Rajmonda S. Caceres

Lin Li, Esther Gupta, John Spaeth et al.

Therapeutic antibody development has become an increasingly popular approach for drug development. To date, antibody therapeutics are largely developed using large scale experimental screens of antibody libraries containing hundreds of millions of antibody sequences. The high cost and difficulty of developing therapeutic antibodies create a pressing need for computational methods to predict antibody properties and create bespoke designs. However, the relationship between antibody sequence and activity is a complex physical process and traditional iterative design approaches rely on large scale assays and random mutagenesis. Deep learning methods have emerged as a promising way to learn antibody property predictors, but predicting antibody properties and target-specific activities depends critically on the choice of antibody representations and data linking sequences to properties is often limited. Existing works have not yet investigated the value, limitations and opportunities of these methods in application to antibody-based drug discovery. In this paper, we present results on a novel SARS-CoV-2 antibody binding dataset and an additional benchmark dataset. We compare three classes of models: conventional statistical sequence models, supervised learning on each dataset independently, and fine-tuning an antibody specific pre-trained language model. Experimental results suggest that self-supervised pretraining of feature representation consistently offers significant improvement in over previous approaches. We also investigate the impact of data size on the model performance, and discuss challenges and opportunities that the machine learning community can address to advance in silico engineering and design of therapeutic antibodies.

Zohair Shafi, Benjamin A. Miller, Ayan Chatterjee et al.

Recent advances in machine learning (ML) have shown promise in aiding and accelerating classical combinatorial optimization algorithms. ML-based speed ups that aim to learn in an end to end manner (i.e., directly output the solution) tend to trade off run time with solution quality. Therefore, solutions that are able to accelerate existing solvers while maintaining their performance guarantees, are of great interest. We consider an APX-hard problem, where an adversary aims to attack shortest paths in a graph by removing the minimum number of edges. We propose the GRASP algorithm: Graph Attention Accelerated Shortest Path Attack, an ML aided optimization algorithm that achieves run times up to 10x faster, while maintaining the quality of solution generated. GRASP uses a graph attention network to identify a smaller subgraph containing the combinatorial solution, thus effectively reducing the input problem size. Additionally, we demonstrate how careful representation of the input graph, including node features that correlate well with the optimization task, can highlight important structure in the optimization solution.

Zohair Shafi, Benjamin A. Miller, Tina Eliassi-Rad et al.

Machine learning (ML) approaches are increasingly being used to accelerate combinatorial optimization (CO) problems. We investigate the Set Cover Problem (SCP) and propose Graph-SCP, a graph neural network method that augments existing optimization solvers by learning to identify a smaller sub-problem that contains the solution space. Graph-SCP uses both supervised learning from prior solved instances and unsupervised learning to minimize the SCP objective. We evaluate the performance of Graph-SCP on synthetically weighted and unweighted SCP instances with diverse problem characteristics and complexities, and on instances from the OR Library, a canonical benchmark for SCP. We show that Graph-SCP reduces the problem size by 60-80% and achieves runtime speedups of up to 10x on average when compared to Gurobi (a state-of-the-art commercial solver), while maintaining solution quality. This is in contrast to fast greedy solutions that significantly compromise solution quality to achieve guaranteed polynomial runtime. We showcase Graph-SCP's ability to generalize to larger problem sizes, training on SCP instances with up to 3,000 subsets and testing on SCP instances with up to 10,000 subsets.

Josué Martínez-Martínez, Olivia Brown, Giselle Zeno et al.

Robustness to natural corruptions remains a critical challenge for reliable deep learning, particularly in safety-sensitive domains. We study a family of model-based training approaches that leverage a learned nuisance variation model to generate realistic corruptions, as well as new hybrid strategies that combine random coverage with adversarial refinement in nuisance space. Using the Challenging Unreal and Real Environments for Traffic Sign Recognition dataset (CURE-TSR), with Snow and Rain corruptions, we evaluate accuracy, calibration, and training complexity across corruption severities. Our results show that model-based methods consistently outperform baselines Vanilla, Adversarial Training, and AugMix baselines, with model-based adversarial training providing the strongest robustness under across all corruptions but at the expense of higher computation and model-based data augmentation achieving comparable robustness with $T$ less computational complexity without incurring a statistically significant drop in performance. These findings highlight the importance of learned nuisance models for capturing natural variability, and suggest a promising path toward more resilient and calibrated models under challenging conditions.

Virginia H. Goodwin, Rajmonda S. Caceres

The irresponsible use of ML algorithms in practical settings has received a lot of deserved attention in the recent years. We posit that the traditional system analysis perspective is needed when designing and implementing ML algorithms and systems. Such perspective can provide a formal way for evaluating and enabling responsible ML practices. In this paper, we review components of the System Analysis methodology and highlight how they connect and enable responsible practices of ML design.

Donald Loveland, Rajmonda Caceres

Graph Neural Network (GNN) research has produced strategies to modify a graph's edges using gradients from a trained GNN, with the goal of network design. However, the factors which govern gradient-based editing are understudied, obscuring why edges are chosen and if edits are grounded in an edge's importance. Thus, we begin by analyzing the gradient computation in previous works, elucidating the factors that influence edits and highlighting the potential over-reliance on structural properties. Specifically, we find that edges can achieve high gradients due to structural biases, rather than importance, leading to erroneous edits when the factors are unrelated to the design task. To improve editing, we propose ORE, an iterative editing method that (a) edits the highest scoring edges and (b) re-embeds the edited graph to refresh gradients, leading to less biased edge choices. We empirically study ORE through a set of proposed design tasks, each with an external validation method, demonstrating that ORE improves upon previous methods by up to 50%.

Neel Sortur, Justin Goodwin, Purvik Patel et al.

Determining the shape of 3D objects from high-frequency radar signals is analytically complex but critical for commercial and aerospace applications. Previous deep learning methods have been applied to radar modeling; however, they often fail to represent arbitrary shapes or have difficulty with real-world radar signals which are collected over limited viewing angles. Existing methods in optical 3D reconstruction can generate arbitrary shapes from limited camera views, but struggle when they naively treat the radar signal as a camera view. In this work, we present Radar2Shape, a denoising diffusion model that handles a partially observable radar signal for 3D reconstruction by correlating its frequencies with multiresolution shape features. Our method consists of a two-stage approach: first, Radar2Shape learns a regularized latent space with hierarchical resolutions of shape features, and second, it diffuses into this latent space by conditioning on the frequencies of the radar signal in an analogous coarse-to-fine manner. We demonstrate that Radar2Shape can successfully reconstruct arbitrary 3D shapes even from partially-observed radar signals, and we show robust generalization to two different simulation methods and real-world data. Additionally, we release two synthetic benchmark datasets to encourage future research in the high-frequency radar domain so that models like Radar2Shape can safely be adapted into real-world radar systems.

Nathan Vaska, Justin Goodwin, Robin Walters et al.

Meshes are used to represent complex objects in high fidelity physics simulators across a variety of domains, such as radar sensing and aerodynamics. There is growing interest in using neural networks to accelerate physics simulations, and also a growing body of work on applying neural networks directly to irregular mesh data. Since multiple mesh topologies can represent the same object, mesh augmentation is typically required to handle topological variation when training neural networks. Due to the sensitivity of physics simulators to small changes in mesh shape, it is challenging to use these augmentations when training neural network-based physics simulators. In this work, we show that variations in mesh topology can significantly reduce the performance of neural network simulators. We evaluate whether pretraining can be used to address this issue, and find that employing an established autoencoder pretraining technique with graph embedding models reduces the sensitivity of neural network simulators to variations in mesh topology. Finally, we highlight future research directions that may further reduce neural simulator sensitivity to mesh topology.

Peter Morales, Rajmonda Sulo Caceres, Tina Eliassi-Rad

Complex networks are often either too large for full exploration, partially accessible, or partially observed. Downstream learning tasks on these incomplete networks can produce low quality results. In addition, reducing the incompleteness of the network can be costly and nontrivial. As a result, network discovery algorithms optimized for specific downstream learning tasks given resource collection constraints are of great interest. In this paper, we formulate the task-specific network discovery problem in an incomplete network setting as a sequential decision making problem. Our downstream task is selective harvesting, the optimal collection of vertices with a particular attribute. We propose a framework, called Network Actor Critic (NAC), which learns a policy and notion of future reward in an offline setting via a deep reinforcement learning algorithm. The NAC paradigm utilizes a task-specific network embedding to reduce the state space complexity. A detailed comparative analysis of popular network embeddings is presented with respect to their role in supporting offline planning. Furthermore, a quantitative study is presented on several synthetic and real benchmarks using NAC and several baselines. We show that offline models of reward and network discovery policies lead to significantly improved performance when compared to competitive online discovery algorithms. Finally, we outline learning regimes where planning is critical in addressing sparse and changing reward signals.

Benjamin Fish, Rajmonda S. Caceres

For any stream of time-stamped edges that form a dynamic network, an important choice is the aggregation granularity that an analyst uses to bin the data. Picking such a windowing of the data is often done by hand, or left up to the technology that is collecting the data. However, the choice can make a big difference in the properties of the dynamic network. This is the time scale detection problem. In previous work, this problem is often solved with a heuristic as an unsupervised task. As an unsupervised problem, it is difficult to measure how well a given algorithm performs. In addition, we show that the quality of the windowing is dependent on which task an analyst wants to perform on the network after windowing. Therefore the time scale detection problem should not be handled independently from the rest of the analysis of the network. We introduce a framework that tackles both of these issues: By measuring the performance of the time scale detection algorithm based on how well a given task is accomplished on the resulting network, we are for the first time able to directly compare different time scale detection algorithms to each other. Using this framework, we introduce time scale detection algorithms that take a supervised approach: they leverage ground truth on training data to find a good windowing of the test data. We compare the supervised approach to previous approaches and several baselines on real data.

Cem Safak Sahin, Rajmonda S. Caceres, Brandon Oselio et al.

Word embedding models offer continuous vector representations that can capture rich contextual semantics based on their word co-occurrence patterns. While these word vectors can provide very effective features used in many NLP tasks such as clustering similar words and inferring learning relationships, many challenges and open research questions remain. In this paper, we propose a solution that aligns variations of the same model (or different models) in a joint low-dimensional latent space leveraging carefully generated synthetic data points. This generative process is inspired by the observation that a variety of linguistic relationships is captured by simple linear operations in embedded space. We demonstrate that our approach can lead to substantial improvements in recovering embeddings of local neighborhoods.

Benjamin Fish, Rajmonda S. Caceres

Oversampling is a common characteristic of data representing dynamic networks. It introduces noise into representations of dynamic networks, but there has been little work so far to compensate for it. Oversampling can affect the quality of many important algorithmic problems on dynamic networks, including link prediction. Link prediction seeks to predict edges that will be added to the network given previous snapshots. We show that not only does oversampling affect the quality of link prediction, but that we can use link prediction to recover from the effects of oversampling. We also introduce a novel generative model of noise in dynamic networks that represents oversampling. We demonstrate the results of our approach on both synthetic and real-world data.

Jeremy Kun, Rajmonda Caceres, Kevin Carter

Learning the right graph representation from noisy, multi-source data has garnered significant interest in recent years. A central tenet of this problem is relational learning. Here the objective is to incorporate the partial information each data source gives us in a way that captures the true underlying relationships. To address this challenge, we present a general, boosting-inspired framework for combining weak evidence of entity associations into a robust similarity metric. Building on previous work, we explore the extent to which different local quality measurements yield graph representations that are suitable for community detection. We present empirical results on a variety of datasets demonstrating the utility of this framework, especially with respect to real datasets where noise and scale present serious challenges. Finally, we prove a convergence theorem in an ideal setting and outline future research into other application domains.

Rajmonda Caceres, Kevin Carter, Jeremy Kun

Learning the right graph representation from noisy, multisource data has garnered significant interest in recent years. A central tenet of this problem is relational learning. Here the objective is to incorporate the partial information each data source gives us in a way that captures the true underlying relationships. To address this challenge, we present a general, boosting-inspired framework for combining weak evidence of entity associations into a robust similarity metric. We explore the extent to which different quality measurements yield graph representations that are suitable for community detection. We then present empirical results on both synthetic and real datasets demonstrating the utility of this framework. Our framework leads to suitable global graph representations from quality measurements local to each edge. Finally, we discuss future extensions and theoretical considerations of learning useful graph representations from weak feedback in general application settings.