Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences

Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures. While Transformers have yielded impressive results, their quadratic runtime dependency on the sequence length complicates their use for long genomic sequences and in-context learning on proteins and chemical sequences. Recently, the recurrent xLSTM architecture has been shown to perform favorably compared to Transformers and modern state-space model (SSM) architectures in the natural language domain. Similar to SSMs, xLSTMs have a linear runtime dependency on the sequence length and allow for constant-memory decoding at inference time, which makes them prime candidates for modeling long-range dependencies in biological and chemical sequences. In this work, we tailor xLSTM towards these domains and propose a suite of architectural variants called Bio-xLSTM. Extensive experiments in three large domains, genomics, proteins, and chemistry, were performed to assess xLSTM's ability to model biological and chemical sequences. The results show that models based on Bio-xLSTM a) can serve as proficient generative models for DNA, protein, and chemical sequences, b) learn rich representations for those modalities, and c) can perform in-context learning for proteins and small molecules.

A Large Recurrent Action Model: xLSTM enables Fast Inference for Robotics Tasks

In recent years, there has been a trend in the field of Reinforcement Learning (RL) towards large action models trained offline on large-scale datasets via sequence modeling. Existing models are primarily based on the Transformer architecture, which result in powerful agents. However, due to slow inference times, Transformer-based approaches are impractical for real-time applications, such as robotics. Recently, modern recurrent architectures, such as xLSTM and Mamba, have been proposed that exhibit parallelization benefits during training similar to the Transformer architecture while offering fast inference. In this work, we study the aptitude of these modern recurrent architectures for large action models. Consequently, we propose a Large Recurrent Action Model (LRAM) with an xLSTM at its core that comes with linear-time inference complexity and natural sequence length extrapolation abilities. Experiments on 432 tasks from 6 domains show that LRAM compares favorably to Transformers in terms of performance and speed.

The Disparate Benefits of Deep Ensembles

Ensembles of Deep Neural Networks, Deep Ensembles, are widely used as a simple way to boost predictive performance. However, their impact on algorithmic fairness is not well understood yet. Algorithmic fairness investigates how a model's performance varies across different groups, typically defined by protected attributes such as age, gender, or race. In this work, we investigate the interplay between the performance gains from Deep Ensembles and fairness. Our analysis reveals that they unevenly favor different groups in what we refer to as a disparate benefits effect. We empirically investigate this effect with Deep Ensembles applied to popular facial analysis and medical imaging datasets, where protected group attributes are given and find that it occurs for multiple established group fairness metrics, including statistical parity and equal opportunity. Furthermore, we identify the per-group difference in predictive diversity of ensemble members as the potential cause of the disparate benefits effect. Finally, we evaluate different approaches to reduce unfairness due to the disparate benefits effect. Our findings show that post-processing is an effective method to mitigate this unfairness while preserving the improved performance of Deep Ensembles.

On Information-Theoretic Measures of Predictive Uncertainty

Reliable estimation of predictive uncertainty is crucial for machine learning applications, particularly in high-stakes scenarios where hedging against risks is essential. Despite its significance, a consensus on the correct measurement of predictive uncertainty remains elusive. In this work, we return to first principles to develop a fundamental framework of information-theoretic predictive uncertainty measures. Our proposed framework categorizes predictive uncertainty measures according to two factors: (I) The predicting model (II) The approximation of the true predictive distribution. Examining all possible combinations of these two factors, we derive a set of predictive uncertainty measures that includes both known and newly introduced ones. We empirically evaluate these measures in typical uncertainty estimation settings, such as misclassification detection, selective prediction, and out-of-distribution detection. The results show that no single measure is universal, but the effectiveness depends on the specific setting. Thus, our work provides clarity about the suitability of predictive uncertainty measures by clarifying their implicit assumptions and relationships.

One Initialization to Rule them All: Fine-tuning via Explained Variance Adaptation

Foundation models (FMs) are pre-trained on large-scale datasets and then fine-tuned on a downstream task for a specific application. The most successful and most commonly used fine-tuning method is to update the pre-trained weights via a low-rank adaptation (LoRA). LoRA introduces new weight matrices that are usually initialized at random with a uniform rank distribution across model weights. Recent works focus on weight-driven initialization or learning of adaptive ranks during training. Both approaches have only been investigated in isolation, resulting in slow convergence or a uniform rank distribution, in turn leading to sub-optimal performance. We propose to enhance LoRA by initializing the new weights in a data-driven manner by computing singular value decomposition on minibatches of activation vectors. Then, we initialize the LoRA matrices with the obtained right-singular vectors and re-distribute ranks among all weight matrices to explain the maximal amount of variance and continue the standard LoRA fine-tuning procedure. This results in our new method Explained Variance Adaptation (EVA). We apply EVA to a variety of fine-tuning tasks ranging from language generation and understanding to image classification and reinforcement learning. EVA exhibits faster convergence than competitors and attains the highest average score across a multitude of tasks per domain.

Retrieval-Augmented Decision Transformer: External Memory for In-context RL

In-context learning (ICL) is the ability of a model to learn a new task by observing a few exemplars in its context. While prevalent in NLP, this capability has recently also been observed in Reinforcement Learning (RL) settings. Prior in-context RL methods, however, require entire episodes in the agent's context. Given that complex environments typically lead to long episodes with sparse rewards, these methods are constrained to simple environments with short episodes. To address these challenges, we introduce Retrieval-Augmented Decision Transformer (RA-DT). RA-DT employs an external memory mechanism to store past experiences from which it retrieves only sub-trajectories relevant for the current situation. The retrieval component in RA-DT does not require training and can be entirely domain-agnostic. We evaluate the capabilities of RA-DT on grid-world environments, robotics simulations, and procedurally-generated video games. On grid-worlds, RA-DT outperforms baselines, while using only a fraction of their context length. Furthermore, we illuminate the limitations of current in-context RL methods on complex environments and discuss future directions. To facilitate future research, we release datasets for four of the considered environments.

Simplified priors for Object-Centric Learning

Humans excel at abstracting data and constructing \emph{reusable} concepts, a capability lacking in current continual learning systems. The field of object-centric learning addresses this by developing abstract representations, or slots, from data without human supervision. Different methods have been proposed to tackle this task for images, whereas most are overly complex, non-differentiable, or poorly scalable. In this paper, we introduce a conceptually simple, fully-differentiable, non-iterative, and scalable method called SAMP Simplified Slot Attention with Max Pool Priors). It is implementable using only Convolution and MaxPool layers and an Attention layer. Our method encodes the input image with a Convolutional Neural Network and then uses a branch of alternating Convolution and MaxPool layers to create specialized sub-networks and extract primitive slots. These primitive slots are then used as queries for a Simplified Slot Attention over the encoded image. Despite its simplicity, our method is competitive or outperforms previous methods on standard benchmarks.

Contrastive Abstraction for Reinforcement Learning

Learning agents with reinforcement learning is difficult when dealing with long trajectories that involve a large number of states. To address these learning problems effectively, the number of states can be reduced by abstract representations that cluster states. In principle, deep reinforcement learning can find abstract states, but end-to-end learning is unstable. We propose contrastive abstraction learning to find abstract states, where we assume that successive states in a trajectory belong to the same abstract state. Such abstract states may be basic locations, achieved subgoals, inventory, or health conditions. Contrastive abstraction learning first constructs clusters of state representations by contrastive learning and then applies modern Hopfield networks to determine the abstract states. The first phase of contrastive abstraction learning is self-supervised learning, where contrastive learning forces states with sequential proximity to have similar representations. The second phase uses modern Hopfield networks to map similar state representations to the same fixed point, i.e.\ to an abstract state. The level of abstraction can be adjusted by determining the number of fixed points of the modern Hopfield network. Furthermore, \textit{contrastive abstraction learning} does not require rewards and facilitates efficient reinforcement learning for a wide range of downstream tasks. Our experiments demonstrate the effectiveness of contrastive abstraction learning for reinforcement learning.

Comparison Visual Instruction Tuning

Comparing two images in terms of Commonalities and Differences (CaD) is a fundamental human capability that forms the basis of advanced visual reasoning and interpretation. It is essential for the generation of detailed and contextually relevant descriptions, performing comparative analysis, novelty detection, and making informed decisions based on visual data. However, surprisingly, little attention has been given to these fundamental concepts in the best current mimic of human visual intelligence - Large Multimodal Models (LMMs). We develop and contribute a new two-phase approach CaD-VI for collecting synthetic visual instructions, together with an instruction-following dataset CaD-Inst containing 349K image pairs with CaD instructions collected using CaD-VI. Our approach significantly improves the CaD spotting capabilities in LMMs, advancing the SOTA on a diverse set of related tasks by up to 17.5%. It is also complementary to existing difference-only instruction datasets, allowing automatic targeted refinement of those resources increasing their effectiveness for CaD tuning by up to 10%. Additionally, we propose an evaluation benchmark with 7.5K open-ended QAs to assess the CaD understanding abilities of LMMs.

Vision-LSTM: xLSTM as Generic Vision Backbone

Transformers are widely used as generic backbones in computer vision, despite initially introduced for natural language processing. Recently, the Long Short-Term Memory (LSTM) has been extended to a scalable and performant architecture - the xLSTM - which overcomes long-standing LSTM limitations via exponential gating and parallelizable matrix memory structure. In this report, we introduce Vision-LSTM (ViL), an adaption of the xLSTM building blocks to computer vision. ViL comprises a stack of xLSTM blocks where odd blocks process the sequence of patch tokens from top to bottom while even blocks go from bottom to top. Experiments show that ViL holds promise to be further deployed as new generic backbone for computer vision architectures.