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Jiří Navrátil

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3 papers

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AAAI Conference 2026 Conference Paper

GP-MoLFormer-Sim: Test Time Molecular Optimization Through Contextual Similarity Guidance

Jiří Navrátil
Jarret Ross
Payel Das
Youssef Mroueh
Samuel C Hoffman
Vijil Chenthamarakshan
Brian Belgodere

The ability to design molecules while preserving similarity to a target molecule and/or property is crucial for various applications in drug discovery, chemical design, and biology. We introduce in this paper an efficient training-free method for navigating and sampling from the molecular space with a generative Chemical Language Model (CLM), while using the molecular similarity to the target as a guide. Our method leverages the contextual representations learned from the CLM itself to estimate the molecular similarity, which is then used to adjust the autoregressive sampling strategy of the CLM. At each step of the decoding process, the method tracks the distance of the current generations from the target and updates the logits to encourage the preservation of similarity in generations. We implement the method using a recently proposed ~47M parameter SMILES-based CLM, GP-MoLFormer, and therefore refer to the method as GP-MoLFormer-Sim, which enables a test-time update of the deep generative policy to reflect the contextual similarity to a set of guide molecules. The method is further integrated into a genetic algorithm (GA) and tested on a set of standard molecular optimization benchmarks involving property optimization, molecular rediscovery, and structure-based drug design. Results show that, GP-MoLFormer-Sim, combined with GA (GP-MoLFormer-Sim+GA) outperforms existing training-free baseline methods, when the oracle remains black-box. The findings in this work are a step forward in understanding and guiding the generative mechanisms of CLMs.

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AAAI Conference 2021 Conference Paper

Anomaly Attribution with Likelihood Compensation

Tsuyoshi Idé
Amit Dhurandhar
Jiří Navrátil
Moninder Singh
Naoki Abe

This paper addresses the task of explaining anomalous predictions of a black-box regression model. When using a black-box model, such as one to predict building energy consumption from many sensor measurements, we often have a situation where some observed samples may significantly deviate from their prediction. It may be due to a sub-optimal black-box model, or simply because those samples are outliers. In either case, one would ideally want to compute a “responsibility score” indicative of the extent to which an input variable is responsible for the anomalous output. In this work, we formalize this task as a statistical inverse problem: Given model deviation from the expected value, infer the responsibility score of each of the input variables. We propose a new method called likelihood compensation (LC), which is founded on the likelihood principle and computes a correction to each input variable. To the best of our knowledge, this is the first principled framework that computes a responsibility score for real valued anomalous model deviations. We apply our approach to a real-world building energy prediction task and confirm its utility based on expert feedback.

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AAAI Conference 2021 Conference Paper

Learning Prediction Intervals for Model Performance

Benjamin Elder
Matthew Arnold
Anupama Murthi
Jiří Navrátil

Understanding model performance on unlabeled data is a fundamental challenge of developing, deploying, and maintaining AI systems. Model performance is typically evaluated using test sets or periodic manual quality assessments, both of which require laborious manual data labeling. Automated performance prediction techniques aim to mitigate this burden, but potential inaccuracy and a lack of trust in their predictions has prevented their widespread adoption. We address this core problem of performance prediction uncertainty with a method to compute prediction intervals for model performance. Our methodology uses transfer learning to train an uncertainty model to estimate the uncertainty of model performance predictions. We evaluate our approach across a wide range of drift conditions and show substantial improvement over competitive baselines. We believe this result makes prediction intervals, and performance prediction in general, significantly more practical for real-world use.

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