Krzysztof Maziarz

Guoqing Liu, Di Xue, Shufang Xie et al.

Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro*, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro*, and from 5.63 to 4.78 for RetroGraph). Our code is available at \url{https://github.com/DiXue98/PDVN}.

Krzysztof Maziarz, Austin Tripp, Guoqing Liu et al.

Automated Synthesis Planning has recently re-emerged as a research area at the intersection of chemistry and machine learning. Despite the appearance of steady progress, we argue that imperfect benchmarks and inconsistent comparisons mask systematic shortcomings of existing techniques, and unnecessarily hamper progress. To remedy this, we present a synthesis planning library with an extensive benchmarking framework, called syntheseus, which promotes best practice by default, enabling consistent meaningful evaluation of single-step models and multi-step planning algorithms. We demonstrate the capabilities of syntheseus by re-evaluating several previous retrosynthesis algorithms, and find that the ranking of state-of-the-art models changes in controlled evaluation experiments. We end with guidance for future works in this area, and call the community to engage in the discussion on how to improve benchmarks for synthesis planning.

Austin Tripp, Krzysztof Maziarz, Sarah Lewis et al.

Retrosynthesis is the task of planning a series of chemical reactions to create a desired molecule from simpler, buyable molecules. While previous works have proposed algorithms to find optimal solutions for a range of metrics (e.g. shortest, lowest-cost), these works generally overlook the fact that we have imperfect knowledge of the space of possible reactions, meaning plans created by algorithms may not work in a laboratory. In this paper we propose a novel formulation of retrosynthesis in terms of stochastic processes to account for this uncertainty. We then propose a novel greedy algorithm called retro-fallback which maximizes the probability that at least one synthesis plan can be executed in the lab. Using in-silico benchmarks we demonstrate that retro-fallback generally produces better sets of synthesis plans than the popular MCTS and retro* algorithms.

Guoqing Liu, Junren Li, Zihan Zhao et al.

Solving computer-aided synthesis planning is essential for enabling fully automated, robot-assisted synthesis workflows and improving the efficiency of drug discovery. A key challenge, however, is bridging the gap between computational route design and practical laboratory execution, particularly the accurate prediction of viable experimental procedures for each synthesis step. In this work, we present QFANG, a scientific reasoning language model capable of generating precise, structured experimental procedures directly from reaction equations, with explicit chain-of-thought reasoning. To develop QFANG, we curated a high-quality dataset comprising 905,990 chemical reactions paired with structured action sequences, extracted and processed from patent literature using large language models. We introduce a Chemistry-Guided Reasoning (CGR) framework that produces chain-of-thought data grounded in chemical knowledge at scale. The model subsequently undergoes supervised fine-tuning to elicit complex chemistry reasoning. Finally, we apply Reinforcement Learning from Verifiable Rewards (RLVR) to further enhance procedural accuracy. Experimental results demonstrate that QFANG outperforms advanced general-purpose reasoning models and nearest-neighbor retrieval baselines, measured by traditional NLP similarity metrics and a chemically aware evaluator using an LLM-as-a-judge. Moreover, QFANG generalizes to certain out-of-domain reaction classes and adapts to variations in laboratory conditions and user-specific constraints. We believe that QFANG's ability to generate high-quality synthesis procedures represents an important step toward bridging the gap between computational synthesis planning and fully automated laboratory synthesis.

Yingce Xia, Peiran Jin, Shufang Xie et al. · microsoft-research

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, RNA and even cells. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) top performance across different domains, matching or surpassing state-of-the-art specialist models. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Krzysztof Maziarz, Guoqing Liu, Hubert Misztela et al.

Chemical synthesis remains a critical bottleneck in the discovery and manufacture of functional small molecules. AI-based synthesis planning models could be a potential remedy to find effective syntheses, and have made progress in recent years. However, they still struggle with less frequent, yet critical reactions for synthetic strategy, as well as hallucinated, incorrect predictions. This hampers multi-step search algorithms that rely on models, and leads to misalignment with chemists' expectations. Here we propose RetroChimera: a frontier retrosynthesis model, built upon two newly developed components with complementary inductive biases, which we fuse together using a new framework for integrating predictions from multiple sources via a learning-based ensembling strategy. Through experiments across several orders of magnitude in data scale and splitting strategy, we show RetroChimera outperforms all major models by a large margin, demonstrating robustness outside the training data, as well as for the first time the ability to learn from even a very small number of examples per reaction class. Moreover, industrial organic chemists prefer predictions from RetroChimera over the reactions it was trained on in terms of quality, revealing high levels of alignment. Finally, we demonstrate zero-shot transfer to an internal dataset from a major pharmaceutical company, showing robust generalization under distribution shift. With the new dimension that our ensembling framework unlocks, we anticipate further acceleration in the development of even more accurate models.

Piotr Gaiński, Michał Koziarski, Krzysztof Maziarz et al.

Single-step retrosynthesis aims to predict a set of reactions that lead to the creation of a target molecule, which is a crucial task in molecular discovery. Although a target molecule can often be synthesized with multiple different reactions, it is not clear how to verify the feasibility of a reaction, because the available datasets cover only a tiny fraction of the possible solutions. Consequently, the existing models are not encouraged to explore the space of possible reactions sufficiently. In this paper, we propose a novel single-step retrosynthesis model, RetroGFN, that can explore outside the limited dataset and return a diverse set of feasible reactions by leveraging a feasibility proxy model during the training. We show that RetroGFN achieves competitive results on standard top-k accuracy while outperforming existing methods on round-trip accuracy. Moreover, we provide empirical arguments in favor of using round-trip accuracy, which expands the notion of feasibility with respect to the standard top-k accuracy metric.

Hagen Muenkler, Hubert Misztela, Michal Pikusa et al.

Many contemporary generative models of molecules are variational auto-encoders of molecular graphs. One term in their training loss pertains to reconstructing the input, yet reconstruction capabilities of state-of-the-art models have not yet been thoroughly compared on a large and chemically diverse dataset. In this work, we show that when several state-of-the-art generative models are evaluated under the same conditions, their reconstruction accuracy is surprisingly low, worse than what was previously reported on seemingly harder datasets. However, we show that improving reconstruction does not directly lead to better sampling or optimization performance. Failed reconstructions from the MoLeR model are usually similar to the inputs, assembling the same motifs in a different way, and possess similar chemical properties such as solubility. Finally, we show that the input molecule and its failed reconstruction are usually mapped by the different encoders to statistically distinguishable posterior distributions, hinting that posterior collapse may not fully explain why VAEs are bad at reconstructing molecular graphs.

Krzysztof Maziarz, Anna Krason, Zbigniew Wojna

Recent advancements in computer vision promise to automate medical image analysis. Rheumatoid arthritis is an autoimmune disease that would profit from computer-based diagnosis, as there are no direct markers known, and doctors have to rely on manual inspection of X-ray images. In this work, we present a multi-task deep learning model that simultaneously learns to localize joints on X-ray images and diagnose two kinds of joint damage: narrowing and erosion. Additionally, we propose a modification of label smoothing, which combines classification and regression cues into a single loss and achieves 5% relative error reduction compared to standard loss functions. Our final model obtained 4th place in joint space narrowing and 5th place in joint erosion in the global RA2 DREAM challenge.

Krzysztof Maziarz, Henry Jackson-Flux, Pashmina Cameron et al.

Recent advancements in deep learning-based modeling of molecules promise to accelerate in silico drug discovery. A plethora of generative models is available, building molecules either atom-by-atom and bond-by-bond or fragment-by-fragment. However, many drug discovery projects require a fixed scaffold to be present in the generated molecule, and incorporating that constraint has only recently been explored. Here, we propose MoLeR, a graph-based model that naturally supports scaffolds as initial seed of the generative procedure, which is possible because it is not conditioned on the generation history. Our experiments show that MoLeR performs comparably to state-of-the-art methods on unconstrained molecular optimization tasks, and outperforms them on scaffold-based tasks, while being an order of magnitude faster to train and sample from than existing approaches. Furthermore, we show the influence of a number of seemingly minor design choices on the overall performance.

Zbigniew Wojna, Krzysztof Maziarz, Łukasz Jocz et al.

We address six different classification tasks related to fine-grained building attributes: construction type, number of floors, pitch and geometry of the roof, facade material, and occupancy class. Tackling such a remote building analysis problem became possible only recently due to growing large-scale datasets of urban scenes. To this end, we introduce a new benchmarking dataset, consisting of 49426 images (top-view and street-view) of 9674 buildings. These photos are further assembled, together with the geometric metadata. The dataset showcases various real-world challenges, such as occlusions, blur, partially visible objects, and a broad spectrum of buildings. We propose a new projection pooling layer, creating a unified, top-view representation of the top-view and the side views in a high-dimensional space. It allows us to utilize the building and imagery metadata seamlessly. Introducing this layer improves classification accuracy -- compared to highly tuned baseline models -- indicating its suitability for building analysis.

Krzysztof Maziarz, Efi Kokiopoulou, Andrea Gesmundo et al.

This paper proposes a novel learning method for multi-task applications. Multi-task neural networks can learn to transfer knowledge across different tasks by using parameter sharing. However, sharing parameters between unrelated tasks can hurt performance. To address this issue, we propose a framework to learn fine-grained patterns of parameter sharing. Assuming that the network is composed of several components across layers, our framework uses learned binary variables to allocate components to tasks in order to encourage more parameter sharing between related tasks, and discourage parameter sharing otherwise. The binary allocation variables are learned jointly with the model parameters by standard back-propagation thanks to the Gumbel-Softmax reparametrization method. When applied to the Omniglot benchmark, the proposed method achieves a 17% relative reduction of the error rate compared to state-of-the-art.

Krzysztof Maziarz, Mingxing Tan, Andrey Khorlin et al.

Neural Architecture Search has shown potential to automate the design of neural networks. Deep Reinforcement Learning based agents can learn complex architectural patterns, as well as explore a vast and compositional search space. On the other hand, evolutionary algorithms offer higher sample efficiency, which is critical for such a resource intensive application. In order to capture the best of both worlds, we propose a class of Evolutionary-Neural hybrid agents (Evo-NAS). We show that the Evo-NAS agent outperforms both neural and evolutionary agents when applied to architecture search for a suite of text and image classification benchmarks. On a high-complexity architecture search space for image classification, the Evo-NAS agent surpasses the accuracy achieved by commonly used agents with only 1/3 of the search cost.

Noam Shazeer, Azalia Mirhoseini, Krzysztof Maziarz et al.

The capacity of a neural network to absorb information is limited by its number of parameters. Conditional computation, where parts of the network are active on a per-example basis, has been proposed in theory as a way of dramatically increasing model capacity without a proportional increase in computation. In practice, however, there are significant algorithmic and performance challenges. In this work, we address these challenges and finally realize the promise of conditional computation, achieving greater than 1000x improvements in model capacity with only minor losses in computational efficiency on modern GPU clusters. We introduce a Sparsely-Gated Mixture-of-Experts layer (MoE), consisting of up to thousands of feed-forward sub-networks. A trainable gating network determines a sparse combination of these experts to use for each example. We apply the MoE to the tasks of language modeling and machine translation, where model capacity is critical for absorbing the vast quantities of knowledge available in the training corpora. We present model architectures in which a MoE with up to 137 billion parameters is applied convolutionally between stacked LSTM layers. On large language modeling and machine translation benchmarks, these models achieve significantly better results than state-of-the-art at lower computational cost.