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Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

Digital twin networks (DTNs) serve as an emerging facilitator in the industrial networking sector, enabling the management of new classes of services, which require tailored support for improved resource utilization, low latencies and accurate data fidelity. In this paper, we explore the intersection between theoretical recommendations and practical implications of applying DTNs to industrial networked environments, sharing empirical findings and lessons learned from our ongoing work. To this end, we first provide experimental examples from selected aspects of data representations and fidelity, mixed-criticality workload support, and application-driven services. Then, we introduce an architectural framework for DTNs, exposing a more practical extension of existing standards; notably the ITU-T Y.3090 (2022) recommendation. Specifically, we explore and discuss the dual nature of DTNs, meant as a digital twin of the network and a network of digital twins, allowing the co-existence of both paradigms., Comment: Funding: (i) European Union under the Italian National Recovery and Resilience Plan (NRRP) of NextGenerationEU, partnership on "Telecommunications of the Future" PE00000001 - program "RESTART", (ii) RA Science Committee grant No. 22rl-052

Conventional methods for outdoor environment reconstruction rely predominantly on vision-based techniques like photogrammetry and LiDAR, facing limitations such as constrained coverage, susceptibility to environmental conditions, and high computational and energy demands. These challenges are particularly pronounced in applications like augmented reality navigation, especially when integrated with wearable devices featuring constrained computational resources and energy budgets. In response, this paper proposes a novel approach harnessing ambient wireless signals for outdoor environment reconstruction. By analyzing radio frequency (RF) data, the paper aims to deduce the environmental characteristics and digitally reconstruct the outdoor surroundings. Investigating the efficacy of selected deep learning (DL) techniques on the synthetic RF dataset WAIR-D, the study endeavors to address the research gap in this domain. Two DL-driven approaches are evaluated (convolutional U-Net and CLIP+ based on vision transformers), with performance assessed using metrics like intersection-over-union (IoU), Hausdorff distance, and Chamfer distance. The results demonstrate promising performance of the RF-based reconstruction method, paving the way towards lightweight and scalable reconstruction solutions., Comment: This work has been submitted to the IEEE for possible publication. Work partly supported by the RA Science Committee grant No. 22rl-052 (DISTAL) and the EU under Italian National Recovery and Resilience Plan of NextGenerationEU on "Telecommunications of the Future" (PE00000001 - program "RESTART")

In this paper, we present a comparative analysis of various self-supervised Vision Transformers (ViTs), focusing on their local representative power. Inspired by large language models, we examine the abilities of ViTs to perform various computer vision tasks with little to no fine-tuning. We design evaluation framework to analyze the quality of local, i.e.\ patch-level, representations in the context of few-shot semantic segmentation, instance identification, object retrieval and tracking. We discover that contrastive learning based methods like DINO produce more universal patch representations that can be immediately applied for downstream tasks with no parameter tuning, compared to masked image modeling. The embeddings learned using the latter approach, e.g. in masked autoencoders, have high variance features that harm distance-based algorithms, such as k-NN, and do not contain useful information for most downstream tasks. Furthermore, we demonstrate that removing these high-variance features enhances k-NN for MAE, as well as for its recent extension Scale-MAE. Finally, we find an object instance retrieval setting where DINOv2, a model pretrained on two orders of magnitude more data, falls short of its less compute intensive counterpart DINO.

Neural networks employ spurious correlations in their predictions, resulting in decreased performance when these correlations do not hold. Recent works suggest fixing pretrained representations and training a classification head that does not use spurious features. We investigate how spurious features are represented in pretrained representations and explore strategies for removing information about spurious features. Considering the Waterbirds dataset and a few pretrained representations, we find that even with full knowledge of spurious features, their removal is not straightforward due to entangled representation. To address this, we propose a linear autoencoder training method to separate the representation into core, spurious, and other features. We propose two effective spurious feature removal approaches that are applied to the encoding and significantly improve classification performance measured by worst group accuracy.

The challenging problem of non-line-of-sight (NLOS) localization is critical for many wireless networking applications. The lack of available datasets has made NLOS localization difficult to tackle with ML-driven methods, but recent developments in synthetic dataset generation have provided new opportunities for research. This paper explores three different input representations: (i) single wireless radio path features, (ii) wireless radio link features (multi-path), and (iii) image-based representations. Inspired by the two latter new representations, we design two convolutional neural networks (CNNs) and we demonstrate that, although not significantly improving the NLOS localization performance, they are able to support richer prediction outputs, thus allowing deeper analysis of the predictions. In particular, the richer outputs enable reliable identification of non-trustworthy predictions and support the prediction of the top-K candidate locations for a given instance. We also measure how the availability of various features (such as angles of signal departure and arrival) affects the model's performance, providing insights about the types of data that should be collected for enhanced NLOS localization. Our insights motivate future work on building more efficient neural architectures and input representations for improved NLOS localization performance, along with additional useful application features., Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible. Work partly supported by the RA Science Committee grant No. 22rl-052 (DISTAL) and the EU under Italian National Recovery and Resilience Plan of NextGenerationEU on "Telecommunications of the Future" (PE00000001 - program "RESTART")

We discover a robust self-supervised strategy tailored towards molecular representations for generative masked language models through a series of tailored, in-depth ablations. Using this pre-training strategy, we train BARTSmiles, a BART-like model with an order of magnitude more compute than previous self-supervised molecular representations. In-depth evaluations show that BARTSmiles consistently outperforms other self-supervised representations across classification, regression, and generation tasks setting a new state-of-the-art on 11 tasks. We then quantitatively show that when applied to the molecular domain, the BART objective learns representations that implicitly encode our downstream tasks of interest. For example, by selecting seven neurons from a frozen BARTSmiles, we can obtain a model having performance within two percentage points of the full fine-tuned model on task Clintox. Lastly, we show that standard attribution interpretability methods, when applied to BARTSmiles, highlight certain substructures that chemists use to explain specific properties of molecules. The code and the pretrained model are publicly available., Comment: 27 pages (including appendix)

Collecting labeled data for many important tasks in chemoinformatics is time consuming and requires expensive experiments. In recent years, machine learning has been used to learn rich representations of molecules using large scale unlabeled molecular datasets and transfer the knowledge to solve the more challenging tasks with limited datasets. Variational autoencoders are one of the tools that have been proposed to perform the transfer for both chemical property prediction and molecular generation tasks. In this work we propose a simple method to improve chemical property prediction performance of machine learning models by incorporating additional information on correlated molecular descriptors in the representations learned by variational autoencoders. We verify the method on three property prediction asks. We explore the impact of the number of incorporated descriptors, correlation between the descriptors and the target properties, sizes of the datasets etc. Finally, we show the relation between the performance of property prediction models and the distance between property prediction dataset and the larger unlabeled dataset in the representation space.

Domain generalization algorithms use training data from multiple domains to learn models that generalize well to unseen domains. While recently proposed benchmarks demonstrate that most of the existing algorithms do not outperform simple baselines, the established evaluation methods fail to expose the impact of various factors that contribute to the poor performance. In this paper we propose an evaluation framework for domain generalization algorithms that allows decomposition of the error into components capturing distinct aspects of generalization. Inspired by the prevalence of algorithms based on the idea of domain-invariant representation learning, we extend the evaluation framework to capture various types of failures in achieving invariance. We show that the largest contributor to the generalization error varies across methods, datasets, regularization strengths and even training lengths. We observe two problems associated with the strategy of learning domain-invariant representations. On Colored MNIST, most domain generalization algorithms fail because they reach domain-invariance only on the training domains. On Camelyon-17, domain-invariance degrades the quality of representations on unseen domains. We hypothesize that focusing instead on tuning the classifier on top of a rich representation can be a promising direction.

Modern data analytics take advantage of ensemble learning and transfer learning approaches to tackle some of the most relevant issues in data analysis, such as lack of labeled data to use to train the analysis models, sparsity of the information, and unbalanced distributions of the records. Nonetheless, when applied to multimodal datasets (i.e., datasets acquired by means of multiple sensing techniques or strategies), the state-of-theart methods for ensemble learning and transfer learning might show some limitations. In fact, in multimodal data analysis, not all observations would show the same level of reliability or information quality, nor an homogeneous distribution of errors and uncertainties. This condition might undermine the classic assumptions ensemble learning and transfer learning methods rely on. In this work, we propose an adaptive approach for dimensionality reduction to overcome this issue. By means of a graph theory-based approach, the most relevant features across variable size subsets of the considered datasets are identified. This information is then used to set-up ensemble learning and transfer learning architectures. We test our approach on multimodal datasets acquired in diverse research fields (remote sensing, brain-computer interfaces, photovoltaic energy). Experimental results show the validity and the robustness of our approach, able to outperform state-of-the-art techniques., Comment: 18 pages, 10 figures, submitted to Pattern Recognition

Transfer learning from pretrained language models recently became the dominant approach for solving many NLP tasks. A common approach to transfer learning for multiple tasks that maximize parameter sharing trains one or more task-specific layers on top of the language model. In this paper, we present an alternative approach based on adversarial reprogramming, which extends earlier work on automatic prompt generation. Adversarial reprogramming attempts to learn task-specific word embeddings that, when concatenated to the input text, instruct the language model to solve the specified task. Using up to 25K trainable parameters per task, this approach outperforms all existing methods with up to 25M trainable parameters on the public leaderboard of the GLUE benchmark. Our method, initialized with task-specific human-readable prompts, also works in a few-shot setting, outperforming GPT-3 on two SuperGLUE tasks with just 32 training samples., Comment: Accepted ACL 2021 Long Paper

Investigation of machine learning algorithms robust to changes between the training and test distributions is an active area of research. In this paper we explore a special type of dataset shift which we call class-dependent domain shift. It is characterized by the following features: the input data causally depends on the label, the shift in the data is fully explained by a known variable, the variable which controls the shift can depend on the label, there is no shift in the label distribution. We define a simple optimization problem with an information theoretic constraint and attempt to solve it with neural networks. Experiments on a toy dataset demonstrate the proposed method is able to learn robust classifiers which generalize well to unseen domains., Comment: Accepted at ICML 2020 workshop on Uncertainty and Robustness in Deep Learning

The success of deep learning in visual recognition tasks has driven advancements in multiple fields of research. Particularly, increasing attention has been drawn towards its application in agriculture. Nevertheless, while visual pattern recognition on farmlands carries enormous economic values, little progress has been made to merge computer vision and crop sciences due to the lack of suitable agricultural image datasets. Meanwhile, problems in agriculture also pose new challenges in computer vision. For example, semantic segmentation of aerial farmland images requires inference over extremely large-size images with extreme annotation sparsity. These challenges are not present in most of the common object datasets, and we show that they are more challenging than many other aerial image datasets. To encourage research in computer vision for agriculture, we present Agriculture-Vision: a large-scale aerial farmland image dataset for semantic segmentation of agricultural patterns. We collected 94,986 high-quality aerial images from 3,432 farmlands across the US, where each image consists of RGB and Near-infrared (NIR) channels with resolution as high as 10 cm per pixel. We annotate nine types of field anomaly patterns that are most important to farmers. As a pilot study of aerial agricultural semantic segmentation, we perform comprehensive experiments using popular semantic segmentation models; we also propose an effective model designed for aerial agricultural pattern recognition. Our experiments demonstrate several challenges Agriculture-Vision poses to both the computer vision and agriculture communities. Future versions of this dataset will include even more aerial images, anomaly patterns and image channels. More information at https://www.agriculture-vision.com., Comment: CVPR 2020

Estimating the covariance structure of multivariate time series is a fundamental problem with a wide-range of real-world applications -- from financial modeling to fMRI analysis. Despite significant recent advances, current state-of-the-art methods are still severely limited in terms of scalability, and do not work well in high-dimensional undersampled regimes. In this work we propose a novel method called Temporal Correlation Explanation, or T-CorEx, that (a) has linear time and memory complexity with respect to the number of variables, and can scale to very large temporal datasets that are not tractable with existing methods; (b) gives state-of-the-art results in highly undersampled regimes on both synthetic and real-world datasets; and (c) makes minimal assumptions about the character of the dynamics of the system. T-CorEx optimizes an information-theoretic objective function to learn a latent factor graphical model for each time period and applies two regularization techniques to induce temporal consistency of estimates. We perform extensive evaluation of T-Corex using both synthetic and real-world data and demonstrate that it can be used for detecting sudden changes in the underlying covariance matrix, capturing transient correlations and analyzing extremely high-dimensional complex multivariate time series such as high-resolution fMRI data.

In this paper, we propose a fast decoder algorithm for uniquely decodable (errorless) code sets for overloaded synchronous optical code-division multiple-access (O-CDMA) systems. The proposed decoder is designed in a such a way that the users can uniquely recover the information bits with a very simple decoder, which uses only a few comparisons. Compared to maximum-likelihood (ML) decoder, which has a high computational complexity for even moderate code lengths, the proposed decoder has much lower computational complexity. Simulation results in terms of bit error rate (BER) demonstrate that the performance of the proposed decoder for a given BER requires only 1-2 dB higher signal-to-noise ratio (SNR) than the ML decoder., Comment: arXiv admin note: substantial text overlap with arXiv:1806.03958

This paper describes our submission to CoNLL 2018 UD Shared Task. We have extended an LSTM-based neural network designed for sequence tagging to additionally generate character-level sequences. The network was jointly trained to produce lemmas, part-of-speech tags and morphological features. Sentence segmentation, tokenization and dependency parsing were handled by UDPipe 1.2 baseline. The results demonstrate the viability of the proposed multitask architecture, although its performance still remains far from state-of-the-art., Comment: System description paper of our system for the CoNLL 2018 shared task on Universal Dependency parsing

We consider the problem of designing a low-complexity decoder for antipodal uniquely decodable (UD) /errorless code sets for overloaded synchronous code-division multiple access (CDMA) systems, where the number of signals Kamax is the largest known for the given code length L. In our complexity analysis, we illustrate that compared to maximum-likelihood (ML) decoder, which has an exponential computational complexity for even moderate code lengths, the proposed decoder has a quasi-quadratic computational complexity. Simulation results in terms of bit-error-rate (BER) demonstrate that the performance of the proposed decoder has only a 1-2 dB degradation in signal-to-noise ratio (SNR) at a BER of 10^-3 when compared to ML. Moreover, we derive the proof of the minimum Manhattan distance of such UD codes and we provide the proofs for the propositions; these proofs constitute the foundation of the formal proof for the maximum number users Kamax for L=8 .

We have tried to reproduce the results of the paper "Natural Language Inference over Interaction Space" submitted to ICLR 2018 conference as part of the ICLR 2018 Reproducibility Challenge. Initially, we were not aware that the code was available, so we started to implement the network from scratch. We have evaluated our version of the model on Stanford NLI dataset and reached 86.38% accuracy on the test set, while the paper claims 88.0% accuracy. The main difference, as we understand it, comes from the optimizers and the way model selection is performed., Comment: as part of ICLR 2018 Reproducibility Challenge

Health care is one of the most exciting frontiers in data mining and machine learning. Successful adoption of electronic health records (EHRs) created an explosion in digital clinical data available for analysis, but progress in machine learning for healthcare research has been difficult to measure because of the absence of publicly available benchmark data sets. To address this problem, we propose four clinical prediction benchmarks using data derived from the publicly available Medical Information Mart for Intensive Care (MIMIC-III) database. These tasks cover a range of clinical problems including modeling risk of mortality, forecasting length of stay, detecting physiologic decline, and phenotype classification. We propose strong linear and neural baselines for all four tasks and evaluate the effect of deep supervision, multitask training and data-specific architectural modifications on the performance of neural models., Comment: This version of the paper adds details about the generation of the benchmark tasks and describes improved neural baselines

An \emph{interval $t$-coloring} of a multigraph $G$ is a proper edge coloring with colors $1,\dots,t$ such that the colors on the edges incident to every vertex of $G$ are colored by consecutive colors. A \emph{cyclic interval $t$-coloring} of a multigraph $G$ is a proper edge coloring with colors $1,\dots,t$ such that the colors on the edges incident to every vertex of $G$ are colored by consecutive colors, under the condition that color $1$ is considered as consecutive to color $t$. Denote by $w(G)$ ($w_{c}(G)$) and $W(G)$ ($W_{c}(G)$) the minimum and maximum number of colors in a (cyclic) interval coloring of a multigraph $G$, respectively. We present some new sharp bounds on $w(G)$ and $W(G)$ for multigraphs $G$ satisfying various conditions. In particular, we show that if $G$ is a $2$-connected multigraph with an interval coloring, then $W(G)\leq 1+\left\lfloor \frac{|V(G)|}{2}\right\rfloor(\Delta(G)-1)$. We also give several results towards the general conjecture that $W_{c}(G)\leq |V(G)|$ for any triangle-free graph $G$ with a cyclic interval coloring; we establish that approximate versions of this conjecture hold for several families of graphs, and we prove that the conjecture is true for graphs with maximum degree at most $4$., Comment: 18 pages, 2 figures

A \emph{proper $t$-edge-coloring} of a graph $G$ is a mapping $\alpha: E(G)\rightarrow \{1,\ldots,t\}$ such that all colors are used, and $\alpha(e)\neq \alpha(e^{\prime})$ for every pair of adjacent edges $e,e^{\prime}\in E(G)$. If $\alpha $ is a proper edge-coloring of a graph $G$ and $v\in V(G)$, then \emph{the spectrum of a vertex $v$}, denoted by $S\left(v,\alpha \right)$, is the set of all colors appearing on edges incident to $v$. \emph{The deficiency of $\alpha$ at vertex $v\in V(G)$}, denoted by $def(v,\alpha)$, is the minimum number of integers which must be added to $S\left(v,\alpha \right)$ to form an interval, and \emph{the deficiency $def\left(G,\alpha\right)$ of a proper edge-coloring $\alpha$ of $G$} is defined as the sum $\sum_{v\in V(G)}def(v,\alpha)$. \emph{The deficiency of a graph $G$}, denoted by $def(G)$, is defined as follows: $def(G)=\min_{\alpha}def\left(G,\alpha\right)$, where minimum is taken over all possible proper edge-colorings of $G$. For a graph $G$, the smallest and the largest values of $t$ for which it has a proper $t$-edge-coloring $\alpha$ with deficiency $def(G,\alpha)=def(G)$ are denoted by $w_{def}(G)$ and $W_{def}(G)$, respectively. In this paper, we obtain some bounds on $w_{def}(G)$ and $W_{def}(G)$. In particular, we show that for any $l\in \mathbb{N}$, there exists a graph $G$ such that $def(G)>0$ and $W_{def}(G)-w_{def}(G)\geq l$. It is known that for the complete graph $K_{2n+1}$, $def(K_{2n+1})=n$ ($n\in \mathbb{N}$). Recently, Borowiecka-Olszewska, Drgas-Burchardt and Ha{\l}uszczak posed the following conjecture on the deficiency of near-complete graphs: if $n\in \mathbb{N}$, then $def(K_{2n+1}-e)=n-1$. In this paper, we confirm this conjecture., Comment: 16 pages, 2 figures

An edge-coloring of a graph $G$ with colors $1,\ldots,t$ is an interval $t$-coloring if all colors are used, and the colors of edges incident to each vertex of $G$ are distinct and form an interval of integers. A graph $G$ is interval colorable if it has an interval $t$-coloring for some positive integer $t$. The problem of deciding whether a bipartite graph is interval colorable is NP-complete. The smallest known examples of interval non-colorable bipartite graphs have $19$ vertices. On the other hand it is known that the bipartite graphs on at most $14$ vertices are interval colorable. In this work we observe that several classes of bipartite graphs of small order have an interval coloring. In particular, we show that all bipartite graphs on $15$ vertices are interval colorable., Comment: Accepted for the CSIT 2015 conference

An edge-coloring of a graph $G$ with colors $1,2,\ldots,t$ is an interval $t$-coloring if all colors are used, and the colors of edges incident to each vertex of $G$ are distinct and form an interval of integers. A graph $G$ is interval colorable if it has an interval $t$-coloring for some positive integer $t$. For an interval colorable graph $G$, $W(G)$ denotes the greatest value of $t$ for which $G$ has an interval $t$-coloring. It is known that the complete graph is interval colorable if and only if the number of its vertices is even. However, the exact value of $W(K_{2n})$ is known only for $n \leq 4$. The second author showed that if $n = p2^q$, where $p$ is odd and $q$ is nonnegative, then $W(K_{2n}) \geq 4n-2-p-q$. Later, he conjectured that if $n \in \mathbb{N}$, then $W(K_{2n}) = 4n - 2 - \left\lfloor\log_2{n}\right\rfloor - \left \| n_2 \right \|$, where $\left \| n_2 \right \|$ is the number of $1$'s in the binary representation of $n$. In this paper we introduce a new technique to construct interval colorings of complete graphs based on their 1-factorizations, which is used to disprove the conjecture, improve lower and upper bounds on $W(K_{2n})$ and determine its exact values for $n \leq 12$.