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Apr 2

Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

  • 5 authors
·
May 31, 2019

Cartridges: Lightweight and general-purpose long context representations via self-study

Large language models are often used to answer queries grounded in large text corpora (e.g. codebases, legal documents, or chat histories) by placing the entire corpus in the context window and leveraging in-context learning (ICL). Although current models support contexts of 100K-1M tokens, this setup is costly to serve because the memory consumption of the KV cache scales with input length. We explore an alternative: training a smaller KV cache offline on each corpus. At inference time, we load this trained KV cache, which we call a Cartridge, and decode a response. Critically, the cost of training a Cartridge can be amortized across all the queries referencing the same corpus. However, we find that the naive approach of training the Cartridge with next-token prediction on the corpus is not competitive with ICL. Instead, we propose self-study, a training recipe in which we generate synthetic conversations about the corpus and train the Cartridge with a context-distillation objective. We find that Cartridges trained with self-study replicate the functionality of ICL, while being significantly cheaper to serve. On challenging long-context benchmarks, Cartridges trained with self-study match ICL performance while using 38.6x less memory and enabling 26.4x higher throughput. Self-study also extends the model's effective context length (e.g. from 128k to 484k tokens on MTOB) and surprisingly, leads to Cartridges that can be composed at inference time without retraining.

  • 11 authors
·
Jun 6, 2025 2