Aleksandra Mojsilovic

Brian Belgodere, Pierre Dognin, Adam Ivankay et al. · ibm-research

Real-world data often exhibits bias, imbalance, and privacy risks. Synthetic datasets have emerged to address these issues. This paradigm relies on generative AI models to generate unbiased, privacy-preserving data while maintaining fidelity to the original data. However, assessing the trustworthiness of synthetic datasets and models is a critical challenge. We introduce a holistic auditing framework that comprehensively evaluates synthetic datasets and AI models. It focuses on preventing bias and discrimination, ensures fidelity to the source data, assesses utility, robustness, and privacy preservation. We demonstrate the framework's effectiveness by auditing various generative models across diverse use cases like education, healthcare, banking, and human resources, spanning different data modalities such as tabular, time-series, vision, and natural language. This holistic assessment is essential for compliance with regulatory safeguards. We introduce a trustworthiness index to rank synthetic datasets based on their safeguards trade-offs. Furthermore, we present a trustworthiness-driven model selection and cross-validation process during training, exemplified with "TrustFormers" across various data types. This approach allows for controllable trustworthiness trade-offs in synthetic data creation. Our auditing framework fosters collaboration among stakeholders, including data scientists, governance experts, internal reviewers, external certifiers, and regulators. This transparent reporting should become a standard practice to prevent bias, discrimination, and privacy violations, ensuring compliance with policies and providing accountability, safety, and performance guarantees.

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.

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.

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.

Swapnaja Achintalwar, Ioana Baldini, Djallel Bouneffouf et al. · ibm-research

The alignment of large language models is usually done by model providers to add or control behaviors that are common or universally understood across use cases and contexts. In contrast, in this article, we present an approach and architecture that empowers application developers to tune a model to their particular values, social norms, laws and other regulations, and orchestrate between potentially conflicting requirements in context. We lay out three main components of such an Alignment Studio architecture: Framers, Instructors, and Auditors that work in concert to control the behavior of a language model. We illustrate this approach with a running example of aligning a company's internal-facing enterprise chatbot to its business conduct guidelines.

Stacy Hobson, Michael Hind, Aleksandra Mojsilovic et al.

The global outbreak of COVID-19 has led to focus on efforts to manage and mitigate the continued spread of the disease. One of these efforts include the use of contact tracing to identify people who are at-risk of developing the disease through exposure to an infected person. Historically, contact tracing has been primarily manual but given the exponential spread of the virus that causes COVID-19, there has been significant interest in the development and use of digital contact tracing solutions to supplement the work of human contact tracers. The collection and use of sensitive personal details by these applications has led to a number of concerns by the stakeholder groups with a vested interest in these solutions. We explore digital contact tracing solutions in detail and propose the use of a transparent reporting mechanism, FactSheets, to provide transparency of and support trust in these applications. We also provide an example FactSheet template with questions that are specific to the contact tracing application domain.

Payel Das, Tom Sercu, Kahini Wadhawan et al.

De novo therapeutic design is challenged by a vast chemical repertoire and multiple constraints, e.g., high broad-spectrum potency and low toxicity. We propose CLaSS (Controlled Latent attribute Space Sampling) - an efficient computational method for attribute-controlled generation of molecules, which leverages guidance from classifiers trained on an informative latent space of molecules modeled using a deep generative autoencoder. We screen the generated molecules for additional key attributes by using deep learning classifiers in conjunction with novel features derived from atomistic simulations. The proposed approach is demonstrated for designing non-toxic antimicrobial peptides (AMPs) with strong broad-spectrum potency, which are emerging drug candidates for tackling antibiotic resistance. Synthesis and testing of only twenty designed sequences identified two novel and minimalist AMPs with high potency against diverse Gram-positive and Gram-negative pathogens, including one multidrug-resistant and one antibiotic-resistant K. pneumoniae, via membrane pore formation. Both antimicrobials exhibit low in vitro and in vivo toxicity and mitigate the onset of drug resistance. The proposed approach thus presents a viable path for faster and efficient discovery of potent and selective broad-spectrum antimicrobials.

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.

Michael Hind, Stephanie Houde, Jacquelyn Martino et al.

AI models and services are used in a growing number of highstakes areas, resulting in a need for increased transparency. Consistent with this, several proposals for higher quality and more consistent documentation of AI data, models, and systems have emerged. Little is known, however, about the needs of those who would produce or consume these new forms of documentation. Through semi-structured developer interviews, and two document creation exercises, we have assembled a clearer picture of these needs and the various challenges faced in creating accurate and useful AI documentation. Based on the observations from this work, supplemented by feedback received during multiple design explorations and stakeholder conversations, we make recommendations for easing the collection and flexible presentation of AI facts to promote transparency.

Vidya Muthukumar, Tejaswini Pedapati, Nalini Ratha et al.

Recent work shows unequal performance of commercial face classification services in the gender classification task across intersectional groups defined by skin type and gender. Accuracy on dark-skinned females is significantly worse than on any other group. In this paper, we conduct several analyses to try to uncover the reason for this gap. The main finding, perhaps surprisingly, is that skin type is not the driver. This conclusion is reached via stability experiments that vary an image's skin type via color-theoretic methods, namely luminance mode-shift and optimal transport. A second suspect, hair length, is also shown not to be the driver via experiments on face images cropped to exclude the hair. Finally, using contrastive post-hoc explanation techniques for neural networks, we bring forth evidence suggesting that differences in lip, eye and cheek structure across ethnicity lead to the differences. Further, lip and eye makeup are seen as strong predictors for a female face, which is a troubling propagation of a gender stereotype.

Payel Das, Kahini Wadhawan, Oscar Chang et al.

Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model learns a rich latent space of the biological peptide context by taking advantage of abundant, unlabeled peptide sequences. The model further learns a disentangled antimicrobial attribute space by using the feedback from a jointly trained AMP classifier that uses limited labeled instances. The disentangled representation allows for controllable generation of AMPs. Extensive analysis of the PepCVAE-generated sequences reveals superior performance of our model in comparison to a plain VAE, as PepCVAE generates novel AMP sequences with higher long-range diversity, while being closer to the training distribution of biological peptides. These features are highly desired in next-generation antimicrobial design.

Matthew Arnold, Rachel K. E. Bellamy, Michael Hind et al.

Accuracy is an important concern for suppliers of artificial intelligence (AI) services, but considerations beyond accuracy, such as safety (which includes fairness and explainability), security, and provenance, are also critical elements to engender consumers' trust in a service. Many industries use transparent, standardized, but often not legally required documents called supplier's declarations of conformity (SDoCs) to describe the lineage of a product along with the safety and performance testing it has undergone. SDoCs may be considered multi-dimensional fact sheets that capture and quantify various aspects of the product and its development to make it worthy of consumers' trust. Inspired by this practice, we propose FactSheets to help increase trust in AI services. We envision such documents to contain purpose, performance, safety, security, and provenance information to be completed by AI service providers for examination by consumers. We suggest a comprehensive set of declaration items tailored to AI and provide examples for two fictitious AI services in the appendix of the paper.

Evan Patterson, Ioana Baldini, Aleksandra Mojsilovic et al.

Your computer is continuously executing programs, but does it really understand them? Not in any meaningful sense. That burden falls upon human knowledge workers, who are increasingly asked to write and understand code. They deserve to have intelligent tools that reveal the connections between code and its subject matter. Towards this prospect, we develop an AI system that forms semantic representations of computer programs, using techniques from knowledge representation and program analysis. To create the representations, we introduce an algorithm for enriching dataflow graphs with semantic information. The semantic enrichment algorithm is undergirded by a new ontology language for modeling computer programs and a new ontology about data science, written in this language. Throughout the paper, we focus on code written by data scientists and we locate our work within a larger movement towards collaborative, open, and reproducible science.

Noel C. F. Codella, Michael Hind, Karthikeyan Natesan Ramamurthy et al.

The adoption of machine learning in high-stakes applications such as healthcare and law has lagged in part because predictions are not accompanied by explanations comprehensible to the domain user, who often holds the ultimate responsibility for decisions and outcomes. In this paper, we propose an approach to generate such explanations in which training data is augmented to include, in addition to features and labels, explanations elicited from domain users. A joint model is then learned to produce both labels and explanations from the input features. This simple idea ensures that explanations are tailored to the complexity expectations and domain knowledge of the consumer. Evaluation spans multiple modeling techniques on a game dataset, a (visual) aesthetics dataset, a chemical odor dataset and a Melanoma dataset showing that our approach is generalizable across domains and algorithms. Results demonstrate that meaningful explanations can be reliably taught to machine learning algorithms, and in some cases, also improve modeling accuracy.