Shape assembly is a ubiquitous task in daily life, integral for constructing complex 3D structures like IKEA furniture. While significant progress has been made in developing autonomous agents for shape assembly, existing datasets have not yet tackled the 4D grounding of assembly instructions in videos, essential for a holistic understanding of assembly in 3D space over time. We introduce IKEA Video Manuals, a dataset that features 3D models of furniture parts, instructional manuals, assembly videos from the Internet, and most importantly, annotations of dense spatio-temporal alignments between these data modalities. To demonstrate the utility of IKEA Video Manuals, we present five applications essential for shape assembly: assembly plan generation, part-conditioned segmentation, part-conditioned pose estimation, video object segmentation, and furniture assembly based on instructional video manuals. For each application, we provide evaluation metrics and baseline methods. Through experiments on our annotated data, we highlight many challenges in grounding assembly instructions in videos to improve shape assembly, including handling occlusions, varying viewpoints, and extended assembly sequences.

Neuroscience research has made immense progress over the last decade, but our understanding of the brain remains fragmented and piecemeal: the dream of probing an arbitrary brain region and automatically reading out the information encoded in its neural activity remains out of reach. In this work, we build towards a first foundation model for neural spiking data that can solve a diverse set of tasks across multiple brain areas. We introduce a novel self-supervised modeling approach for population activity in which the model alternates between masking out and reconstructing neural activity across different time steps, neurons, and brain regions. To evaluate our approach, we design unsupervised and supervised prediction tasks using the International Brain Laboratory repeated site dataset, which is comprised of Neuropixels recordings targeting the same brain locations across 48 animals and experimental sessions. The prediction tasks include single-neuron and region-level activity prediction, forward prediction, and behavior decoding. We demonstrate that our multi-task-masking (MtM) approach significantly improves the performance of current state-of-the-art population models and enables multi-task learning. We also show that by training on multiple animals, we can improve the generalization ability of the model to unseen animals, paving the way for a foundation model of the brain at single-cell, single-spike resolution.

Data-driven inference of the generative dynamics underlying a set of observed time series is of growing interest in machine learning and the natural sciences. In neuroscience, such methods promise to alleviate the need to handcraft models based on biophysical principles and allow to automatize the inference of inter-individual differences in brain dynamics. Recent breakthroughs in training techniques for state space models (SSMs) specifically geared toward dynamical systems (DS) reconstruction (DSR) enable to recover the underlying system including its geometrical (attractor) and long-term statistical invariants from even short time series. These techniques are based on control-theoretic ideas, like modern variants of teacher forcing (TF), to ensure stable loss gradient propagation while training. However, as it currently stands, these techniques are not directly applicable to data modalities where current observations depend on an entire history of previous states due to a signal's filtering properties, as common in neuroscience (and physiology more generally). Prominent examples are the blood oxygenation level dependent (BOLD) signal in functional magnetic resonance imaging (fMRI) or Ca$^{2+}$ imaging data. Such types of signals render the SSM's decoder model non-invertible, a requirement for previous TF-based methods.Here, exploiting the recent success of control techniques for training SSMs, we propose a novel algorithm that solves this problem and scales exceptionally well with model dimensionality and filter length. We demonstrate its efficiency in reconstructing dynamical systems, including their state space geometry and long-term temporal properties, from just short BOLD time series.

Due to the recent remarkable advances in artificial intelligence, researchers have begun to consider challenging learning problems such as learning to generalize behavior from large offline datasets or learning online in non-Markovian environments. Meanwhile, recent advances in both of these areas have increasingly relied on conditioning policies on large context lengths. A natural question is if there is a limit to the performance benefits of increasing the context length if the computation needed is available. In this work, we establish a novel theoretical result that links the context length of a policy to the time needed to reliably evaluate its performance (i.e., its mixing time) in large scale partially observable reinforcement learning environments that exhibit latent sub-task structure. This analysis underscores a key tradeoff: when we extend the context length, our policy can more effectively model non-Markovian dependencies, but this comes at the cost of potentially slower policy evaluation and as a result slower downstream learning. Moreover, our empirical results highlight the relevance of this analysis when leveraging Transformer based neural networks. This perspective will become increasingly pertinent as the field scales towards larger and more realistic environments, opening up a number of potential future directions for improving the way we design learning agents.

Invasive brain-computer interfaces with Electrocorticography (ECoG) have shown promise for high-performance speech decoding in medical applications, but less damaging methods like intracranial stereo-electroencephalography (sEEG) remain underexplored. With rapid advances in representation learning, leveraging abundant recordings to enhance speech decoding is increasingly attractive. However, popular methods often pre-train temporal models based on brain-level tokens, overlooking that brain activities in different regions are highly desynchronized during tasks. Alternatively, they pre-train spatial-temporal models based on channel-level tokens but fail to evaluate them on challenging tasks like speech decoding, which requires intricate processing in specific language-related areas. To address this issue, we collected a well-annotated Chinese word-reading sEEG dataset targeting language-related brain networks from 12 subjects. Using this benchmark, we developed the Du-IN model, which extracts contextual embeddings based on region-level tokens through discrete codex-guided mask modeling. Our model achieves state-of-the-art performance on the 61-word classification task, surpassing all baselines. Model comparisons and ablation studies reveal that our design choices, including (\romannumeral1) temporal modeling based on region-level tokens by utilizing 1D depthwise convolution to fuse channels in the ventral sensorimotor cortex (vSMC) and superior temporal gyrus (STG) and (\romannumeral2) self-supervision through discrete codex-guided mask modeling, significantly contribute to this performance. Overall, our approach -- inspired by neuroscience findings and capitalizing on region-level representations from specific brain regions -- is suitable for invasive brain modeling and represents a promising neuro-inspired AI approach in brain-computer interfaces.

Whole slide image (WSI) analysis is gaining prominence within the medical imaging field. Recent advances in pathology foundation models have shown the potential to extract powerful feature representations from WSIs for downstream tasks. However, these foundation models are usually designed for general-purpose pathology image analysis and may not be optimal for specific downstream tasks or cancer types. In this work, we present Concept Anchor-guided Task-specific Feature Enhancement (CATE), an adaptable paradigm that can boost the expressivity and discriminativeness of pathology foundation models for specific downstream tasks. Based on a set of task-specific concepts derived from the pathology vision-language model with expert-designed prompts, we introduce two interconnected modules to dynamically calibrate the generic image features extracted by foundation models for certain tasks or cancer types. Specifically, we design a Concept-guided Information Bottleneck module to enhance task-relevant characteristics by maximizing the mutual information between image features and concept anchors while suppressing superfluous information. Moreover, a Concept-Feature Interference module is proposed to utilize the similarity between calibrated features and concept anchors to further generate discriminative task-specific features. The extensive experiments on public WSI datasets demonstrate that CATE significantly enhances the performance and generalizability of MIL models. Additionally, heatmap and umap visualization results also reveal the effectiveness and interpretability of CATE.

Studying protein mutations within amino acid sequences holds tremendous significance in life sciences. Protein language models (PLMs) have demonstrated strong capabilities in broad biological applications. However, due to architectural design and lack of supervision, PLMs model mutations implicitly with evolutionary plausibility, which is not satisfactory to serve as explainable and engineerable tools in real-world studies. To address these issues, we present MutaPLM, a unified framework for interpreting and navigating protein mutations with protein language models. MutaPLM introduces a protein network that captures explicit protein mutation representations within a unified feature space, and a transfer learning pipeline with a chain-of-thought (CoT) strategy to harvest protein mutation knowledge from biomedical texts. We also construct MutaDescribe, the first large-scale protein mutation dataset with rich textual annotations, which provides cross-modal supervision signals. Through comprehensive experiments, we demonstrate that MutaPLM excels at providing human-understandable explanations for mutational effects and prioritizing novel mutations with desirable properties.

Machine unlearning has raised significant interest with the adoption of laws ensuring the ``right to be forgotten''. Researchers have provided a probabilistic notion of approximate unlearning under a similar definition of Differential Privacy (DP), where privacy is defined as statistical indistinguishability to retraining from scratch. We propose Langevin unlearning, an unlearning framework based on noisy gradient descent with privacy guarantees for approximate unlearning problems.

Foundation models are becoming valuable tools in medicine. Yet despite their promise, the best way to leverage Large Language Models (LLMs) in complex medical tasks remains an open question. We introduce a novel multi-agent framework, named **M**edical **D**ecision-making **Agents** (**MDAgents**) that helps to address this gap by automatically assigning a collaboration structure to a team of LLMs. The assigned solo or group collaboration structure is tailored to the medical task at hand, a simple emulation inspired by the way real-world medical decision-making processes are adapted to tasks of different complexities. We evaluate our framework and baseline methods using state-of-the-art LLMs across a suite of real-world medical knowledge and clinical diagnosis benchmarks, including a comparison ofLLMs' medical complexity classification against human physicians. MDAgents achieved the **best performance in seven out of ten** benchmarks on tasks requiring an understanding of medical knowledge and multi-modal reasoning, showing a significant **improvement of up to 4.2\%** ($p$ < 0.05) compared to previous methods' best performances. Ablation studies reveal that MDAgents effectively determines medical complexity to optimize for efficiency and accuracy across diverse medical tasks. Notably, the combination of moderator review and external medical knowledge in group collaboration resulted in an average accuracy **improvement of 11.8\%**.

Image segmentation is a crucial vision task that groups pixels within an image into semantically meaningful segments, which is pivotal in obtaining a fine-grained understanding of real-world scenes. However, an increasing privacy concern exists regarding training large-scale image segmentation models on unauthorized private data. In this work, we exploit the concept of unlearnable examples to make images unusable to model training by generating and adding unlearnable noise into the original images. Particularly, we propose a novel Unlearnable Segmentation (UnSeg) framework to train a universal unlearnable noise generator that is capable of transforming any downstream images into their unlearnable version. The unlearnable noise generator is finetuned from the Segment Anything Model (SAM) via bilevel optimization on an interactive segmentation dataset towards minimizing the training error of a surrogate model that shares the same architecture with SAM (but trains from scratch). We empirically verify the effectiveness of UnSeg across 6 mainstream image segmentation tasks, 10 widely used datasets, and 7 different network architectures, and show that the unlearnable images can reduce the segmentation performance by a large margin. Our work provides useful insights into how to leverage foundation models in a data-efficient and computationally affordable manner to protect images against image segmentation models.