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Jan 7

SimpleFold: Folding Proteins is Simpler than You Think

Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Nonetheless, given the success of generative models across different but related problems, it is natural to question whether these architectural designs are a necessary condition to build performant models. In this paper, we introduce SimpleFold, the first flow-matching based protein folding model that solely uses general purpose transformer blocks. Protein folding models typically employ computationally expensive modules involving triangular updates, explicit pair representations or multiple training objectives curated for this specific domain. Instead, SimpleFold employs standard transformer blocks with adaptive layers and is trained via a generative flow-matching objective with an additional structural term. We scale SimpleFold to 3B parameters and train it on approximately 9M distilled protein structures together with experimental PDB data. On standard folding benchmarks, SimpleFold-3B achieves competitive performance compared to state-of-the-art baselines, in addition SimpleFold demonstrates strong performance in ensemble prediction which is typically difficult for models trained via deterministic reconstruction objectives. Due to its general-purpose architecture, SimpleFold shows efficiency in deployment and inference on consumer-level hardware. SimpleFold challenges the reliance on complex domain-specific architectures designs in protein folding, opening up an alternative design space for future progress.

  • 5 authors
·
Sep 22, 2025 5

Alljoined-1.6M: A Million-Trial EEG-Image Dataset for Evaluating Affordable Brain-Computer Interfaces

We present a new large-scale electroencephalography (EEG) dataset as part of the THINGS initiative, comprising over 1.6 million visual stimulus trials collected from 20 participants, and totaling more than twice the size of the most popular current benchmark dataset, THINGS-EEG2. Crucially, our data was recorded using a 32-channel consumer-grade wet electrode system costing ~$2.2k, around 27x cheaper than research-grade EEG systems typically used in cognitive neuroscience labs. Our work is one of the first open-source, large-scale EEG resource designed to closely reflect the quality of hardware that is practical to deploy in real-world, downstream applications of brain-computer interfaces (BCIs). We aim to explore the specific question of whether deep neural network-based BCI research and semantic decoding methods can be effectively conducted with such affordable systems, filling an important gap in current literature that is extremely relevant for future research. In our analysis, we not only demonstrate that decoding of high-level semantic information from EEG of visualized images is possible at consumer-grade hardware, but also that our data can facilitate effective EEG-to-Image reconstruction even despite significantly lower signal-to-noise ratios. In addition to traditional benchmarks, we also conduct analyses of EEG-to-Image models that demonstrate log-linear decoding performance with increasing data volume on our data, and discuss the trade-offs between hardware cost, signal fidelity, and the scale of data collection efforts in increasing the size and utility of currently available datasets. Our contributions aim to pave the way for large-scale, cost-effective EEG research with widely accessible equipment, and position our dataset as a unique resource for the democratization and development of effective deep neural models of visual cognition.

  • 8 authors
·
Aug 25, 2025

Characterizing State Space Model (SSM) and SSM-Transformer Hybrid Language Model Performance with Long Context Length

The demand for machine intelligence capable of processing continuous, long-context inputs on local devices is growing rapidly. However, the quadratic complexity and memory requirements of traditional Transformer architectures make them inefficient and often unusable for these tasks. This has spurred a paradigm shift towards new architectures like State Space Models (SSMs) and hybrids, which promise near-linear scaling. While most current research focuses on the accuracy and theoretical throughput of these models, a systematic performance characterization on practical consumer hardware is critically needed to guide system-level optimization and unlock new applications. To address this gap, we present a comprehensive, comparative benchmarking of carefully selected Transformer, SSM, and hybrid models specifically for long-context inference on consumer and embedded GPUs. Our analysis reveals that SSMs are not only viable but superior for this domain, capable of processing sequences up to 220K tokens on a 24GB consumer GPU-approximately 4x longer than comparable Transformers. While Transformers may be up to 1.8x faster at short sequences, SSMs demonstrate a dramatic performance inversion, becoming up to 4x faster at very long contexts (~57K tokens). Our operator-level analysis reveals that custom, hardware-aware SSM kernels dominate the inference runtime, accounting for over 55% of latency on edge platforms, identifying them as a primary target for future hardware acceleration. We also provide detailed, device-specific characterization results to guide system co-design for the edge. To foster further research, we will open-source our characterization framework.

  • 5 authors
·
Jul 16, 2025