arXiv subjects

Thorben Prein

Publications and source records attributed to Thorben Prein.

7 recordsLinked to original sources

arXiv2026

HASSL: Hierarchy-Aware Self-Supervised Learning Framework for Single Cell Microscopy

Hierarchical structure is common in image data, where fine-grained clusters often merge into larger, coarser semantic groups. In biological cell images, current self-supervised learning models often suppress this hierarchy, as coarse factors such as imaging modality can obscure finer morphological attributes in the latent space. We propose a hierarchy-aware self-supervised training framework to address this problem. Our method combines two components: a distillation framework with a segmentation teacher to improve morphological awareness in the latent space, and a hierarchy-aware contrastive loss based on HDBSCAN to improve decision boundaries between closely related subtypes at different hierarchical levels. Together, these components reduce the tendency of self-supervised learning to overemphasize coarse factors and instead align embeddings with semantic and morphological cues. This yields biologically meaningful sub-clusters driven by fine morphological detail. We train and evaluate our method on a curated corpus of 2.3 million single cells aggregated from 20 microscopy datasets, both labeled and unlabeled, covering 208 cell classes. Our method improves over baseline and counterpart methods, increasing average top-K accuracy by 2.8%, top-9 retrieval on the dataset with the deepest hierarchy by 6.3%, and downstream F1-score for biologically relevant drug classification from perturbed cell morphology by 7.8%.

cs.CV↗

arXiv2025

A Synthesizability-Guided Pipeline for Materials Discovery

Computational materials discovery relies on the generation of plausible crystal structures. The plausibility is typically judged through density functional theory methods which, while typically accurate at zero Kelvin, often favor low-energy structures that are not experimentally accessible. We develop a combined compositional and structural synthesizability score which provides an accurate way of predicting which compounds can actually be synthesized in a laboratory. We use it to evaluate non-synthesized structures from the Materials Project, GNoME, and Alexandria, and identified several hundred highly synthesizable candidates. We then predict synthesis pathways, conduct corresponding experiments, and characterize the products across 16 targets, successfully synthesizing 7 of 16. The entire experimental process was completed in only three days. Our results highlight omissions in lists of known synthesized structures, deliver insights into the practical utility of current materials databases, and showcase the central role synthesizability prediction can play in materials discovery.

cs.CE↗

arXiv2025

DiffSyn: A Generative Diffusion Approach to Materials Synthesis Planning

The synthesis of crystalline materials, such as zeolites, remains a significant challenge due to a high-dimensional synthesis space, intricate structure-synthesis relationships and time-consuming experiments. Considering the one-to-many relationship between structure and synthesis, we propose DiffSyn, a generative diffusion model trained on over 23,000 synthesis recipes spanning 50 years of literature. DiffSyn generates probable synthesis routes conditioned on a desired zeolite structure and an organic template. DiffSyn achieves state-of-the-art performance by capturing the multi-modal nature of structure-synthesis relationships. We apply DiffSyn to differentiate among competing phases and generate optimal synthesis routes. As a proof of concept, we synthesize a UFI material using DiffSyn-generated synthesis routes. These routes, rationalized by density functional theory binding energies, resulted in the successful synthesis of a UFI material with a high Si/Al$_{\text{ICP}}$ of 19.0, which is expected to improve thermal stability and is higher than that of any previously recorded.

cond-mat.mtrl-sci↗

arXiv2025

Language Models Enable Data-Augmented Synthesis Planning for Inorganic Materials

Inorganic synthesis planning currently relies primarily on heuristic approaches or machine-learning models trained on limited datasets, which constrains its generality. We demonstrate that language models, without task-specific fine-tuning, can recall synthesis conditions. Off-the-shelf models, such as GPT-4.1, Gemini 2.0 Flash and Llama 4 Maverick, achieve a Top-1 precursor-prediction accuracy of up to 53.8 % and a Top-5 performance of 66.1 % on a held-out set of 1,000 reactions. They also predict calcination and sintering temperatures with mean absolute errors below 126 {\deg}C, matching specialized regression methods. Ensembling these language models further enhances predictive accuracy and reduces inference cost per prediction by up to 70 %. We subsequently employ language models to generate 28,548 synthetic reaction recipes, which we combine with literature-mined examples to pretrain a transformer-based model, SyntMTE. After fine-tuning on the combined dataset, SyntMTE reduces mean-absolute error in sintering temperature prediction to 73 {\deg}C and in calcination temperature to 98 {\deg}C. This strategy improves models by up to 8.7 % compared with baselines trained exclusively on experimental data. Finally, in a case study on Li7La3Zr2O12 solid-state electrolytes, we demonstrate that SyntMTE reproduces the experimentally observed dopant-dependent sintering trends. Our hybrid workflow enables scalable, data-efficient inorganic synthesis planning.

cond-mat.mtrl-sci↗

arXiv2025

Retro-Rank-In: A Ranking-Based Approach for Inorganic Materials Synthesis Planning

Retrosynthesis strategically plans the synthesis of a chemical target compound from simpler, readily available precursor compounds. This process is critical for synthesizing novel inorganic materials, yet traditional methods in inorganic chemistry continue to rely on trial-and-error experimentation. Emerging machine-learning approaches struggle to generalize to entirely new reactions due to their reliance on known precursors, as they frame retrosynthesis as a multi-label classification task. To address these limitations, we propose Retro-Rank-In, a novel framework that reformulates the retrosynthesis problem by embedding target and precursor materials into a shared latent space and learning a pairwise ranker on a bipartite graph of inorganic compounds. We evaluate Retro-Rank-In's generalizability on challenging retrosynthesis dataset splits designed to mitigate data duplicates and overlaps. For instance, for Cr2AlB2, it correctly predicts the verified precursor pair CrB + Al despite never seeing them in training, a capability absent in prior work. Extensive experiments show that Retro-Rank-In sets a new state-of-the-art, particularly in out-of-distribution generalization and candidate set ranking, offering a powerful tool for accelerating inorganic material synthesis.

physics.chem-ph↗

arXiv2024

Regress, Don't Guess -- A Regression-like Loss on Number Tokens for Language Models

While language models have exceptional capabilities at text generation, they lack a natural inductive bias for emitting numbers and thus struggle in tasks involving quantitative reasoning, especially arithmetic. One fundamental limitation is the nature of the cross-entropy (CE) loss, which assumes a nominal scale and thus cannot convey proximity between generated number tokens. In response, we here present a regression-like loss that operates purely on token level. Our proposed Number Token Loss (NTL) comes in two flavors and minimizes either the $L_p$ norm or the Wasserstein distance between the numerical values of the real and predicted number tokens. NTL can easily be added to any language model and extend the CE objective during training without runtime overhead. We evaluate the proposed scheme on various mathematical datasets and find that it consistently improves performance in math-related tasks. In a direct comparison on a regression task, we find that NTL can match the performance of a regression head, despite operating on token level. Finally, we scale NTL up to 3B parameter models and observe improved performance, demonstrating its potential for seamless integration into LLMs. We hope to inspire LLM developers to improve their pretraining objectives and distribute NTL as a minimalistic and lightweight PyPI package $ntloss$: https://github.com/ai4sd/number-token-loss. Development code for full paper reproduction is available separately.

cs.CL↗

arXiv2022

Augmenting Scientific Creativity with Retrieval across Knowledge Domains

Exposure to ideas in domains outside a scientist's own may benefit her in reformulating existing research problems in novel ways and discovering new application domains for existing solution ideas. While improved performance in scholarly search engines can help scientists efficiently identify relevant advances in domains they may already be familiar with, it may fall short of helping them explore diverse ideas \textit{outside} such domains. In this paper we explore the design of systems aimed at augmenting the end-user ability in cross-domain exploration with flexible query specification. To this end, we develop an exploratory search system in which end-users can select a portion of text core to their interest from a paper abstract and retrieve papers that have a high similarity to the user-selected core aspect but differ in terms of domains. Furthermore, end-users can `zoom in' to specific domain clusters to retrieve more papers from them and understand nuanced differences within the clusters. Our case studies with scientists uncover opportunities and design implications for systems aimed at facilitating cross-domain exploration and inspiration.

cs.IR↗