Related papers: Test-Time Tuned Language Models Enable End-to-end …
Identification of experimentally acquired mass spectra of unknown compounds presents a~particular challenge because reliable spectral databases do not cover the potential chemical space with sufficient density. Therefore machine learning…
We explore the effectiveness of an LLM-guided query refinement paradigm for extending the usability of embedding models to challenging zero-shot search and classification tasks. Our approach refines the embedding representation of a user…
The static ``train then deploy" paradigm fundamentally limits Large Language Models (LLMs) from dynamically adapting their weights in response to continuous streams of new information inherent in real-world tasks. Test-Time Training (TTT)…
The synthesis of inorganic crystalline materials is essential for modern technology, especially in quantum materials development. However, designing efficient synthesis workflows remains a significant challenge due to the precise…
We propose a new finetuning method to provide pre-trained large language models (LMs) the ability to scale test-time compute through the diffusion framework. By increasing the number of diffusion steps, we show our finetuned models achieve…
Frontier AI models have achieved remarkable progress, yet recent studies suggest they struggle with compositional reasoning, often performing at or below random chance on established benchmarks. We revisit this problem and show that widely…
Tandem mass spectrometry (MS/MS) stands as the predominant high-throughput technique for comprehensively analyzing protein content within biological samples. This methodology is a cornerstone driving the advancement of proteomics. In recent…
Masked diffusion models (MDMs) generate discrete sequences by iterative denoising under an absorbing masking process. In standard masked diffusion, if a token remains masked after a reverse update, the model discards its clean-state…
Transition Matching (TM) is an emerging paradigm for generative modeling that generalizes diffusion and flow-matching models as well as continuous-state autoregressive models. TM, similar to previous paradigms, gradually transforms noise…
De novo peptide sequencing aims to recover amino acid sequences of a peptide from tandem mass spectrometry (MS) data. Existing approaches for de novo analysis enumerate MS evidence for all amino acid classes during inference. It leads to…
Through end-to-end training to predict the next token, LLMs have become valuable tools for various tasks. Enhancing their core training in language modeling can improve numerous downstream applications. A successful approach to enhance…
Molecular property prediction (MPP) is integral to drug discovery and material science, but often faces the challenge of data scarcity in real-world scenarios. Addressing this, few-shot molecular property prediction (FSMPP) has been…
Foundation medical segmentation models, with MedSAM being the most popular, have achieved promising performance across organs and lesions. However, MedSAM still suffers from compromised performance on specific lesions with intricate…
Post-translational modifications (PTMs) form a combinatorial "code" that regulates protein function, yet deciphering this code - linking modified sites to their catalytic enzymes - remains a central unsolved problem in understanding…
Text-guided molecule generation is a task where molecules are generated to match specific textual descriptions. Recently, most existing SMILES-based molecule generation methods rely on an autoregressive architecture. In this work, we…
Numerical simulation of non-linear partial differential equations plays a crucial role in modeling physical science and engineering phenomena, such as weather, climate, and aerodynamics. Recent Machine Learning (ML) models trained on…
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…
Alternating minimization methods have recently been proposed as alternatives to the gradient descent for deep neural network optimization. Alternating minimization methods can typically decompose a deep neural network into layerwise…
Pretraining DNA language models (DNALMs) on the full human genome is resource-intensive, yet often considered necessary for strong downstream performance. Inspired by recent findings in NLP and long-context modeling, we explore an…
Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…