从时间序列数据中推断化学反应网络（CRN）是细胞水平上定量时间数据的可用性日益增长的挑战。这激发了算法的设计，以推断给定生化过程中观察到的分子物种之间的占主导反应，并有助于构建CRN模型结构和动力学。现有的基于ODE的推理方法，例如Sindy诉讼至少正方形回归，结合了稀疏性强制性惩罚，例如Lasso。但是，当仅在存在所有反应的野生型条件下提供输入时间序列时，我们观察到当前方法无法学习稀疏模型。结果：我们提出了一种Reactmine，这是一种CRN学习算法，该算法通过在有界深度的搜索树中以连续的方式推断反应来实现稀疏性，根据其动力学的差异对推断反应候选者进行排名，并重新计算CRN动力学参数在最后一遍中，整个痕迹对推断的CRN候选人进行排名。我们首先评估其在隐藏CRN基准的模拟数据上的性能，以及算法高参数敏感性分析，然后在两组真实的实验数据上进行评估：一组来自细胞周期和昼夜节律标记的蛋白质荧光视频，一个来自生物医学测量值。系统的昼夜节律生物标志物可能作用于外周器官中的时钟基因表达。我们表明，Reactmine通过检索Sindy失败的隐藏CRN以及通过与以前的研究一致的反应来取得成功。

In this paper, we address the problem of multimodal emotion recognition from multiple physiological signals. We demonstrate that a Transformer-based approach is suitable for this task. In addition, we present how such models may be pretrained in a multimodal scenario to improve emotion recognition performances. We evaluate the benefits of using multimodal inputs and pre-training with our approach on a state-ofthe-art dataset.

Contrastive representation learning has proven to be an effective self-supervised learning method for images and videos. Most successful approaches are based on Noise Contrastive Estimation (NCE) and use different views of an instance as positives that should be contrasted with other instances, called negatives, that are considered as noise. However, several instances in a dataset are drawn from the same distribution and share underlying semantic information. A good data representation should contain relations between the instances, or semantic similarity and dissimilarity, that contrastive learning harms by considering all negatives as noise. To circumvent this issue, we propose a novel formulation of contrastive learning using semantic similarity between instances called Similarity Contrastive Estimation (SCE). Our training objective is a soft contrastive one that brings the positives closer and estimates a continuous distribution to push or pull negative instances based on their learned similarities. We validate empirically our approach on both image and video representation learning. We show that SCE performs competitively with the state of the art on the ImageNet linear evaluation protocol for fewer pretraining epochs and that it generalizes to several downstream image tasks. We also show that SCE reaches state-of-the-art results for pretraining video representation and that the learned representation can generalize to video downstream tasks.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Information spread on networks can be efficiently modeled by considering three features: documents' content, time of publication relative to other publications, and position of the spreader in the network. Most previous works model up to two of those jointly, or rely on heavily parametric approaches. Building on recent Dirichlet-Point processes literature, we introduce the Houston (Hidden Online User-Topic Network) model, that jointly considers all those features in a non-parametric unsupervised framework. It infers dynamic topic-dependent underlying diffusion networks in a continuous-time setting along with said topics. It is unsupervised; it considers an unlabeled stream of triplets shaped as \textit{(time of publication, information's content, spreading entity)} as input data. Online inference is conducted using a sequential Monte-Carlo algorithm that scales linearly with the size of the dataset. Our approach yields consequent improvements over existing baselines on both cluster recovery and subnetworks inference tasks.

The publication time of a document carries a relevant information about its semantic content. The Dirichlet-Hawkes process has been proposed to jointly model textual information and publication dynamics. This approach has been used with success in several recent works, and extended to tackle specific challenging problems --typically for short texts or entangled publication dynamics. However, the prior in its current form does not allow for complex publication dynamics. In particular, inferred topics are independent from each other --a publication about finance is assumed to have no influence on publications about politics, for instance. In this work, we develop the Multivariate Powered Dirichlet-Hawkes Process (MPDHP), that alleviates this assumption. Publications about various topics can now influence each other. We detail and overcome the technical challenges that arise from considering interacting topics. We conduct a systematic evaluation of MPDHP on a range of synthetic datasets to define its application domain and limitations. Finally, we develop a use case of the MPDHP on Reddit data. At the end of this article, the interested reader will know how and when to use MPDHP, and when not to.

Time series is the most prevalent form of input data for educational prediction tasks. The vast majority of research using time series data focuses on hand-crafted features, designed by experts for predictive performance and interpretability. However, extracting these features is labor-intensive for humans and computers. In this paper, we propose an approach that utilizes irregular multivariate time series modeling with graph neural networks to achieve comparable or better accuracy with raw time series clickstreams in comparison to hand-crafted features. Furthermore, we extend concept activation vectors for interpretability in raw time series models. We analyze these advances in the education domain, addressing the task of early student performance prediction for downstream targeted interventions and instructional support. Our experimental analysis on 23 MOOCs with millions of combined interactions over six behavioral dimensions show that models designed with our approach can (i) beat state-of-the-art educational time series baselines with no feature extraction and (ii) provide interpretable insights for personalized interventions. Source code: https://github.com/epfl-ml4ed/ripple/.

This paper reviews existing work in software engineering that applies statistical causal inference methods. These methods aim at estimating causal effects from observational data. The review covers 32 papers published between 2010 and 2022. Our results show that the application of statistical causal inference methods is relatively recent and that the corresponding research community remains relatively fragmented.

Large language models (LLMs) show excellent performance but are compute- and memory-intensive. Quantization can reduce memory and accelerate inference. However, for LLMs beyond 100 billion parameters, existing methods cannot maintain accuracy or do not run efficiently on hardware. We propose SmoothQuant, a training-free, accuracy-preserving, and general-purpose post-training quantization (PTQ) solution to enable 8-bit weight, 8-bit activation (W8A8) quantization for LLMs that can be implemented efficiently. We observe that systematic outliers appear at fixed activation channels. Based on the fact that weights are easy to quantize while activations are not, SmoothQuant smooths the activation outliers by offline migrating the quantization difficulty from activations to weights with a mathematically equivalent transformation. SmoothQuant enables an INT8 quantization of both weights and activations for all the GEMMs in LLMs, including OPT-175B, BLOOM-176B, and GLM-130B. SmoothQuant has better hardware efficiency than existing techniques using mixed-precision activation quantization or weight-only quantization. We demonstrate up to 1.56x speedup and 2x memory reduction for LLMs with negligible loss in accuracy. Thanks to the hardware-friendly design, we integrate SmoothQuant into FasterTransformer, a state-of-the-art LLM serving framework, and achieve faster inference speed with half the number of GPUs compared to FP16. Our work offers a turn-key solution that reduces hardware costs and democratizes LLMs. Code is available at: https://github.com/mit-han-lab/smoothquant.

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License.