Samuel C. Hoffman

Matteo Manica, Jannis Born, Joris Cadow et al. · mit

With the growing availability of data within various scientific domains, generative models hold enormous potential to accelerate scientific discovery. They harness powerful representations learned from datasets to speed up the formulation of novel hypotheses with the potential to impact material discovery broadly. We present the Generative Toolkit for Scientific Discovery (GT4SD). This extensible open-source library enables scientists, developers, and researchers to train and use state-of-the-art generative models to accelerate scientific discovery focused on material design.

Michael Feffer, Martin Hirzel, Samuel C. Hoffman et al.

Bias mitigators can improve algorithmic fairness in machine learning models, but their effect on fairness is often not stable across data splits. A popular approach to train more stable models is ensemble learning, but unfortunately, it is unclear how to combine ensembles with mitigators to best navigate trade-offs between fairness and predictive performance. To that end, we built an open-source library enabling the modular composition of 8 mitigators, 4 ensembles, and their corresponding hyperparameters, and we empirically explored the space of configurations on 13 datasets. We distilled our insights from this exploration in the form of a guidance diagram for practitioners that we demonstrate is robust and reproducible.

Vijil Chenthamarakshan, Samuel C. Hoffman, C. David Owen et al.

The discovery of novel inhibitor molecules for emerging drug-target proteins is widely acknowledged as a challenging inverse design problem: Exhaustive exploration of the vast chemical search space is impractical, especially when the target structure or active molecules are unknown. Here we validate experimentally the broad utility of a deep generative framework trained at-scale on protein sequences, small molecules, and their mutual interactions -- that is unbiased toward any specific target. As demonstrators, we consider two dissimilar and relevant SARS-CoV-2 targets: the main protease and the spike protein (receptor binding domain, RBD). To perform target-aware design of novel inhibitor molecules, a protein sequence-conditioned sampling on the generative foundation model is performed. Despite using only the target sequence information, and without performing any target-specific adaptation of the generative model, micromolar-level inhibition was observed in in vitro experiments for two candidates out of only four synthesized for each target. The most potent spike RBD inhibitor also exhibited activity against several variants in live virus neutralization assays. These results therefore establish that a single, broadly deployable generative foundation model for accelerated hit discovery is effective and efficient, even in the most general case where neither target structure nor binder information is available.

Samuel C. Hoffman, Payel Das, Karthikeyan Shanmugam et al.

Training generative models that capture rich semantics of the data and interpreting the latent representations encoded by such models are very important problems in un-/self-supervised learning. In this work, we provide a simple algorithm that relies on perturbation experiments on latent codes of a pre-trained generative autoencoder to uncover an attribute graph that is implied by the generative model. We perform perturbation experiments to check for influence of a given latent variable on a subset of attributes. Given this, we show that one can fit an effective graphical model that models a structural equation model between latent codes taken as exogenous variables and attributes taken as observed variables. One interesting aspect is that a single latent variable controls multiple overlapping subsets of attributes unlike conventional approaches that try to impose full independence. Using a pre-trained generative autoencoder trained on a large dataset of small molecules, we demonstrate that the graphical model between various molecular attributes and latent codes learned by our algorithm can be used to predict a specific property for molecules which are drawn from a different distribution. We compare prediction models trained on various feature subsets chosen by simple baselines, as well as existing causal discovery and sparse learning/feature selection methods, with the ones in the derived Markov blanket from our method. Results show empirically that the predictor that relies on our Markov blanket attributes is robust to distribution shifts when transferred or fine-tuned with a few samples from the new distribution, especially when training data is limited.

Manish Nagireddy, Moninder Singh, Samuel C. Hoffman et al.

Ensuring trustworthiness in machine learning (ML) models is a multi-dimensional task. In addition to the traditional notion of predictive performance, other notions such as privacy, fairness, robustness to distribution shift, adversarial robustness, interpretability, explainability, and uncertainty quantification are important considerations to evaluate and improve (if deficient). However, these sub-disciplines or 'pillars' of trustworthiness have largely developed independently, which has limited us from understanding their interactions in real-world ML pipelines. In this paper, focusing specifically on compositions of functions arising from the different pillars, we aim to reduce this gap, develop new insights for trustworthy ML, and answer questions such as the following. Does the composition of multiple fairness interventions result in a fairer model compared to a single intervention? How do bias mitigation algorithms for fairness affect local post-hoc explanations? Does a defense algorithm for untargeted adversarial attacks continue to be effective when composed with a privacy transformation? Toward this end, we report initial empirical results and new insights from 9 different compositions of functions (or pipelines) on 7 real-world datasets along two trustworthy dimensions - fairness and explainability. We also report progress, and implementation choices, on an extensible composer tool to encourage the combination of functionalities from multiple pillars. To-date, the tool supports bias mitigation algorithms for fairness and post-hoc explainability methods. We hope this line of work encourages the thoughtful consideration of multiple pillars when attempting to formulate and resolve a trustworthiness problem.

Michael Feffer, Martin Hirzel, Samuel C. Hoffman et al.

There are several bias mitigators that can reduce algorithmic bias in machine learning models but, unfortunately, the effect of mitigators on fairness is often not stable when measured across different data splits. A popular approach to train more stable models is ensemble learning. Ensembles, such as bagging, boosting, voting, or stacking, have been successful at making predictive performance more stable. One might therefore ask whether we can combine the advantages of bias mitigators and ensembles? To explore this question, we first need bias mitigators and ensembles to work together. We built an open-source library enabling the modular composition of 10 mitigators, 4 ensembles, and their corresponding hyperparameters. Based on this library, we empirically explored the space of combinations on 13 datasets, including datasets commonly used in fairness literature plus datasets newly curated by our library. Furthermore, we distilled the results into a guidance diagram for practitioners. We hope this paper will contribute towards improving stability in bias mitigation.

Vijay Arya, Rachel K. E. Bellamy, Pin-Yu Chen et al.

As artificial intelligence and machine learning algorithms become increasingly prevalent in society, multiple stakeholders are calling for these algorithms to provide explanations. At the same time, these stakeholders, whether they be affected citizens, government regulators, domain experts, or system developers, have different explanation needs. To address these needs, in 2019, we created AI Explainability 360 (Arya et al. 2020), an open source software toolkit featuring ten diverse and state-of-the-art explainability methods and two evaluation metrics. This paper examines the impact of the toolkit with several case studies, statistics, and community feedback. The different ways in which users have experienced AI Explainability 360 have resulted in multiple types of impact and improvements in multiple metrics, highlighted by the adoption of the toolkit by the independent LF AI & Data Foundation. The paper also describes the flexible design of the toolkit, examples of its use, and the significant educational material and documentation available to its users.

Vijay Arya, Rachel K. E. Bellamy, Pin-Yu Chen et al.

As artificial intelligence and machine learning algorithms make further inroads into society, calls are increasing from multiple stakeholders for these algorithms to explain their outputs. At the same time, these stakeholders, whether they be affected citizens, government regulators, domain experts, or system developers, present different requirements for explanations. Toward addressing these needs, we introduce AI Explainability 360 (http://aix360.mybluemix.net/), an open-source software toolkit featuring eight diverse and state-of-the-art explainability methods and two evaluation metrics. Equally important, we provide a taxonomy to help entities requiring explanations to navigate the space of explanation methods, not only those in the toolkit but also in the broader literature on explainability. For data scientists and other users of the toolkit, we have implemented an extensible software architecture that organizes methods according to their place in the AI modeling pipeline. We also discuss enhancements to bring research innovations closer to consumers of explanations, ranging from simplified, more accessible versions of algorithms, to tutorials and an interactive web demo to introduce AI explainability to different audiences and application domains. Together, our toolkit and taxonomy can help identify gaps where more explainability methods are needed and provide a platform to incorporate them as they are developed.

Rachel K. E. Bellamy, Kuntal Dey, Michael Hind et al.

Fairness is an increasingly important concern as machine learning models are used to support decision making in high-stakes applications such as mortgage lending, hiring, and prison sentencing. This paper introduces a new open source Python toolkit for algorithmic fairness, AI Fairness 360 (AIF360), released under an Apache v2.0 license {https://github.com/ibm/aif360). The main objectives of this toolkit are to help facilitate the transition of fairness research algorithms to use in an industrial setting and to provide a common framework for fairness researchers to share and evaluate algorithms. The package includes a comprehensive set of fairness metrics for datasets and models, explanations for these metrics, and algorithms to mitigate bias in datasets and models. It also includes an interactive Web experience (https://aif360.mybluemix.net) that provides a gentle introduction to the concepts and capabilities for line-of-business users, as well as extensive documentation, usage guidance, and industry-specific tutorials to enable data scientists and practitioners to incorporate the most appropriate tool for their problem into their work products. The architecture of the package has been engineered to conform to a standard paradigm used in data science, thereby further improving usability for practitioners. Such architectural design and abstractions enable researchers and developers to extend the toolkit with their new algorithms and improvements, and to use it for performance benchmarking. A built-in testing infrastructure maintains code quality.

Jerret Ross, Brian Belgodere, Samuel C. Hoffman et al.

Transformer-based models trained on large and general purpose datasets consisting of molecular strings have recently emerged as a powerful tool for successfully modeling various structure-property relations. Inspired by this success, we extend the paradigm of training chemical language transformers on large-scale chemical datasets to generative tasks in this work. Specifically, we propose GP-MoLFormer, an autoregressive molecular string generator that is trained on more than 1.1B (billion) chemical SMILES. GP-MoLFormer uses a 46.8M parameter transformer decoder model with linear attention and rotary positional encodings as the base architecture. GP-MoLFormer's utility is evaluated and compared with that of existing baselines on three different tasks: de novo generation, scaffold-constrained molecular decoration, and unconstrained property-guided optimization. While the first two are handled with no additional training, we propose a parameter-efficient fine-tuning method for the last task, which uses property-ordered molecular pairs as input. We call this new approach pair-tuning. Our results show GP-MoLFormer performs better or comparable with baselines across all three tasks, demonstrating its general utility for a variety of molecular generation tasks. We further report strong memorization of training data in GP-MoLFormer generations, which has so far remained unexplored for chemical language models. Our analyses reveal that training data memorization and novelty in generations are impacted by the quality and scale of the training data; duplication bias in training data can enhance memorization at the cost of lowering novelty. We further establish a scaling law relating inference compute and novelty in generations.

Samuel C. Hoffman, Vijil Chenthamarakshan, Dmitry Yu. Zubarev et al.

Photo-acid generators (PAGs) are compounds that release acids ($H^+$ ions) when exposed to light. These compounds are critical components of the photolithography processes that are used in the manufacture of semiconductor logic and memory chips. The exponential increase in the demand for semiconductors has highlighted the need for discovering novel photo-acid generators. While de novo molecule design using deep generative models has been widely employed for drug discovery and material design, its application to the creation of novel photo-acid generators poses several unique challenges, such as lack of property labels. In this paper, we highlight these challenges and propose a generative modeling approach that utilizes conditional generation from a pre-trained deep autoencoder and expert-in-the-loop techniques. The validity of the proposed approach was evaluated with the help of subject matter experts, indicating the promise of such an approach for applications beyond the creation of novel photo-acid generators.

Vijil Chenthamarakshan, Payel Das, Samuel C. Hoffman et al.

The novel nature of SARS-CoV-2 calls for the development of efficient de novo drug design approaches. In this study, we propose an end-to-end framework, named CogMol (Controlled Generation of Molecules), for designing new drug-like small molecules targeting novel viral proteins with high affinity and off-target selectivity. CogMol combines adaptive pre-training of a molecular SMILES Variational Autoencoder (VAE) and an efficient multi-attribute controlled sampling scheme that uses guidance from attribute predictors trained on latent features. To generate novel and optimal drug-like molecules for unseen viral targets, CogMol leverages a protein-molecule binding affinity predictor that is trained using SMILES VAE embeddings and protein sequence embeddings learned unsupervised from a large corpus. CogMol framework is applied to three SARS-CoV-2 target proteins: main protease, receptor-binding domain of the spike protein, and non-structural protein 9 replicase. The generated candidates are novel at both molecular and chemical scaffold levels when compared to the training data. CogMol also includes insilico screening for assessing toxicity of parent molecules and their metabolites with a multi-task toxicity classifier, synthetic feasibility with a chemical retrosynthesis predictor, and target structure binding with docking simulations. Docking reveals favorable binding of generated molecules to the target protein structure, where 87-95 % of high affinity molecules showed docking free energy < -6 kcal/mol. When compared to approved drugs, the majority of designed compounds show low parent molecule and metabolite toxicity and high synthetic feasibility. In summary, CogMol handles multi-constraint design of synthesizable, low-toxic, drug-like molecules with high target specificity and selectivity, and does not need target-dependent fine-tuning of the framework or target structure information.

Prasanna Sattigeri, Samuel C. Hoffman, Vijil Chenthamarakshan et al.

In this paper, we introduce the Fairness GAN, an approach for generating a dataset that is plausibly similar to a given multimedia dataset, but is more fair with respect to protected attributes in allocative decision making. We propose a novel auxiliary classifier GAN that strives for demographic parity or equality of opportunity and show empirical results on several datasets, including the CelebFaces Attributes (CelebA) dataset, the Quick, Draw!\ dataset, and a dataset of soccer player images and the offenses they were called for. The proposed formulation is well-suited to absorbing unlabeled data; we leverage this to augment the soccer dataset with the much larger CelebA dataset. The methodology tends to improve demographic parity and equality of opportunity while generating plausible images.