Correction

The attention mechanism of a transformer has a quadratic complexity, leading to high inference costs and latency for long sequences. However, attention matrices are mostly sparse, which implies that many entries may be omitted from computation for efficient inference. Sparse attention inference methods aim to reduce this computational burden; however, they also come with a troublesome performance degradation. We discover that one reason for this degradation is that the sparse calculation induces a distributional shift in the attention outputs. The distributional shift causes decoding-time queries to fail to align well with the appropriate keys from the prefill stage, leading to a drop in performance. We propose a simple, novel, and effective procedure for correcting this distributional shift, bringing the distribution of sparse attention outputs closer to that of quadratic attention. Our method can be applied on top of any sparse attention method, and results in an average 36%pt performance increase, recovering 88% of quadratic attention accuracy on the 131K RULER benchmark when applied on top of sliding window attention with sink tokens while only adding a small overhead. Our method can maintain approximately 98.5% sparsity over full quadratic attention, making our model 32 times faster than Flash Attention 2 when processing 1M token prefills.

cs.LG↗

arXiv2024

Training-Free Exponential Context Extension via Cascading KV Cache

The transformer's context window is vital for tasks such as few-shot learning and conditional generation as it preserves previous tokens for active memory. However, as the context lengths increase, the computational costs grow quadratically, hindering the deployment of large language models (LLMs) in real-world, long sequence scenarios. Although some recent key-value caching (KV Cache) methods offer linear inference complexity, they naively manage the stored context, prematurely evicting tokens and losing valuable information. Moreover, they lack an optimized prefill/prompt stage strategy, resulting in higher latency than even quadratic attention for realistic context sizes. In response, we introduce a novel mechanism that leverages cascading sub-cache buffers to selectively retain the most relevant tokens, enabling the model to maintain longer context histories without increasing the cache size. Our approach outperforms linear caching baselines across key benchmarks, including streaming perplexity, question answering, book summarization, and passkey retrieval, where it retains better retrieval accuracy at 1M tokens after four doublings of the cache size of 65K. Additionally, our method reduces prefill stage latency by a factor of 6.8 when compared to flash attention on 1M tokens. These innovations not only enhance the computational efficiency of LLMs but also pave the way for their effective deployment in resource-constrained environments, enabling large-scale, real-time applications with significantly reduced latency.

cs.CL↗

arXiv2024

SEA: Sparse Linear Attention with Estimated Attention Mask

The transformer architecture has driven breakthroughs in recent years on tasks which require modeling pairwise relationships between sequential elements, as is the case in natural language understanding. However, long seqeuences pose a problem due to the quadratic complexity of the attention operation. Previous research has aimed to lower the complexity by sparsifying or linearly approximating the attention matrix. Yet, these approaches cannot straightforwardly distill knowledge from a teacher's attention matrix and often require complete retraining from scratch. Furthermore, previous sparse and linear approaches lose interpretability if they cannot produce full attention matrices. To address these challenges, we propose SEA: Sparse linear attention with an Estimated Attention mask. SEA estimates the attention matrix with linear complexity via kernel-based linear attention, then subsequently creates a sparse attention matrix with a top-k selection to perform a sparse attention operation. For language modeling tasks (Wikitext2), previous linear and sparse attention methods show roughly two-fold worse perplexity scores over the quadratic OPT-1.3B baseline, while SEA achieves better perplexity than OPT-1.3B, using roughly half the memory of OPT-1.3B, providing interpretable attention matrix. We believe that our work will have a large practical impact, as it opens the possibility of running large transformers on resource-limited devices with less memory.

cs.CL↗

arXiv2023

Scalable Set Encoding with Universal Mini-Batch Consistency and Unbiased Full Set Gradient Approximation

Recent work on mini-batch consistency (MBC) for set functions has brought attention to the need for sequentially processing and aggregating chunks of a partitioned set while guaranteeing the same output for all partitions. However, existing constraints on MBC architectures lead to models with limited expressive power. Additionally, prior work has not addressed how to deal with large sets during training when the full set gradient is required. To address these issues, we propose a Universally MBC (UMBC) class of set functions which can be used in conjunction with arbitrary non-MBC components while still satisfying MBC, enabling a wider range of function classes to be used in MBC settings. Furthermore, we propose an efficient MBC training algorithm which gives an unbiased approximation of the full set gradient and has a constant memory overhead for any set size for both train- and test-time. We conduct extensive experiments including image completion, text classification, unsupervised clustering, and cancer detection on high-resolution images to verify the efficiency and efficacy of our scalable set encoding framework. Our code is available at github.com/jeffwillette/umbc

cs.LG↗

arXiv2022

Exploring The Role of Mean Teachers in Self-supervised Masked Auto-Encoders

Masked image modeling (MIM) has become a popular strategy for self-supervised learning~(SSL) of visual representations with Vision Transformers. A representative MIM model, the masked auto-encoder (MAE), randomly masks a subset of image patches and reconstructs the masked patches given the unmasked patches. Concurrently, many recent works in self-supervised learning utilize the student/teacher paradigm which provides the student with an additional target based on the output of a teacher composed of an exponential moving average (EMA) of previous students. Although common, relatively little is known about the dynamics of the interaction between the student and teacher. Through analysis on a simple linear model, we find that the teacher conditionally removes previous gradient directions based on feature similarities which effectively acts as a conditional momentum regularizer. From this analysis, we present a simple SSL method, the Reconstruction-Consistent Masked Auto-Encoder (RC-MAE) by adding an EMA teacher to MAE. We find that RC-MAE converges faster and requires less memory usage than state-of-the-art self-distillation methods during pre-training, which may provide a way to enhance the practicality of prohibitively expensive self-supervised learning of Vision Transformer models. Additionally, we show that RC-MAE achieves more robustness and better performance compared to MAE on downstream tasks such as ImageNet-1K classification, object detection, and instance segmentation.

cs.CV↗

arXiv2022

Meta Learning Low Rank Covariance Factors for Energy-Based Deterministic Uncertainty

Numerous recent works utilize bi-Lipschitz regularization of neural network layers to preserve relative distances between data instances in the feature spaces of each layer. This distance sensitivity with respect to the data aids in tasks such as uncertainty calibration and out-of-distribution (OOD) detection. In previous works, features extracted with a distance sensitive model are used to construct feature covariance matrices which are used in deterministic uncertainty estimation or OOD detection. However, in cases where there is a distribution over tasks, these methods result in covariances which are sub-optimal, as they may not leverage all of the meta information which can be shared among tasks. With the use of an attentive set encoder, we propose to meta learn either diagonal or diagonal plus low-rank factors to efficiently construct task specific covariance matrices. Additionally, we propose an inference procedure which utilizes scaled energy to achieve a final predictive distribution which is well calibrated under a distributional dataset shift.

stat.ML↗

arXiv2021

Mini-Batch Consistent Slot Set Encoder for Scalable Set Encoding

Most existing set encoding algorithms operate under the implicit assumption that all the set elements are accessible, and that there are ample computational and memory resources to load the set into memory during training and inference. However, both assumptions fail when the set is excessively large such that it is impossible to load all set elements into memory, or when data arrives in a stream. To tackle such practical challenges in large-scale set encoding, the general set-function constraints of permutation invariance and equivariance are not sufficient. We introduce a new property termed Mini-Batch Consistency (MBC) that is required for large scale mini-batch set encoding. Additionally, we present a scalable and efficient attention-based set encoding mechanism that is amenable to mini-batch processing of sets, and capable of updating set representations as data arrives. The proposed method adheres to the required symmetries of invariance and equivariance as well as maintaining MBC for any partition of the input set. We perform extensive experiments and show that our method is computationally efficient and results in rich set encoding representations for set-structured data.

cs.LG↗

arXiv2021

Improving Uncertainty Calibration via Prior Augmented Data

Neural networks have proven successful at learning from complex data distributions by acting as universal function approximators. However, they are often overconfident in their predictions, which leads to inaccurate and miscalibrated probabilistic predictions. The problem of overconfidence becomes especially apparent in cases where the test-time data distribution differs from that which was seen during training. We propose a solution to this problem by seeking out regions of feature space where the model is unjustifiably overconfident, and conditionally raising the entropy of those predictions towards that of the prior distribution of the labels. Our method results in a better calibrated network and is agnostic to the underlying model structure, so it can be applied to any neural network which produces a probability density as an output. We demonstrate the effectiveness of our method and validate its performance on both classification and regression problems, applying it to recent probabilistic neural network models.

cs.LG↗