Empowering Biomedical Discovery with AI Agents

We envision 'AI scientists' as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate machine learning tools with experimental platforms. Rather than taking humans out of the discovery process, biomedical AI agents combine human creativity and expertise with AI's ability to analyze large datasets, navigate hypothesis spaces, and execute repetitive tasks. AI agents are proficient in a variety of tasks, including self-assessment and planning of discovery workflows. These agents use large language models and generative models to feature structured memory for continual learning and use machine learning tools to incorporate scientific knowledge, biological principles, and theories. AI agents can impact areas ranging from hybrid cell simulation, programmable control of phenotypes, and the design of cellular circuits to the development of new therapies.

Unleashing the Power of Meta-tuning for Few-shot Generalization Through Sparse Interpolated Experts

Conventional wisdom suggests parameter-efficient fine-tuning of foundation models as the state-of-the-art method for transfer learning in vision, replacing the rich literature of alternatives such as meta-learning. In trying to harness the best of both worlds, meta-tuning introduces a subsequent optimization stage of foundation models but has so far only shown limited success and crucially tends to underperform on out-of-domain (OOD) tasks. In this paper, we introduce Sparse MetA-Tuning (SMAT), a method inspired by sparse mixture-of-experts approaches and trained to isolate subsets of pre-trained parameters automatically for meta-tuning on each task. SMAT successfully overcomes OOD sensitivity and delivers on the promise of enhancing the transfer abilities of vision foundation models beyond parameter-efficient finetuning. We establish new state-of-the-art results on a challenging combination of Meta-Dataset augmented with additional OOD tasks in both zero-shot and gradient-based adaptation settings. In addition, we provide a thorough analysis of the superiority of learned over hand-designed sparsity patterns for sparse expert methods and the pivotal importance of the sparsity level in balancing between in-domain and out-of-domain generalization. Our code is publicly available.

Online Adaptation of Language Models with a Memory of Amortized Contexts

Due to the rapid generation and dissemination of information, large language models (LLMs) quickly run out of date despite enormous development costs. Due to this crucial need to keep models updated, online learning has emerged as a critical necessity when utilizing LLMs for real-world applications. However, given the ever-expanding corpus of unseen documents and the large parameter space of modern LLMs, efficient adaptation is essential. To address these challenges, we propose Memory of Amortized Contexts (MAC), an efficient and effective online adaptation framework for LLMs with strong knowledge retention. We propose an amortized feature extraction and memory-augmentation approach to compress and extract information from new documents into compact modulations stored in a memory bank. When answering questions, our model attends to and extracts relevant knowledge from this memory bank. To learn informative modulations in an efficient manner, we utilize amortization-based meta-learning, which substitutes the optimization process with a single forward pass of the encoder. Subsequently, we learn to choose from and aggregate selected documents into a single modulation by conditioning on the question, allowing us to adapt a frozen language model during test time without requiring further gradient updates. Our experiment demonstrates the superiority of MAC in multiple aspects, including online adaptation performance, time, and memory efficiency. Code is available at: https://github.com/jihoontack/MAC.

C3: High-performance and low-complexity neural compression from a single image or video

Most neural compression models are trained on large datasets of images or videos in order to generalize to unseen data. Such generalization typically requires large and expressive architectures with a high decoding complexity. Here we introduce C3, a neural compression method with strong rate-distortion (RD) performance that instead overfits a small model to each image or video separately. The resulting decoding complexity of C3 can be an order of magnitude lower than neural baselines with similar RD performance. C3 builds on COOL-CHIC (Ladune et al.) and makes several simple and effective improvements for images. We further develop new methodology to apply C3 to videos. On the CLIC2020 image benchmark, we match the RD performance of VTM, the reference implementation of the H.266 codec, with less than 3k MACs/pixel for decoding. On the UVG video benchmark, we match the RD performance of the Video Compression Transformer (Mentzer et al.), a well-established neural video codec, with less than 5k MACs/pixel for decoding.

Spatial Functa: Scaling Functa to ImageNet Classification and Generation

Neural fields, also known as implicit neural representations, have emerged as a powerful means to represent complex signals of various modalities. Based on this Dupont et al. (2022) introduce a framework that views neural fields as data, termed *functa*, and proposes to do deep learning directly on this dataset of neural fields. In this work, we show that the proposed framework faces limitations when scaling up to even moderately complex datasets such as CIFAR-10. We then propose *spatial functa*, which overcome these limitations by using spatially arranged latent representations of neural fields, thereby allowing us to scale up the approach to ImageNet-1k at 256x256 resolution. We demonstrate competitive performance to Vision Transformers (Steiner et al., 2022) on classification and Latent Diffusion (Rombach et al., 2022) on image generation respectively.

Efficient Meta-Learning via Error-based Context Pruning for Implicit Neural Representations

We introduce an efficient optimization-based meta-learning technique for learning large-scale implicit neural representations (INRs). Our main idea is designing an online selection of context points, which can significantly reduce memory requirements for meta-learning in any established setting. By doing so, we expect additional memory savings which allows longer per-signal adaptation horizons (at a given memory budget), leading to better meta-initializations by reducing myopia and, more crucially, enabling learning on high-dimensional signals. To implement such context pruning, our technical novelty is three-fold. First, we propose a selection scheme that adaptively chooses a subset at each adaptation step based on the predictive error, leading to the modeling of the global structure of the signal in early steps and enabling the later steps to capture its high-frequency details. Second, we counteract any possible information loss from context pruning by minimizing the parameter distance to a bootstrapped target model trained on a full context set. Finally, we suggest using the full context set with a gradient scaling scheme at test-time. Our technique is model-agnostic, intuitive, and straightforward to implement, showing significant reconstruction improvements for a wide range of signals. Code is available at https://github.com/jihoontack/ECoP

Modality-Agnostic Variational Compression of Implicit Neural Representations

We introduce a modality-agnostic neural data compression algorithm based on a functional view of data and parameterised as an Implicit Neural Representation (INR). Bridging the gap between latent coding and sparsity, we obtain compact latent representations which are non-linearly mapped to a soft gating mechanism capable of specialising a shared INR base network to each data item through subnetwork selection. After obtaining a dataset of such compact latent representations, we directly optimise the rate/distortion trade-off in this modality-agnostic space using non-linear transform coding. We term this method Variational Compression of Implicit Neural Representation (VC-INR) and show both improved performance given the same representational capacity pre quantisation while also outperforming previous quantisation schemes used for other INR-based techniques. Our experiments demonstrate strong results over a large set of diverse data modalities using the same algorithm without any modality-specific inductive biases. We show results on images, climate data, 3D shapes and scenes as well as audio and video, introducing VC-INR as the first INR-based method to outperform codecs as well-known and diverse as JPEG 2000, MP3 and AVC/HEVC on their respective modalities.

Meta-Learning Sparse Compression Networks

Recent work in Deep Learning has re-imagined the representation of data as functions mapping from a coordinate space to an underlying continuous signal. When such functions are approximated by neural networks this introduces a compelling alternative to the more common multi-dimensional array representation. Recent work on such Implicit Neural Representations (INRs) has shown that - following careful architecture search - INRs can outperform established compression methods such as JPEG (e.g. Dupont et al., 2021). In this paper, we propose crucial steps towards making such ideas scalable: Firstly, we employ stateof-the-art network sparsification techniques to drastically improve compression. Secondly, introduce the first method allowing for sparsification to be employed in the inner-loop of commonly used Meta-Learning algorithms, drastically improving both compression and the computational cost of learning INRs. The generality of this formalism allows us to present results on diverse data modalities such as images, manifolds, signed distance functions, 3D shapes and scenes, several of which establish new state-of-the-art results.