Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts make sense of the complex outputs of folding pathway simulations of such reactions. Here we present ViDa, a new approach for visualizing DNA reaction folding trajectories over the energy landscape of secondary structures. We integrate a deep graph embedding model with common dimensionality reduction approaches, to map high-dimensional data onto 2D Euclidean space. We assess ViDa on two well-studied and contrasting DNA hybridization reactions. Our preliminary results suggest that ViDa's visualization successfully separates trajectories with different folding mechanisms, thereby providing useful insight to users, and is a big improvement over the current state-of-the-art in DNA kinetics visualization.
相關內容
We study semantic models of probabilistic programming languages over graphs, and establish a connection to graphons from graph theory and combinatorics. We show that every well-behaved equational theory for our graph probabilistic programming language corresponds to a graphon, and conversely, every graphon arises in this way. We provide three constructions for showing that every graphon arises from an equational theory. The first is an abstract construction, using Markov categories and monoidal indeterminates. The second and third are more concrete. The second is in terms of traditional measure theoretic probability, which covers 'black-and-white' graphons. The third is in terms of probability monads on the nominal sets of Gabbay and Pitts. Specifically, we use a variation of nominal sets induced by the theory of graphs, which covers Erd\H{o}s-R\'enyi graphons. In this way, we build new models of graph probabilistic programming from graphons.
Multi-modal Magnetic Resonance Imaging (MRI) offers complementary diagnostic information, but some modalities are limited by the long scanning time. To accelerate the whole acquisition process, MRI reconstruction of one modality from highly undersampled k-space data with another fully-sampled reference modality is an efficient solution. However, the misalignment between modalities, which is common in clinic practice, can negatively affect reconstruction quality. Existing deep learning-based methods that account for inter-modality misalignment perform better, but still share two main common limitations: (1) The spatial alignment task is not adaptively integrated with the reconstruction process, resulting in insufficient complementarity between the two tasks; (2) the entire framework has weak interpretability. In this paper, we construct a novel Deep Unfolding Network with Spatial Alignment, termed DUN-SA, to appropriately embed the spatial alignment task into the reconstruction process. Concretely, we derive a novel joint alignment-reconstruction model with a specially designed cross-modal spatial alignment term. By relaxing the model into cross-modal spatial alignment and multi-modal reconstruction tasks, we propose an effective algorithm to solve this model alternatively. Then, we unfold the iterative steps of the proposed algorithm and design corresponding network modules to build DUN-SA with interpretability. Through end-to-end training, we effectively compensate for spatial misalignment using only reconstruction loss, and utilize the progressively aligned reference modality to provide inter-modality prior to improve the reconstruction of the target modality. Comprehensive experiments on three real datasets demonstrate that our method exhibits superior reconstruction performance compared to state-of-the-art methods.
Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper, rather than pursuing state-of-the-art performance, we aim to evaluate capabilities of LLMs in a wide range of tasks across the chemistry domain. We identify three key chemistry-related capabilities including understanding, reasoning and explaining to explore in LLMs and establish a benchmark containing eight chemistry tasks. Our analysis draws on widely recognized datasets facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Five LLMs (GPT-4, GPT-3.5, Davinci-003, Llama and Galactica) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. Our investigation found that GPT-4 outperformed other models and LLMs exhibit different competitive levels in eight chemistry tasks. In addition to the key findings from the comprehensive benchmark analysis, our work provides insights into the limitation of current LLMs and the impact of in-context learning settings on LLMs' performance across various chemistry tasks. The code and datasets used in this study are available at //github.com/ChemFoundationModels/ChemLLMBench.
Multi-modal language models (LM) have recently shown promising performance in high-level reasoning tasks on videos. However, existing methods still fall short in tasks like causal or compositional spatiotemporal reasoning over actions, in which model predictions need to be grounded in fine-grained low-level details, such as object motions and object interactions. In this work, we propose training an LM end-to-end on low-level surrogate tasks, including object detection, re-identification, and tracking, to endow the model with the required low-level visual capabilities. We show that a two-stream video encoder with spatiotemporal attention is effective at capturing the required static and motion-based cues in the video. By leveraging the LM's ability to perform the low-level surrogate tasks, we can cast reasoning in videos as the three-step process of Look, Remember, Reason wherein visual information is extracted using low-level visual skills step-by-step and then integrated to arrive at a final answer. We demonstrate the effectiveness of our framework on diverse visual reasoning tasks from the ACRE, CATER, and Something-Else datasets. Our approach is trainable end-to-end and surpasses state-of-the-art task-specific methods across these tasks by a large margin.
This paper addresses category-agnostic instance segmentation for robotic manipulation, focusing on segmenting objects independent of their class to enable versatile applications like bin-picking in dynamic environments. Existing methods often lack generalizability and object-specific information, leading to grasp failures. We present a novel approach leveraging object-centric instance segmentation and simulation-based training for effective transfer to real-world scenarios. Notably, our strategy overcomes challenges posed by noisy depth sensors, enhancing the reliability of learning. Our solution accommodates transparent and semi-transparent objects which are historically difficult for depth-based grasping methods. Contributions include domain randomization for successful transfer, our collected dataset for warehouse applications, and an integrated framework for efficient bin-picking. Our trained instance segmentation model achieves state-of-the-art performance over WISDOM public benchmark [1] and also over the custom-created dataset. In a real-world challenging bin-picking setup our bin-picking framework method achieves 98% accuracy for opaque objects and 97% accuracy for non-opaque objects, outperforming the state-of-the-art baselines with a greater margin.
Speech emotion recognition (SER) systems aim to recognize human emotional state during human-computer interaction. Most existing SER systems are trained based on utterance-level labels. However, not all frames in an audio have affective states consistent with utterance-level label, which makes it difficult for the model to distinguish the true emotion of the audio and perform poorly. To address this problem, we propose a frame-level emotional state alignment method for SER. First, we fine-tune HuBERT model to obtain a SER system with task-adaptive pretraining (TAPT) method, and extract embeddings from its transformer layers to form frame-level pseudo-emotion labels with clustering. Then, the pseudo labels are used to pretrain HuBERT. Hence, the each frame output of HuBERT has corresponding emotional information. Finally, we fine-tune the above pretrained HuBERT for SER by adding an attention layer on the top of it, which can focus only on those frames that are emotionally more consistent with utterance-level label. The experimental results performed on IEMOCAP indicate that our proposed method performs better than state-of-the-art (SOTA) methods.
The application of deep learning techniques on aroma-chemicals has resulted in models more accurate than human experts at predicting olfactory qualities. However, public research in this domain has been limited to predicting the qualities of single molecules, whereas in industry applications, perfumers and food scientists are often concerned with blends of many odorants. In this paper, we apply both existing and novel approaches to a dataset we gathered consisting of labeled pairs of molecules. We present a publicly available model capable of generating accurate predictions for the non-linear qualities arising from blends of aroma-chemicals.
There exist multiple regression applications in engineering and industry where the outcomes are not conditionally independent given the covariates, but where instead the covariates follow a sequential experimental design in which the next measurement depends on the previous outcomes, introducing dependence. Such designs are commonly employed for example for choosing test values when estimating the sensitivity of a material under physical stimulus. Apart from the extensive study of the Robbins--Monro procedure, virtually no attention has been given to verifying asymptotic normality of the maximum likelihood estimator in the general sequential setting, despite the wide use of such designs in industry since at least the 1940s. This is a considerable gap in the literature, since said properties underlie the construction of confidence intervals and hypothesis testing. In this paper we close this gap by establishing a large-sample theory for sequential experimental designs other than the Robbins--Monro procedure. First, we use martingale theory to prove a general result for when such asymptotic normality may be asserted. Second, we consider the special case where the covariate process forms a Markov chain. In doing so, we verify asymptotic normality for the widely applied Bruceton design and a proposed Markovian version of the Langlie design.
We develop a theory for the representation of opaque solids as volumetric models. Starting from a stochastic representation of opaque solids as random indicator functions, we prove the conditions under which such solids can be modeled using exponential volumetric transport. We also derive expressions for the volumetric attenuation coefficient as a functional of the probability distributions of the underlying indicator functions. We generalize our theory to account for isotropic and anisotropic scattering at different parts of the solid, and for representations of opaque solids as implicit surfaces. We derive our volumetric representation from first principles, which ensures that it satisfies physical constraints such as reciprocity and reversibility. We use our theory to explain, compare, and correct previous volumetric representations, as well as propose meaningful extensions that lead to improved performance in 3D reconstruction tasks.
Scientific claims gain credibility by replicability, especially if replication under different circumstances and varying designs yields equivalent results. Aggregating results over multiple studies is, however, not straightforward, and when the heterogeneity between studies increases, conventional methods such as (Bayesian) meta-analysis and Bayesian sequential updating become infeasible. *Bayesian Evidence Synthesis*, built upon the foundations of the Bayes factor, allows to aggregate support for conceptually similar hypotheses over studies, regardless of methodological differences. We assess the performance of Bayesian Evidence Synthesis over multiple effect and sample sizes, with a broad set of (inequality-constrained) hypotheses using Monte Carlo simulations, focusing explicitly on the complexity of the hypotheses under consideration. The simulations show that this method can evaluate complex (informative) hypotheses regardless of methodological differences between studies, and performs adequately if the set of studies considered has sufficient statistical power. Additionally, we pinpoint challenging conditions that can lead to unsatisfactory results, and provide suggestions on handling these situations. Ultimately, we show that Bayesian Evidence Synthesis is a promising tool that can be used when traditional research synthesis methods are not applicable due to insurmountable between-study heterogeneity.
小貼士
登錄享
相關主題
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191