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Aug 11

MIMIC: A Generative Multimodal Foundation Model for Biomolecules

Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained within one modality or for a fixed forward task. We present MIMIC, a generative multimodal foundation model trained on our newly curated and aligned dataset, LORE, linking nucleic acid, protein, evolutionary, structural, regulatory, and semantic/contextual modalities within partially observed biomolecular states. MIMIC uses a split-track encoder-decoder architecture to condition on arbitrary subsets of observed modalities and reconstruct or generate missing components of molecular state across the genome, transcriptome, and proteome. Multimodal conditioning consistently improves MIMIC's sequence reconstruction relative to sequence-only inputs, while its learned representations enable state-of-the-art performance on RNA and protein downstream tasks. MIMIC achieves state-of-the-art splicing prediction, and its joint generative formulation enables isoform-aware inference that further improves performance. Beyond prediction, the same generative framework supports constrained design. For RNA, MIMIC identifies corrective edits in a clinically relevant HBB splice-disrupting mutation without reverting it by using evolutionary and structural signals. For proteins, jointly conditioning on shape and surface chemistry of PD-L1 and hACE2 binding sites produces diverse, high-confidence sequences with strong in silico support for target binding. Finally, MIMIC uses experimental context as semantic conditioning to model assay-dependent RNA chemical probing, rather than treating context as a fixed output. Together, these results position MIMIC's aligned multimodal generative modeling as a strong foundation for unifying representation learning, conditional prediction, and constrained biomolecular design within a single model.

  • 31 authors
·
Apr 26

Visual IRL for Human-Like Robotic Manipulation

We present a novel method for collaborative robots (cobots) to learn manipulation tasks and perform them in a human-like manner. Our method falls under the learn-from-observation (LfO) paradigm, where robots learn to perform tasks by observing human actions, which facilitates quicker integration into industrial settings compared to programming from scratch. We introduce Visual IRL that uses the RGB-D keypoints in each frame of the observed human task performance directly as state features, which are input to inverse reinforcement learning (IRL). The inversely learned reward function, which maps keypoints to reward values, is transferred from the human to the cobot using a novel neuro-symbolic dynamics model, which maps human kinematics to the cobot arm. This model allows similar end-effector positioning while minimizing joint adjustments, aiming to preserve the natural dynamics of human motion in robotic manipulation. In contrast with previous techniques that focus on end-effector placement only, our method maps multiple joint angles of the human arm to the corresponding cobot joints. Moreover, it uses an inverse kinematics model to then minimally adjust the joint angles, for accurate end-effector positioning. We evaluate the performance of this approach on two different realistic manipulation tasks. The first task is produce processing, which involves picking, inspecting, and placing onions based on whether they are blemished. The second task is liquid pouring, where the robot picks up bottles, pours the contents into designated containers, and disposes of the empty bottles. Our results demonstrate advances in human-like robotic manipulation, leading to more human-robot compatibility in manufacturing applications.

  • 2 authors
·
Dec 15, 2024

Saliency-Guided Deep Learning Network for Automatic Tumor Bed Volume Delineation in Post-operative Breast Irradiation

Efficient, reliable and reproducible target volume delineation is a key step in the effective planning of breast radiotherapy. However, post-operative breast target delineation is challenging as the contrast between the tumor bed volume (TBV) and normal breast tissue is relatively low in CT images. In this study, we propose to mimic the marker-guidance procedure in manual target delineation. We developed a saliency-based deep learning segmentation (SDL-Seg) algorithm for accurate TBV segmentation in post-operative breast irradiation. The SDL-Seg algorithm incorporates saliency information in the form of markers' location cues into a U-Net model. The design forces the model to encode the location-related features, which underscores regions with high saliency levels and suppresses low saliency regions. The saliency maps were generated by identifying markers on CT images. Markers' locations were then converted to probability maps using a distance-transformation coupled with a Gaussian filter. Subsequently, the CT images and the corresponding saliency maps formed a multi-channel input for the SDL-Seg network. Our in-house dataset was comprised of 145 prone CT images from 29 post-operative breast cancer patients, who received 5-fraction partial breast irradiation (PBI) regimen on GammaPod. The performance of the proposed method was compared against basic U-Net. Our model achieved mean (standard deviation) of 76.4 %, 6.76 mm, and 1.9 mm for DSC, HD95, and ASD respectively on the test set with computation time of below 11 seconds per one CT volume. SDL-Seg showed superior performance relative to basic U-Net for all the evaluation metrics while preserving low computation cost. The findings demonstrate that SDL-Seg is a promising approach for improving the efficiency and accuracy of the on-line treatment planning procedure of PBI, such as GammaPod based PBI.

  • 8 authors
·
May 6, 2021

Neural networks for abstraction and reasoning: Towards broad generalization in machines

For half a century, artificial intelligence research has attempted to reproduce the human qualities of abstraction and reasoning - creating computer systems that can learn new concepts from a minimal set of examples, in settings where humans find this easy. While specific neural networks are able to solve an impressive range of problems, broad generalisation to situations outside their training data has proved elusive.In this work, we look at several novel approaches for solving the Abstraction & Reasoning Corpus (ARC), a dataset of abstract visual reasoning tasks introduced to test algorithms on broad generalization. Despite three international competitions with $100,000 in prizes, the best algorithms still fail to solve a majority of ARC tasks and rely on complex hand-crafted rules, without using machine learning at all. We revisit whether recent advances in neural networks allow progress on this task. First, we adapt the DreamCoder neurosymbolic reasoning solver to ARC. DreamCoder automatically writes programs in a bespoke domain-specific language to perform reasoning, using a neural network to mimic human intuition. We present the Perceptual Abstraction and Reasoning Language (PeARL) language, which allows DreamCoder to solve ARC tasks, and propose a new recognition model that allows us to significantly improve on the previous best implementation.We also propose a new encoding and augmentation scheme that allows large language models (LLMs) to solve ARC tasks, and find that the largest models can solve some ARC tasks. LLMs are able to solve a different group of problems to state-of-the-art solvers, and provide an interesting way to complement other approaches. We perform an ensemble analysis, combining models to achieve better results than any system alone. Finally, we publish the arckit Python library to make future research on ARC easier.

  • 2 authors
·
Feb 4, 2024

Geolocation with Real Human Gameplay Data: A Large-Scale Dataset and Human-Like Reasoning Framework

Geolocation, the task of identifying an image's location, requires complex reasoning and is crucial for navigation, monitoring, and cultural preservation. However, current methods often produce coarse, imprecise, and non-interpretable localization. A major challenge lies in the quality and scale of existing geolocation datasets. These datasets are typically small-scale and automatically constructed, leading to noisy data and inconsistent task difficulty, with images that either reveal answers too easily or lack sufficient clues for reliable inference. To address these challenges, we introduce a comprehensive geolocation framework with three key components: GeoComp, a large-scale dataset; GeoCoT, a novel reasoning method; and GeoEval, an evaluation metric, collectively designed to address critical challenges and drive advancements in geolocation research. At the core of this framework is GeoComp (Geolocation Competition Dataset), a large-scale dataset collected from a geolocation game platform involving 740K users over two years. It comprises 25 million entries of metadata and 3 million geo-tagged locations spanning much of the globe, with each location annotated thousands to tens of thousands of times by human users. The dataset offers diverse difficulty levels for detailed analysis and highlights key gaps in current models. Building on this dataset, we propose Geographical Chain-of-Thought (GeoCoT), a novel multi-step reasoning framework designed to enhance the reasoning capabilities of Large Vision Models (LVMs) in geolocation tasks. GeoCoT improves performance by integrating contextual and spatial cues through a multi-step process that mimics human geolocation reasoning. Finally, using the GeoEval metric, we demonstrate that GeoCoT significantly boosts geolocation accuracy by up to 25% while enhancing interpretability.

  • 9 authors
·
Feb 19, 2025 2